Package ‘netmeta’

May 6, 2023
Title Network Meta-Analysis using Frequentist Methods
Version 2.8-2
Date 2023-05-06
Depends R (>= 4.0.0), meta (>= 6.2-0)
Imports magic, MASS, ggplot2 (>= 3.0.0), metafor
Suggests colorspace, rgl, hasseDiagram (>= 0.1.3), grid, mvtnorm,
gridExtra, igraph (>= 1.0.1), tictoc, writexl, R.rsp

URL https://github.com/guido-s/netmeta
https://link.springer.com/book/10.1007/978-3-319-21416-0
Description A comprehensive set of functions providing frequentist methods for network meta-
analysis (Balduzzi et al., 2023) <doi:10.18637/jss.v106.i02> and support-
ing Schwarzer et al. (2015) <doi:10.1007/978-3-319-21416-0>, Chapter 8 ``Network Meta-
Analysis'':
- frequentist network meta-analysis following Rücker (2012) <doi:10.1002/jrsm.1058>;
- additive network meta-
analysis for combinations of treatments (Rücker et al., 2020) <doi:10.1002/bimj.201800167>;
- network meta-analysis of binary data using the Mantel-Haenszel or non-
central hypergeometric distribution method (Efthimiou et al., 2019) <doi:10.1002/sim.8158>;
- rankograms and ranking of treatments by the Surface under the cumulative ranking curve (SU-
CRA) (Salanti et al., 2013) <doi:10.1016/j.jclinepi.2010.03.016>;
- ranking of treatments using P-scores (frequentist analogue of SUCRAs without resampling) ac-
cording to Rücker & Schwarzer (2015) <doi:10.1186/s12874-015-0060-8>;
- split direct and indirect evidence to check consis-
tency (Dias et al., 2010) <doi:10.1002/sim.3767>, (Efthimiou et al., 2019) <doi:10.1002/sim.8158>;
- league table with network meta-analysis results;
- 'comparison-adjusted' funnel plot (Chaimani & Salanti, 2012) <doi:10.1002/jrsm.57>;
- net heat plot and design-
based decomposition of Cochran's Q according to Krahn et al. (2013) <doi:10.1186/1471-2288-
13-35>;
- measures characterizing the flow of evidence between two treat-
ments by König et al. (2013) <doi:10.1002/sim.6001>;
- automated drawing of network graphs de-
scribed in Rücker & Schwarzer (2016) <doi:10.1002/jrsm.1143>;

1
2 R topics documented:

- partial order of treatment rankings ('poset') and Hasse diagram for 'poset' (Carlsen & Brugge-
mann, 2014) <doi:10.1002/cem.2569>; (Rücker & Schwarzer, 2017) <doi:10.1002/jrsm.1270>;
- contribution matrix as described in Papakonstanti-
nou et al. (2018) <doi:10.12688/f1000research.14770.3> and Davies et al. (2022) <doi:10.1002/sim.9346>.
License GPL (>= 2)
Encoding UTF-8
VignetteBuilder R.rsp
RoxygenNote 7.2.3
NeedsCompilation no
Author Gerta Rücker [aut] (<https://orcid.org/0000-0002-2192-2560>),
Ulrike Krahn [aut],
Jochem König [aut] (<https://orcid.org/0000-0003-4683-0360>),
Orestis Efthimiou [aut] (<https://orcid.org/0000-0002-0955-7572>),
Annabel Davies [aut] (<https://orcid.org/0000-0003-2320-7701>),
Theodoros Papakonstantinou [aut]
(<https://orcid.org/0000-0002-6630-6817>),
Guido Schwarzer [aut, cre] (<https://orcid.org/0000-0001-6214-9087>)
Maintainer Guido Schwarzer <[email protected]>
Repository CRAN
Date/Publication 2023-05-06 10:10:05 UTC

R topics documented:
netmeta-package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
as.data.frame.netconnection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
as.data.frame.netmeta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Baker2009 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
decomp.design . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
dietaryfat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
discomb . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Dogliotti2014 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Dong2013 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
forest.netbind . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
forest.netcomb . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
forest.netcomparison . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
forest.netcomplex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
forest.netmeta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
forest.netsplit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Franchini2012 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
funnel.netmeta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Gurusamy2011 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
hasse . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
hatmatrix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
heatplot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
heatplot.netmeta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
R topics documented: 3

invmat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
Linde2015 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Linde2016 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
metabias.netmeta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
netbind . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
netcomb . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
netcomparison . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
netcomplex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
netconnection.default . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
netcontrib . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
netdistance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
netgraph . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
netgraph.discomb . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
netgraph.netcomb . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
netgraph.netconnection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
netgraph.netimpact . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
netgraph.netmeta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
netheat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
netimpact . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
netleague . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
netmatrix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
netmeasures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
netmeta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
netmetabin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
netpairwise . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
netposet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
netrank . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
netsplit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
nettable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155
pairwise . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158
plot.netposet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
plot.netrank . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
plot.rankogram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173
print.decomp.design . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
print.netbind . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
print.netcomb . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
print.netimpact . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180
print.summary.netcomb . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
print.summary.netmeta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183
radial.netmeta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
rankogram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190
Senn2013 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193
smokingcessation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195
Stowe2010 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196
subset.pairwise . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
summary.netcomb . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 198
summary.netmeta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200
treats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203
4 netmeta-package

Woods2010 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 205

Index 207

netmeta-package netmeta: Brief overview of methods and general hints

Description
R package netmeta (Balduzzi et al., 2023) provides frequentist methods for network meta-analysis
and supports Schwarzer et al. (2015), Chapter 8 on network meta-analysis https://link.springer.
com/book/10.1007/978-3-319-21416-0.

Details
R package netmeta is an add-on package for meta providing the following network meta-analysis
models:

• frequentist network meta-analysis (function netmeta) based on Rücker (2012) and Rücker &
Schwarzer (2014);
• additive network meta-analysis for combinations of treatments (netcomb for connected net-
works, discomb for disconnected networks) (Rücker et al., 2020a);
• network meta-analysis of binary data (netmetabin) using the Mantel-Haenszel or non-central
hypergeometric distribution method (Efthimiou et al., 2019).

The following methods are available to present results of a network meta-analysis:

• network graphs (netgraph) described in Rücker & Schwarzer (2016);

• forest plots (forest.netmeta, forest.netcomb);
• league tables with network meta-analysis results (netleague);
• tables with network, direct and indirect estimates (nettable) looking similar to the statistical
part of a GRADE table for a network meta-analysis (Puhan et al., 2014).

The following methods are implemented to rank treatments:

• rankograms (rankogram) (Salanti et al., 2011);

• ranking of treatments (netrank) based on P-scores (Rücker & Schwarzer, 2015) or the Surface
Under the Cumulative RAnking curve (SUCRA) (Salanti et al., 2011);
• partial order of treatment rankings (netposet, plot.netposet) and Hasse diagram (hasse)
according to Carlsen & Bruggemann (2014) and Rücker & Schwarzer (2017).

Available functions to evaluate network inconsistency:

• split direct and indirect evidence (netsplit) to check for consistency (Dias et al., 2010;
Efthimiou et al., 2019);
• net heat plot (netheat) and design-based decomposition of Cochran’s Q (decomp.design)
described in Krahn et al. (2013).
netmeta-package 5

Additional methods and functions:

• information on network connectivity (netconnection);

• contribution of direct comparisons to network estimates (netcontrib) (Papakonstantinou et
al., 2018; Davies et al., 2022);
• importance of individual studies measured by reduction of precision if removed from network
(netimpact) (Rücker et al., 2020b);
• ‘comparison-adjusted’ funnel plot (funnel.netmeta) to assess funnel plot asymmetry in net-
work meta-analysis (Chaimani & Salanti, 2012);
• conduct pairwise meta-analyses for all comparisons with direct evidence in a network meta-
analysis (netpairwise);
• results of several network meta-analyses can be combined with netbind to show these results
in a forest plot (forest.netbind).
• measures characterizing the flow of evidence between two treatments (netmeasures) de-
scribed in König et al. (2013);
• calculate comparison effects of two arbitrary complex interventions in component network
meta-analysis (netcomparison);
• calculate effect of arbitrary complex interventions in component network meta-analysis (netcomplex).

Functions and datasets from netmeta are utilised in Schwarzer et al. (2015), Chapter 8 "Network
Meta-Analysis", https://link.springer.com/book/10.1007/978-3-319-21416-0.
Type help(package = "netmeta") for a listing of all R functions available in netmeta.
Type citation("netmeta") on how to cite netmeta in publications.
To report problems and bugs

• type bug.report(package = "netmeta") if you do not use RStudio,

• send an email to Guido Schwarzer <[email protected]> if you use
RStudio.

The development version of netmeta is available on GitHub https://github.com/guido-s/

netmeta.

Author(s)
Guido Schwarzer <[email protected]>, Gerta Rücker <[email protected]

References
Balduzzi S, Rücker G, Nikolakopoulou A, Papakonstantinou T, Salanti G, Efthimiou O, Schwarzer
G (2023): netmeta: An R Package for network meta-analysis using frequentist methods. Journal of
Statistical Software, 106, 1–40
Carlsen L, Bruggemann R (2014): Partial order methodology: a valuable tool in chemometrics.
Journal of Chemometrics, 28, 226–34
Chaimani A & Salanti G (2012): Using network meta-analysis to evaluate the existence of small-
study effects in a network of interventions. Research Synthesis Methods, 3, 161–76
6 netmeta-package

Davies AL, Papakonstantinou T, Nikolakopoulou A, Rücker G, Galla T (2022): Network meta-

analysis and random walks. Statistics in Medicine, 41, 2091–2114
Dias S, Welton NJ, Caldwell DM, Ades AE (2010): Checking consistency in mixed treatment
comparison meta-analysis. Statistics in Medicine, 29, 932–44
Efthimiou O, Rücker G, Schwarzer G, Higgins J, Egger M, Salanti G (2019): A Mantel-Haenszel
model for network meta-analysis of rare events. Statistics in Medicine, 38, 2992–3012
König J, Krahn U, Binder H (2013): Visualizing the flow of evidence in network meta-analysis and
characterizing mixed treatment comparisons. Statistics in Medicine, 32, 5414–29
Krahn U, Binder H, König J (2013): A graphical tool for locating inconsistency in network meta-
analyses. BMC Medical Research Methodology, 13, 35
Papakonstantinou, T., Nikolakopoulou, A., Rücker, G., Chaimani, A., Schwarzer, G., Egger, M.,
Salanti, G. (2018): Estimating the contribution of studies in network meta-analysis: paths, flows
and streams. F1000Research
Puhan MA, Schünemann HJ, Murad MH, et al. (2014): A GRADE working group approach for rat-
ing the quality of treatment effect estimates from network meta-analysis. British Medical Journal,
349, g5630
Rücker G (2012): Network meta-analysis, electrical networks and graph theory. Research Synthesis
Methods, 3, 312–24
Rücker G, Schwarzer G (2014): Reduce dimension or reduce weights? Comparing two approaches
to multi-arm studies in network meta-analysis. Statistics in Medicine, 33, 4353–69
Rücker G, Schwarzer G (2015): Ranking treatments in frequentist network meta-analysis works
without resampling methods. BMC Medical Research Methodology, 15, 58
Rücker G, Schwarzer G (2016): Automated drawing of network plots in network meta-analysis.
Research Synthesis Methods, 7, 94–107
Rücker G, Schwarzer G (2017): Resolve conflicting rankings of outcomes in network meta-analysis:
Partial ordering of treatments. Research Synthesis Methods, 8, 526–36
Rücker G, Petropoulou M, Schwarzer G (2020a): Network meta-analysis of multicomponent inter-
ventions. Biometrical Journal, 62, 808–21
Rücker G, Nikolakopoulou A, Papakonstantinou T, Salanti G, Riley RD, Schwarzer G (2020b):
The statistical importance of a study for a network meta-analysis estimate. BMC Medical Research
Methodology, 20, 190
Salanti G, Ades AE, Ioannidis JP (2011): Graphical methods and numerical summaries for present-
ing results from multiple-treatment meta-analysis: an overview and tutorial. Journal of Clinical
Epidemiology, 64, 163–71
Schwarzer G, Carpenter JR and Rücker G (2015): Meta-Analysis with R (Use R!). Springer Inter-
national Publishing, Switzerland.
as.data.frame.netconnection 7

as.data.frame.netconnection
Create a data frame from an object of class netconnection

Description

The as.data.frame method returns a data frame containing information on membership of studies
/ pairwise comparisons to a (sub)network.

Usage

## S3 method for class 'netconnection'

as.data.frame(x, ...)

Arguments

x An object of class netconnection.

... Additional arguments (ignored).

Value

A data frame is returned by the function as.data.frame.

Author(s)

Guido Schwarzer <[email protected]>

See Also

netconnection

Examples
# Artificial example with two subnetworks
#
t1 <- c("G", "B", "B", "D", "A", "F")
t2 <- c("B", "C", "E", "E", "H", "A")
#
nc2 <- netconnection(t1, t2)
print(nc2, details = TRUE)

as.data.frame(nc2)
8 as.data.frame.netmeta

as.data.frame.netmeta Create a data frame from an object of class netmeta

Description
The as.data.frame method returns a data frame containing information on individual studies, e.g.,
estimated treatment effect and its standard error.

Usage
## S3 method for class 'netmeta'
as.data.frame(x, row.names = NULL, optional = FALSE, details = FALSE, ...)

Arguments
x An object of class netmeta.
row.names NULL or a character vector giving the row names for the data frame.
optional A logical. If TRUE, setting row names and converting column names (to syntactic
names) is optional.
details A logical. If TRUE, additional variables of less interest are included in data frame.
... Additional arguments.

Value
A data frame is returned by the function as.data.frame.

Author(s)
Guido Schwarzer <[email protected]>

See Also
netmeta

Examples
data(smokingcessation)

# Transform data from arm-based format to contrast-based format

#
p1 <- pairwise(list(treat1, treat2, treat3),
event = list(event1, event2, event3), n = list(n1, n2, n3),
data = smokingcessation, sm = "OR")

# Conduct random effects network meta-analysis and show data frame

#
net1 <- netmeta(p1, common = FALSE)
Baker2009 9

as.data.frame(net1)

## Not run:
data(Senn2013)

# Conduct network meta-analysis

#
net2 <- netmeta(TE, seTE, treat1, treat2, studlab,
data = Senn2013, sm = "MD")

as.data.frame(net2)
as.data.frame(net2, details = TRUE)

## End(Not run)

Baker2009 Network meta-analysis of pharmacologic treatments for chronic ob-

structive pulmonary disease

Description
This data set comes from a systematic review of randomized controlled trials on pharmacologic
treatments for chronic obstructive pulmonary disease (COPD) (Baker et al., 2009).
The primary outcome, occurrence of one or more episodes of COPD exacerbation, is binary (yes
/ no). For this outcome, five drug treatments (fluticasone, budesonide, salmeterol, formoterol,
tiotropium) and two combinations (fluticasone + salmeterol, budesonide + formoterol) were com-
pared to placebo. The authors considered the two combinations as separate treatments instead of
evaluating the individual components.

Format
A data frame with the following columns:

study study label

year year of publication
id study ID
treatment treatment
exac one or more episodes of COPD exacerbation
total number of individuals in treatment arm

Source

Baker WL, Baker EL, Coleman CI (2009): Pharmacologic Treatments for Chronic Obstructive Pul-
monary Disease: A Mixed-Treatment Comparison Meta-analysis. Pharmacotherapy: The Journal
of Human Pharmacology and Drug Therapy, 29, 891–905
10 decomp.design

See Also

pairwise, metabin, netmetabin

Examples
data(Baker2009)
Baker2009

## Not run:
# Transform data from long arm-based format to contrast-based
# format. Argument 'sm' has to be used for odds ratio as summary
# measure; by default the risk ratio is used in the metabin
# function called internally.
#
p1 <- pairwise(treatment, exac, total, studlab = paste(study, year),
data = Baker2009, sm = "OR")

# Conduct network meta-analysis

#
net1 <- netmeta(p1, ref = "plac")

# Conduct component network meta-analysis

#
cnet1 <- netcomb(net1)
cnet1

## End(Not run)

decomp.design Design-based decomposition of Cochran’s Q in network meta-analysis

Description

This function performs a design-based decomposition of Cochran’s Q for assessing the homogeneity
in the whole network, the homogeneity within designs, and the homogeneity/consistency between
designs. It allows also an assessment of the consistency assumption after detaching the effect of
single designs.

Usage

decomp.design(
x,
tau.preset = x$tau.preset,
warn = TRUE,
nchar.trts = x$nchar.trts
)
decomp.design 11

Arguments
x An object of class netmeta.
tau.preset An optional value for the square-root of the between-study variance τ 2 (see
Details).
warn A logical indicating whether warnings should be printed.
nchar.trts A numeric defining the minimum number of characters used to create unique
treatment names.

Details
In the context of network meta-analysis and the assessment of the homogeneity and consistency
assumption, a generalized Cochran’s Q statistic for multivariate meta-analysis can be used as shown
in Krahn et al. (2013). This Q statistic can be decomposed in a sum of within-design Q statistics and
one between-designs Q statistic that incorporates the concept of design inconsistency, see Higgins
et al. (2012).
For assessing the inconsistency in a random effects model, the between-designs Q statistic can be
calculated based on a full design-by-treatment interaction random effects model (see Higgins et al.,
2012). This Q statistic will be automatically given in the output (τ 2 estimated by the method of mo-
ments (see Jackson et al., 2012). Alternatively, the square-root of the between-study variance can be
prespecified by argument tau.preset to obtain a between-designs Q statistic (in Q.inc.random),
its design-specific contributions Q.inc.design.random.preset) as well as residuals after detach-
ing of single designs (residuals.inc.detach.random.preset).
Since an inconsistent treatment effect of one design can simultaneously inflate several residuals,
Krahn et al. (2013) suggest for locating the inconsistency in a network to fit a set of extended models
allowing for example for a deviating effect of each study design in turn. The recalculated between-
designs Q statistics are given in list component Q.inc.detach. The change of the inconsistency
contribution of single designs can be investigated in more detail by a net heat plot (see function
netheat). Designs where only one treatment is involved in other designs of the network or where
the removal of corresponding studies would lead to a splitting of the network do not contribute to
the inconsistency assessment. These designs are not included in Q.inc.detach.

Value
Network meta-analysis with a single design: NULL. Otherwise, a list containing the following com-
ponents:

Q.decomp Data frame with Q statistics (variable Q) based on the common effects model to
assess the homogeneity/consistency in the whole network, within designs, and
between designs. Corresponding degrees of freedom (df) and p-values (p.val)
are also given.
Q.het.design Data frame with design-specific decomposition of the within-designs Q statistic
(Q) of the common effects model, corresponding degrees of freedom (df) and
p-values (p.val) are given.
Q.inc.detach Data frame with between-designs Q statistics (Q) of the common effects model
after detaching of single designs, corresponding degrees of freedom (df) and
p-values (p.val) are given.
12 decomp.design

Q.inc.design A named vector with contributions of single designs to the between design Q
statistic given in Q.decomp.
Q.inc.random Data frame with between-designs Q statistic (Q) based on a random effects
model with square-root of between-study variance tau.within estimated em-
bedded in a full design-by-treatment interaction model, corresponding degrees
of freedom (df) and p-value (p.val).
Q.inc.random.preset
Data frame with between-designs Q statistic (Q) based on a random effects
model with prespecified square-root of between-study variance tau.preset in
the case if argument tau.preset is not NULL, corresponding degrees of free-
dom (df) and p-value (p.val).
Q.inc.design.random.preset
A named vector with contributions of single designs to the between design
Q statistic based on a random effects model with prespecified square-root of
between-study variance tau.preset in the case if argument tau.preset is
given.
residuals.inc.detach
Matrix with residuals, i.e. design-specific direct estimates minus the correspond-
ing network estimates after detaching the design of the column.
residuals.inc.detach.random.preset
Matrix with residuals analogous to residuals.inc.detach but based on a
random effects model with prespecified square-root of between-study variance
tau.preset in the case if argument tau.preset is not NULL.
call Function call.
version Version of R package netmeta used to create object.

Author(s)

Ulrike Krahn <[email protected]>, Jochem König <[email protected]>

References

Higgins JPT, Jackson D, Barrett JK, Lu G, Ades AE, White IR (2012): Consistency and inconsis-
tency in network meta-analysis: concepts and models for multi-arm studies. Research Synthesis
Methods, 3, 98–110
Krahn U, Binder H, König J (2013): A graphical tool for locating inconsistency in network meta-
analyses. BMC Medical Research Methodology, 13, 35
Jackson D, White IR and Riley RD (2012): Quantifying the impact of between-study heterogeneity
in multivariate meta-analyses. Statistics in Medicine, 31, 3805–20

See Also

netmeta, netheat
dietaryfat 13

Examples
data(Senn2013)

# Only consider first five studies (to reduce runtime of example)

#
studies <- unique(Senn2013$studlab)
Senn2013.5 <- subset(Senn2013, studlab %in% studies[1:5])

# Conduct network meta-analysis with placebo as reference treatment

#
net1 <- netmeta(TE, seTE, treat1, treat2, studlab,
data = Senn2013.5, sm = "MD", reference = "plac")

# Decomposition of Cochran's Q
#
decomp.design(net1)

dietaryfat Network meta-analysis of dietary fat

Description
Network meta-analysis comparing the effects of two diets to control on mortality.
The data are rates, given as the number of deaths and person-years. These data are used as an
example in the supplemental material of Dias et al. (2013).

Format
A data frame with the following columns:

treat1 treatment 1
treat2 treatment 2
treat3 treatment 3
years1 person years arm 1
years2 person years arm 2
years3 person years arm 3
d1 events (deaths) arm 1
d2 events (deaths) arm 2
d3 events (deaths) arm 3
ID study ID

Source

Dias S, Sutton AJ, Ades AE and Welton NJ (2013): Evidence synthesis for decision making 2:
A generalized linear modeling framework for pairwise and network meta-analysis of randomized
controlled trials. Medical Decision Making, 33, 607–17
14 discomb

See Also
pairwise, metainc, netmeta, netgraph.netmeta

Examples
data(dietaryfat)

# Transform data from arm-based format to contrast-based format

# Using incidence rate ratios (sm = "IRR") as effect measure.
# Note, the argument 'sm' is not necessary as this is the default
# in R function metainc() called internally
#
p1 <- pairwise(list(treat1, treat2, treat3),
list(d1, d2, d3), time = list(years1, years2, years3),
studlab = ID, data = dietaryfat, sm = "IRR")
p1

# Conduct network meta-analysis

#
net1 <- netmeta(p1)
net1

# Conduct network meta-analysis using incidence rate differences

# (sm = "IRD")
#
p2 <- pairwise(list(treat1, treat2, treat3),
list(d1, d2, d3), time = list(years1, years2, years3),
studlab = ID, data = dietaryfat, sm = "IRD")
net2 <- netmeta(p2)
net2

# Draw network graph

#
netgraph(net1, points = TRUE, cex.points = 3, cex = 1.25)

netgraph(net1, points = TRUE, cex.points = 3, cex = 1.25,

labels = c("Control","Diet", "Diet 2"))

discomb Additive network meta-analysis for combinations of treatments (dis-

connected networks)

Description
Some treatments in a network meta-analysis may be combinations of other treatments or have com-
mon components. The influence of individual components can be evaluated in an additive network
meta-analysis model assuming that the effect of treatment combinations is the sum of the effects of
its components. This function implements this additive model in a frequentist way and is particu-
larly intended for disconnected networks.
discomb 15

Usage
discomb(
TE,
seTE,
treat1,
treat2,
studlab,
data = NULL,
subset = NULL,
inactive = NULL,
sep.comps = "+",
C.matrix,
sm,
level = gs("level"),
level.ma = gs("level.ma"),
common = gs("common"),
random = gs("random") | !is.null(tau.preset),
reference.group,
baseline.reference = TRUE,
seq = NULL,
tau.preset = NULL,
tol.multiarm = 0.001,
tol.multiarm.se = NULL,
details.chkmultiarm = FALSE,
details.chkident = FALSE,
sep.trts = ":",
nchar.comps = 666,
func.inverse = invmat,
backtransf = gs("backtransf"),
title = "",
warn = TRUE,
warn.deprecated = gs("warn.deprecated"),
nchar.trts = nchar.comps,
...
)

Arguments
TE Estimate of treatment effect, i.e. difference between first and second treatment
(e.g. log odds ratio, mean difference, or log hazard ratio). Or an R object created
with pairwise.
seTE Standard error of treatment estimate.
treat1 Label/Number for first treatment.
treat2 Label/Number for second treatment.
studlab An optional - but important! - vector with study labels (see netmeta).
data An optional data frame containing the study information.
subset An optional vector specifying a subset of studies to be used.
16 discomb

inactive A character string defining the inactive treatment component (see Details).
sep.comps A single character to define separator between treatment components.
C.matrix C matrix (see Details).
sm A character string indicating underlying summary measure, e.g., "RD", "RR",
"OR", "ASD", "HR", "MD", "SMD", or "ROM".
level The level used to calculate confidence intervals for individual comparisons.
level.ma The level used to calculate confidence intervals for network estimates.
common A logical indicating whether a common effects / common effects network meta-
analysis should be conducted.
random A logical indicating whether a random effects network meta-analysis should be
conducted.
reference.group
Reference treatment (first treatment is used if argument is missing).
baseline.reference
A logical indicating whether results should be expressed as comparisons of other
treatments versus the reference treatment (default) or vice versa. This argument
is only considered if reference.group has been specified.
seq A character or numerical vector specifying the sequence of treatments in print-
outs.
tau.preset An optional value for the square-root of the between-study variance τ 2 .
tol.multiarm A numeric for the tolerance for consistency of treatment estimates in multi-arm
studies which are consistent by design.
tol.multiarm.se
A numeric for the tolerance for consistency of standard errors in multi-arm stud-
ies which are consistent by design. This check is not conducted if the argument
is NULL.
details.chkmultiarm
A logical indicating whether treatment estimates and / or variances of multi-
arm studies with inconsistent results or negative multi-arm variances should be
printed.
details.chkident
A logical indicating whether details on unidentifiable components should be
printed.
sep.trts A character used in comparison names as separator between treatment labels.
nchar.comps A numeric defining the minimum number of characters used to create unique
names for components (see Details).
func.inverse R function used to calculate the pseudoinverse of the Laplacian matrix L (see
netmeta).
backtransf A logical indicating whether results should be back transformed in printouts and
forest plots. If backtransf = TRUE, results for sm = "OR" are presented as odds
ratios rather than log odds ratios, for example.
title Title of meta-analysis / systematic review.
discomb 17

warn A logical indicating whether warnings should be printed (e.g., if studies are
excluded from meta-analysis due to zero standard errors).
warn.deprecated
A logical indicating whether warnings should be printed if deprecated arguments
are used.
nchar.trts Deprecated argument (replaced by nchar.comps).
... Additional arguments (to catch deprecated arguments).

Details
Treatments in network meta-analysis (NMA) can be complex interventions. Some treatments may
be combinations of others or have common components. The standard analysis provided by netmeta
is a NMA where all existing (single or combined) treatments are considered as different nodes in
the network. Exploiting the fact that some treatments are combinations of common components, an
additive component network meta-analysis (CNMA) model can be used to evaluate the influence of
individual components. This model assumes that the effect of a treatment combination is the sum of
the effects of its components which implies that common components cancel out in comparisons.
This R function can be used for disconnected networks. Use netmeta and netcomb for connected
networks.
The additive CNMA model has been implemented using Bayesian methods (Mills et al., 2012;
Welton et al., 2013). This function implements the additive model in a frequentist way (Rücker et
al., 2020).
The underlying multivariate model is given by

δ = Bθ, θ = Cβ

with
δ vector of true treatment effects (differences) from individual studies,
B design matrix describing the structure of the network,
θ parameter vector that represents the existing combined treatments,
C matrix describing how the treatments are composed,
β parameter vector representing the treatment components.
All parameters are estimated using weighted least squares regression.
Argument inactive can be used to specify a single component that does not have any therapeutic
value. Accordingly, it is assumed that the treatment effect of the combination of this component
with an additional treatment component is equal to the treatment effect of the additional component
alone.
Argument sep.comps can be used to specify the separator between individual components. By
default, the matrix C is calculated internally from treatment names. However, it is possible to
specify a different matrix using argument C.matrix.
By default, component names are not abbreviated in printouts. However, in order to get more
concise printouts, argument nchar.comps can be used to define the minimum number of characters
for abbreviated component names (see abbreviate, argument minlength). R function treats is
utilised internally to create abbreviated component names.
18 discomb

Value
An object of classes discomb and netcomb with corresponding print, summary, and forest func-
tions. The object is a list containing the following components:

studlab Study labels.

treat1 Label/Number for first treatment.
treat2 Label/Number for second treatment.
TE Estimate of treatment effect, i.e. difference between first and second treatment.
seTE Standard error of treatment estimate.
seTE.adj.common, seTE.adj.random
Standard error of treatment estimate, adjusted for multi-arm studies.
event1 Number of events in first treatment group.
event2 Number of events in second treatment group.
n1 Number of observations in first treatment group.
n2 Number of observations in second treatment group.
k Total number of studies.
m Total number of pairwise comparisons.
n Total number of treatments.
d Total number of designs (corresponding to the unique set of treatments com-
pared within studies).
c Total number of components.
trts Treatments included in network meta-analysis.
comps Unique list of components present in the network.
TE.cnma.common, TE.cnma.random
A vector of length m of consistent treatment effects estimated by the additive
(common and random effects) model.
seTE.cnma.common, seTE.cnma.random
A vector of length m with standard errors estimated by the additive (common
and random effects) model.
lower.cnma.common, lower.cnma.random
A vector of length m of lower confidence interval limits for consistent treatment
effects estimated by the additive (common and random effects) model.
upper.cnma.common, upper.cnma.random
A vector of length m of upper confidence interval limits for consistent treatment
effects estimated by the additive (common and random effects) model.
statistic.cnma.common, statistic.cnma.random
A vector of length m of z-values for the test of an overall effect estimated by the
additive (common and random effects) model.
pval.cnma.common, pval.cnma.random
A vector of length m of p-values for the test of an overall effect estimated by the
additive (common and random effects) model.
discomb 19

TE.common, TE.random
nxn matrix with overall treatment effects estimated by the additive (common
and random effects) model.
seTE.common, seTE.random
nxn matrix with standard errors estimated by the additive (common and random
effects) model.
lower.common, upper.common, lower.random, upper.random
nxn matrices with lower and upper confidence interval limits estimated by the
additive (common and random effects) model.
statistic.common, pval.common, statistic.random, pval.random
nxn matrices with z-values and p-values for test of overall effect estimated by
the additive (common and random effects) model.
Comp.common, Comp.random
A vector of component effects (common and random effects model).
seComp.common, seComp.random
A vector with corresponding standard errors (common and random effects model).
lower.Comp.common, lower.Comp.random
A vector with lower confidence limits for components (common and random
effects model).
upper.Comp.common, upper.Comp.random
A vector with upper confidence limits for components (common and random
effects model).
statistic.Comp.common, statistic.Comp.random
A vector with z-values for the overall effect of components (common and ran-
dom effects model).
pval.Comp.common, pval.Comp.random
A vector with p-values for the overall effect of components (common and ran-
dom effects model).
Comb.common, Comb.random
A vector of combination effects (common and random effects model).
seComb.common, seComb.random
A vector with corresponding standard errors (common and random effects model).
lower.Comb.common, lower.Comb.random
A vector with lower confidence limits for combinations (common and random
effects model).
upper.Comb.common, upper.Comb.random
A vector with upper confidence limits for combinations (common and random
effects model).
statistic.Comb.common, statistic.Comb.random
A vector with z-values for the overall effect of combinations (common and ran-
dom effects model).
pval.Comb.common, pval.Comb.random
A vector with p-values for the overall effect of combinations (common and ran-
dom effects model).
Q.additive Overall heterogeneity / inconsistency statistic (additive model).
df.Q.additive Degrees of freedom for test of heterogeneity / inconsistency (additive model).
20 discomb

pval.Q.additive
P-value for test of heterogeneity / inconsistency (additive model).
tau Square-root of between-study variance (additive model).
I2 I-squared (additive model).
Q.standard Overall heterogeneity / inconsistency statistic (standard model).
df.Q.standard Degrees of freedom for test of heterogeneity / inconsistency (standard model).
pval.Q.standard
P-value for test of heterogeneity / inconsistency (standard model).
Q.diff Test statistic for difference in goodness of fit between standard and additive
model.
df.Q.diff Degrees of freedom for difference in goodness of fit between standard and addi-
tive model.
pval.Q.diff P-value for difference in goodness of fit between standard and additive model.
X.matrix Design matrix (mxn).
B.matrix Edge-vertex incidence matrix (mxn).
C.matrix As defined above.
sm Summary measure.
level.ma Level for confidence intervals.
common, random, tau.preset
As defined above.
sep.trts A character used in comparison names as separator between treatment labels.
nchar.comps A numeric defining the minimum number of characters used to create unique
component names.
inactive, sep.comps
As defined above.
backtransf A logical indicating whether results should be back transformed in printouts and
forest plots.
title Title of meta-analysis / systematic review.
x As defined above.
call Function call.
version Version of R package netmeta used to create object.

Note
This function calculates effects for individual components and complex interventions present in the
network.
R function netcomplex can be used to calculate the effect for arbitrary complex interventions in
a component network meta-analysis. Furthermore, R function netcomparison can be used to cal-
culate the effect for comparisons of two arbitrary complex intervention in a component network
meta-analysis.

Author(s)
Gerta Rücker <[email protected]>, Guido Schwarzer <[email protected]
discomb 21

References
König J, Krahn U, Binder H (2013): Visualizing the flow of evidence in network meta-analysis and
characterizing mixed treatment comparisons. Statistics in Medicine, 32, 5414–29
Mills EJ, Thorlund K, Ioannidis JP (2012): Calculating additive treatment effects from multiple
randomized trials provides useful estimates of combination therapies. Journal of Clinical Epidemi-
ology, 65, 1282–8
Rücker G, Petropoulou M, Schwarzer G (2020): Network meta-analysis of multicomponent inter-
ventions. Biometrical Journal, 62, 808–21
Welton NJ, Caldwell DM, Adamopoulos E, Vedhara K (2009): Mixed treatment comparison meta-
analysis of complex interventions: psychological interventions in coronary heart disease. American
Journal of Epidemiology, 169: 1158–65

See Also
netcomb, forest.netcomb, summary.netcomb, netmeta, netconnection, netcomplex, netcomparison

Examples
# Artificial dataset
#
t1 <- c("A + B", "A + C", "A" , "A" , "D", "D", "E")
t2 <- c("C" , "B" , "B + C", "A + D", "E", "F", "F")
#
mean <- c(4.1, 2.05, 0, 0, 0.1, 0.1, 0.05)
se.mean <- rep(0.1, 7)
#
study <- paste("study", c(1:4, 5, 5, 5))
#
dat <- data.frame(mean, se.mean, t1, t2, study,
stringsAsFactors = FALSE)
#
trts <- c("A", "A + B", "A + C", "A + D",
"B", "B + C", "C", "D", "E", "F")
#
comps <- LETTERS[1:6]

# Use netconnection() to display network information

#
netconnection(t1, t2, study)

dc1 <- discomb(mean, se.mean, t1, t2, study, seq = trts)

dc1

forest(dc1, ref = "F")

# Define C matrix manually (which will produce the same results)

#
C <- rbind(c(1, 0, 0, 0, 0, 0), # A
c(1, 1, 0, 0, 0, 0), # A + B
c(1, 0, 1, 0, 0, 0), # A + C
22 Dogliotti2014

c(1, 0, 0, 1, 0, 0), # A + D
c(0, 1, 0, 0, 0, 0), # B
c(0, 1, 1, 0, 0, 0), # B + C
c(0, 0, 1, 0, 0, 0), # C
c(0, 0, 0, 1, 0, 0), # D
c(0, 0, 0, 0, 1, 0), # E
c(0, 0, 0, 0, 0, 1)) # F
#
colnames(C) <- comps
rownames(C) <- trts
#
dc2 <- discomb(mean, se.mean, t1, t2, study, seq = trts,
C.matrix = C)
#
# Compare C matrices
#
all.equal(dc1$C.matrix, dc2$C.matrix)

Dogliotti2014 Network meta-analysis of antithrombotic treatments in patients with

non-valvular atrial fibrillation

Description
This data set comes from a systematic review aiming to determine the effects of eight antithrombotic
treatments in reducing the incidence of major thrombotic events in patients with non-valvular atrial
fibrillation (Dogliotti et al., 2014). The review included 20 studies (79,808 participants), four of
which were three-arm studies. The primary outcome is stroke reduction.

Format
A data frame with the following columns:

study study label

id study ID
treatment treatment
stroke number of strokes
total number of individuals in treatment arm

Source
Dogliotti A, Paolasso E, Giugliano RP (2014): Current and new oral antithrombotics in non-valvular
atrial fibrillation: a network meta-analysis of 79 808 patients. Heart, 100, 396–405

See Also
pairwise, metabin, netmetabin
Dong2013 23

Examples
data(Dogliotti2014)
Dogliotti2014

## Not run:
# Transform data from long arm-based format to contrast-based
# format. Argument 'sm' has to be used for odds ratio as summary
# measure; by default the risk ratio is used in the metabin
# function called internally.
#
p1 <- pairwise(treatment, stroke, total, studlab = study,
data = Dogliotti2014, sm = "OR")

# Conduct Mantel-Haenszel network meta-analysis

#
netmetabin(p1, ref = "plac")

## End(Not run)

Dong2013 Network meta-analysis for chronic obstructive pulmonary disease

Description
Network meta-analysis comparing inhaled medications in patients with chronic obstructive pul-
monary disease.

Format
A data frame with the following columns:

id study ID
treatment treatment
death mortality
randomized number of individuals in treatment arm

Source
Dong Y-H, Lin H-H, Shau W-Y, Wu Y-C, Chang C-H, Lai M-S (2013): Comparative safety of
inhaled medications in patients with chronic obstructive pulmonary disease: systematic review and
mixed treatment comparison meta-analysis of randomised controlled trials. Thorax, 68, 48–56

See Also
pairwise, metabin, netmetabin

Examples
data(Dong2013)
24 forest.netbind

# Only consider first ten studies (to reduce runtime of example)

#
first10 <- subset(Dong2013, id <= 10)

# Transform data from long arm-based format to contrast-based

# format. Argument 'sm' has to be used for odds ratio as summary
# measure; by default the risk ratio is used in the metabin
# function called internally.
#
p1 <- pairwise(treatment, death, randomized, studlab = id,
data = first10, sm = "OR")

# Conduct Mantel-Haenszel network meta-analysis

#
netmetabin(p1, ref = "plac")

## Not run:
# Conduct Mantel-Haenszel network meta-analysis for the whole
# dataset
#
p2 <- pairwise(treatment, death, randomized, studlab = id,
data = Dong2013, sm = "OR")
netmetabin(p2, ref = "plac")

## End(Not run)

forest.netbind Forest plot showing results of two or more network meta-analyses

Description
Forest plot to show network estimates of two or more network meta-analyses.

Usage
## S3 method for class 'netbind'
forest(
x,
pooled = ifelse(x$x$random, "random", "common"),
equal.size = TRUE,
leftcols = "studlab",
leftlabs = "Treatment",
rightcols = c("effect", "ci"),
rightlabs = NULL,
subset.treatments,
digits = gs("digits.forest"),
digits.prop = max(gs("digits.pval") - 2, 2),
backtransf = x$backtransf,
forest.netbind 25

lab.NA = "",
smlab,
...
)

## S3 method for class 'netbind'

plot(x, ...)

Arguments
x An object of class netbind.
pooled A character string indicating whether results for the common ("common") or
random effects model ("random") should be plotted. Can be abbreviated.
equal.size A logical indicating whether all squares should be of equal size. Otherwise, the
square size is proportional to the precision of estimates.
leftcols A character vector specifying columns to be plotted on the left side of the forest
plot (see Details).
leftlabs A character vector specifying labels for columns on left side of the forest plot.
rightcols A character vector specifying columns to be plotted on the right side of the forest
plot (see Details).
rightlabs A character vector specifying labels for columns on right side of the forest plot.
subset.treatments
A character vector specifying treatments to show in forest plot as comparators
to the reference.
digits Minimal number of significant digits for treatment effects and confidence inter-
vals, see print.default.
digits.prop Minimal number of significant digits for the direct evidence proportion.
backtransf A logical indicating whether results should be back transformed in forest plots.
If backtransf = TRUE, results for sm = "OR" are presented as odds ratios rather
than log odds ratios, for example.
lab.NA A character string to label missing values.
smlab A label printed at top of figure. By default, text indicating either common or
random effects model is printed.
... Additional arguments for forest.meta function.

Details
A forest plot, also called confidence interval plot, is drawn in the active graphics window.
The arguments leftcols and rightcols can be used to specify columns which are plotted on the
left and right side of the forest plot, respectively. If argument rightcols is FALSE, no columns will
be plotted on the right side.
For more information see help page of forest.meta function.

Author(s)
Guido Schwarzer <[email protected]>
26 forest.netcomb

See Also
netbind, netcomb, forest.meta

Examples
data(Linde2016)

# Only consider studies including Face-to-face PST (to reduce

# runtime of example)
#
face <- subset(Linde2016, id %in% c(16, 24, 49, 118))

# Standard random effects NMA model (with placebo as reference

# treatment)
#
net1 <- netmeta(lnOR, selnOR, treat1, treat2, id,
data = face, reference.group = "placebo",
sm = "OR", common = FALSE)

# Additive CNMA model with placebo as inactive component and

# reference
#
nc1 <- netcomb(net1, inactive = "placebo")

# Combine results of standard NMA and CNMA

#
nb1 <- netbind(nc1, net1,
name = c("Additive CNMA", "Standard NMA"),
col.study = c("red", "black"),
col.square = c("red", "black"))
forest(nb1,
col.by = "black", addrow.subgroups = FALSE,
fontsize = 10, spacing = 0.7, squaresize = 0.9,
label.left = "Favours Placebo",
label.right = "Favours other")

forest.netcomb Forest plot for additive network meta-analysis

Description
Draws a forest plot in the active graphics window (using grid graphics system).

Usage
## S3 method for class 'netcomb'
forest(
x,
forest.netcomb 27

pooled = ifelse(x$random, "random", "common"),

reference.group = x$reference.group,
baseline.reference = x$baseline.reference,
leftcols = "studlab",
leftlabs = "Treatment",
rightcols = c("effect", "ci"),
rightlabs = NULL,
digits = gs("digits.forest"),
smlab = NULL,
sortvar = x$seq,
backtransf = x$backtransf,
lab.NA = ".",
add.data,
drop.reference.group = FALSE,
weight.study = "same",
...
)

## S3 method for class 'netcomb'

plot(x, ...)

Arguments
x An object of class netcomb.
pooled A character string indicating whether results for the common ("common") or
random effects model ("random") should be plotted. Can be abbreviated.
reference.group
Reference treatment(s).
baseline.reference
A logical indicating whether results should be expressed as comparisons of other
treatments versus the reference treatment (default) or vice versa.
leftcols A character vector specifying (additional) columns to be plotted on the left side
of the forest plot or a logical value (see forest.meta help page for details).
leftlabs A character vector specifying labels for (additional) columns on left side of the
forest plot (see forest.meta help page for details).
rightcols A character vector specifying (additional) columns to be plotted on the right side
of the forest plot or a logical value (see forest.meta help page for details).
rightlabs A character vector specifying labels for (additional) columns on right side of the
forest plot (see forest.meta help page for details).
digits Minimal number of significant digits for treatment effects and confidence inter-
vals, see print.default.
smlab A label printed at top of figure. By default, text indicating either common or
random effects model is printed.
sortvar An optional vector used to sort the individual studies (must be of same length as
the total number of treatments).
28 forest.netcomb

backtransf A logical indicating whether results should be back transformed in forest plots.
If backtransf = TRUE, results for sm = "OR" are presented as odds ratios rather
than log odds ratios, for example.
lab.NA A character string to label missing values.
add.data An optional data frame with additional columns to print in forest plot (see De-
tails).
drop.reference.group
A logical indicating whether the reference group should be printed in the forest
plot.
weight.study A character string indicating weighting used to determine size of squares or
diamonds.
... Additional arguments for forest.meta function.

Details
A forest plot, also called confidence interval plot, is drawn in the active graphics window.
Argument sortvar can be either a numeric or character vector with length of number of treatments.
If sortvar is numeric the order function is utilised internally to determine the order of values. If
sortvar is character it must be a permutation of the treatment names. It is also possible to to sort
by treatment comparisons (sortvar = TE, etc.), standard error (sortvar = seTE), and number of
studies with direct treatment comparisons (sortvar = k).
Argument add.data can be used to add additional columns to the forest plot. This argument must
be a data frame with the same row names as the treatment effects matrices in R object x, i.e.,
x$TE.common or x$TE.random.
For more information see help page of forest.meta function.

Author(s)
Guido Schwarzer <[email protected]>

See Also
netcomb, discomb, forest.meta

Examples
data(Linde2016)

# Only consider studies including Face-to-face PST (to reduce

# runtime of example)
#
face <- subset(Linde2016, id %in% c(16, 24, 49, 118))

# Conduct random effects network meta-analysis

#
net1 <- netmeta(lnOR, selnOR, treat1, treat2, id,
data = face, ref = "placebo", sm = "OR", common = FALSE)
forest.netcomparison 29

# Additive model for treatment components (with placebo as inactive

# treatment)
#
nc1 <- netcomb(net1, inactive = "placebo")
#
forest(nc1)

## Not run:
# Specify, order of treatments
#
trts <- c("TCA", "SSRI", "SNRI", "NRI", "Low-dose SARI", "NaSSa",
"rMAO-A", "Ind drug", "Hypericum", "Face-to-face CBT",
"Face-to-face PST", "Face-to-face interpsy", "Face-to-face psychodyn",
"Other face-to-face", "Remote CBT", "Self-help CBT", "No contact CBT",
"Face-to-face CBT + SSRI", "Face-to-face interpsy + SSRI",
"Face-to-face PST + SSRI", "UC", "Placebo")
#
# Note, three treatments are actually combinations of 'SSRI' with
# other components:
# "Face-to-face CBT + SSRI",
# "Face-to-face interpsy + SSRI",
# "Face-to-face PST + SSRI"

# Conduct random effects network meta-analysis

#
net2 <- netmeta(lnOR, selnOR, treat1, treat2, id,
data = Linde2016, ref = "placebo",
seq = trts, sm = "OR", common = FALSE)
#
net2

# Additive model for treatment components (with placebo as inactive

# treatment)
#
nc2 <- netcomb(net2, inactive = "placebo")
#
forest(nc2)

## End(Not run)

forest.netcomparison Forest plot for complex interventions in component network meta-

analysis

Description

Draws a forest plot in the active graphics window (using grid graphics system).
30 forest.netcomparison

Usage
## S3 method for class 'netcomparison'
forest(
x,
pooled = ifelse(x$random, "random", "common"),
leftcols = c("studlab", "treat1", "treat2"),
leftlabs = c("Comparison", "Trt 1", "Trt 2"),
rightcols = c("effect", "ci", "statistic", "pval"),
rightlabs = c(NA, NA, "z", "p-value"),
nchar.comps = x$nchar.trts,
digits = gs("digits.forest"),
digits.stat = gs("digits.stat"),
digits.pval = gs("digits.pval"),
smlab = NULL,
backtransf = x$backtransf,
lab.NA = ".",
weight.study = "same",
...
)

## S3 method for class 'netcomparison'

plot(x, ...)

Arguments
x An object of class netcomparison.
pooled A character string indicating whether results for the common ("common") or
random effects model ("random") should be plotted. Can be abbreviated.
leftcols A character vector specifying (additional) columns to be plotted on the left side
of the forest plot or a logical value (see forest.meta help page for details).
leftlabs A character vector specifying labels for (additional) columns on left side of the
forest plot (see forest.meta help page for details).
rightcols A character vector specifying (additional) columns to be plotted on the right side
of the forest plot or a logical value (see forest.meta help page for details).
rightlabs A character vector specifying labels for (additional) columns on right side of the
forest plot (see forest.meta help page for details).
nchar.comps A numeric defining the minimum number of characters used to create unique
names for components.
digits Minimal number of significant digits for treatment effects and confidence inter-
vals, see print.default.
digits.stat Minimal number of significant digits for tests of overall effect, see print.default.
digits.pval Minimal number of significant digits for p-value of overall effects, see print.default.
smlab A label printed at top of figure. By default, text indicating either common or
random effects model is printed.
forest.netcomparison 31

backtransf A logical indicating whether results should be back transformed in forest plots.
If backtransf = TRUE, results for sm = "OR" are presented as odds ratios rather
than log odds ratios, for example.
lab.NA A character string to label missing values.
weight.study A character string indicating weighting used to determine size of squares or
diamonds.
... Additional arguments for forest.meta function.

Details
A forest plot, also called confidence interval plot, is drawn in the active graphics window. For more
information see help page of forest.meta function.

Author(s)
Guido Schwarzer <[email protected]>

See Also
netcomparison, netcomb, discomb, forest.meta

Examples
data(Linde2016)

# Only consider studies including Face-to-face PST (to reduce

# runtime of example)
#
face <- subset(Linde2016, id %in% c(16, 24, 49, 118))

# Conduct random effects network meta-analysis

#
net1 <- netmeta(lnOR, selnOR, treat1, treat2, id,
data = face, ref = "placebo", sm = "OR", common = FALSE)

# Additive model for treatment components (with placebo as inactive

# treatment)
#
nc1 <- netcomb(net1, inactive = "placebo")

# Some comparisons
#
t1 <- c("F + TCA", "F + Plac", "SSRI + Plac + TCA")
t2 <- c("UC", "Plac", "UC")
#
netcomparison(nc1, t1, t2)
#
forest(netcomparison(nc1, t1, t2))
forest(netcomparison(nc1, t1, t2), nchar.comps = 4)
forest(netcomparison(nc1, c("F", "TCA"), "UC"), nchar.comps = 4)
32 forest.netcomplex

forest.netcomplex Forest plot for complex interventions in component network meta-

analysis

Description
Draws a forest plot in the active graphics window (using grid graphics system).

Usage
## S3 method for class 'netcomplex'
forest(
x,
pooled = ifelse(x$random, "random", "common"),
leftcols = "studlab",
leftlabs = NULL,
rightcols = c("effect", "ci", "statistic", "pval"),
rightlabs = c(NA, NA, "z", "p-value"),
nchar.comps = x$nchar.trts,
digits = gs("digits.forest"),
digits.stat = gs("digits.stat"),
digits.pval = gs("digits.pval"),
smlab = NULL,
backtransf = x$backtransf,
lab.NA = ".",
weight.study = "same",
...
)

## S3 method for class 'netcomplex'

plot(x, ...)

Arguments
x An object of class netcomplex.
pooled A character string indicating whether results for the common ("common") or
random effects model ("random") should be plotted. Can be abbreviated.
leftcols A character vector specifying (additional) columns to be plotted on the left side
of the forest plot or a logical value (see forest.meta help page for details).
leftlabs A character vector specifying labels for (additional) columns on left side of the
forest plot (see forest.meta help page for details).
rightcols A character vector specifying (additional) columns to be plotted on the right side
of the forest plot or a logical value (see forest.meta help page for details).
rightlabs A character vector specifying labels for (additional) columns on right side of the
forest plot (see forest.meta help page for details).
forest.netcomplex 33

nchar.comps A numeric defining the minimum number of characters used to create unique
names for components.
digits Minimal number of significant digits for treatment effects and confidence inter-
vals, see print.default.
digits.stat Minimal number of significant digits for tests of overall effect, see print.default.
digits.pval Minimal number of significant digits for p-value of overall effects, see print.default.
smlab A label printed at top of figure. By default, text indicating either common or
random effects model is printed.
backtransf A logical indicating whether results should be back transformed in forest plots.
If backtransf = TRUE, results for sm = "OR" are presented as odds ratios rather
than log odds ratios, for example.
lab.NA A character string to label missing values.
weight.study A character string indicating weighting used to determine size of squares or
diamonds.
... Additional arguments for forest.meta function.

Details
A forest plot, also called confidence interval plot, is drawn in the active graphics window. For more
information see help page of forest.meta function.

Author(s)
Guido Schwarzer <[email protected]>

See Also
netcomplex, netcomb, discomb, forest.meta

Examples
data(Linde2016)

# Only consider studies including Face-to-face PST (to reduce

# runtime of example)
#
face <- subset(Linde2016, id %in% c(16, 24, 49, 118))

# Conduct random effects network meta-analysis

#
net1 <- netmeta(lnOR, selnOR, treat1, treat2, id,
data = face, ref = "placebo", sm = "OR", common = FALSE)

# Additive model for treatment components (with placebo as inactive

# treatment)
#
nc1 <- netcomb(net1, inactive = "placebo")
34 forest.netmeta

# Some complex interventions

#
ints <- c("F + TCA", "F + Plac", "SSRI + Plac + TCA")
netcomplex(nc1, ints)
#
forest(netcomplex(nc1, ints))
forest(netcomplex(nc1, ints), nchar.comps = 4)

# Component effects
#
forest(netcomplex(nc1, nc1$comps))

forest.netmeta Forest plot for network meta-analysis

Description
Draws a forest plot in the active graphics window (using grid graphics system).

Usage
## S3 method for class 'netmeta'
forest(
x,
pooled = ifelse(x$random, "random", "common"),
reference.group = x$reference.group,
baseline.reference = x$baseline.reference,
labels = x$trts,
equal.size = TRUE,
leftcols = "studlab",
leftlabs,
rightcols = c("effect", "ci"),
rightlabs,
digits = gs("digits.forest"),
small.values = x$small.values,
nsim = 1000,
digits.prop = 2,
smlab = NULL,
sortvar = x$seq,
backtransf = x$backtransf,
lab.NA = ".",
add.data,
drop.reference.group = FALSE,
col.by = "black",
print.subgroup.name = FALSE,
...
)
forest.netmeta 35

## S3 method for class 'netmeta'

plot(x, ...)

Arguments
x An object of class netmeta.
pooled A character string indicating whether results for the common ("common") or
random effects model ("random") should be plotted. Can be abbreviated.
reference.group
Reference treatment(s).
baseline.reference
A logical indicating whether results should be expressed as comparisons of other
treatments versus the reference treatment (default) or vice versa.
labels An optional vector with treatment labels.
equal.size A logical indicating whether all squares should be of equal size. Otherwise, the
square size is proportional to the precision of estimates.
leftcols A character vector specifying columns to be plotted on the left side of the forest
plot or a logical value (see Details).
leftlabs A character vector specifying labels for (additional) columns on left side of the
forest plot (see Details).
rightcols A character vector specifying columns to be plotted on the right side of the forest
plot or a logical value (see Details).
rightlabs A character vector specifying labels for (additional) columns on right side of the
forest plot (see Details).
digits Minimal number of significant digits for treatment effects and confidence inter-
vals, see print.default.
small.values A character string specifying whether small treatment effects indicate a benefi-
cial ("desirable") or harmful ("undesirable") effect, can be abbreviated; see
netrank.
nsim Number of simulations to calculate SUCRAs.
digits.prop Minimal number of significant digits for P-scores, SUCRAs and direct evidence
proportions, see print.default and netrank.
smlab A label printed at top of figure. By default, text indicating either common or
random effects model is printed.
sortvar An optional vector used to sort treatments (must be of same length as the total
number of treatments).
backtransf A logical indicating whether results should be back transformed in forest plots.
If backtransf = TRUE, results for sm = "OR" are presented as odds ratios rather
than log odds ratios, for example.
lab.NA A character string to label missing values.
add.data An optional data frame with additional columns to print in forest plot (see De-
tails).
36 forest.netmeta

drop.reference.group
A logical indicating whether the reference group should be printed in the forest
plot.
col.by The colour to print information on subgroups.
print.subgroup.name
A logical indicating whether the name of the grouping variable should be printed
in front of the group labels.
... Additional arguments for forest.meta function.

Details
A forest plot, also called confidence interval plot, is drawn in the active graphics window.
Argument sortvar can be either a numeric or character vector with length of number of treatments.
If sortvar is numeric the order function is utilised internally to determine the order of values. If
sortvar is character it must be a permutation of the treatment names. It is also possible to provide
either sortvar = Pscore, sortvar = "Pscore", sortvar = -Pscore, or sortvar = "-Pscore" in
order to sort treatments according to the ranking generated by netrank which is called internally.
It is also possible to use "SUCRA" instead of "Pscore". Similar expressions are possible to sort
by treatment comparisons (sortvar = TE, etc.), standard error (sortvar = seTE), number of stud-
ies with direct treatment comparisons (sortvar = k), and direct evidence proportion (sortvar =
prop.direct, see also netmeasures).
The arguments leftcols and rightcols can be used to specify columns which are plotted on the
left and right side of the forest plot, respectively. The following columns are available:

Name Definition
"studlab" Treatments
"TE" Network estimates (either from common or random effects model)
"seTE" Corresponding standard errors
"Pscore" P-scores (see netrank)
"SUCRA" SUCRAs (see netrank)
"n.trts" Number of participants per treatment arm
"k" Number of studies in pairwise comparisons
"prop.direct" Direct evidence proportions (see netmeasures)
"effect" (Back-transformed) network estimates
"ci" Confidence intervals
"effect.ci" (Back-transformed) network estimates and confidence intervals

As a sidenote, the rather odd column name "studlab" to describe the treatment comparisons comes
from internally calling forest.meta which uses study labels as the essential information.
Argument add.data can be used to add additional columns to the forest plot. This argument must
be a data frame with row names equal to the treatment names in R object x, i.e., x$trts.
See help page of forest.meta for more information on the generation of forest plots and additional
arguments.

Author(s)
Guido Schwarzer <[email protected]>
forest.netmeta 37

See Also
forest.meta

Examples
data(smokingcessation)

# Transform data from arm-based format to contrast-based format

#
p1 <- pairwise(list(treat1, treat2, treat3),
event = list(event1, event2, event3), n = list(n1, n2, n3),
data = smokingcessation, sm = "OR")

# Conduct random effects network meta-analysis

#
net1 <- netmeta(p1, common = FALSE)

forest(net1)

## Not run:
data(Senn2013)

# Conduct network meta-analysis

#
net2 <- netmeta(TE, seTE, treat1, treat2, studlab,
data = Senn2013, sm = "MD")

forest(net2, ref = "plac")

forest(net2, xlim = c(-1.5, 1), ref = "plac",
xlab = "HbA1c difference", rightcols = FALSE)

# Random effects effect model

#
net3 <- netmeta(TE, seTE, treat1, treat2, studlab,
data = Senn2013, sm = "MD", common = FALSE)

forest(net3, xlim = c(-1.5, 1), ref = "plac",

xlab = "HbA1c difference")

# Add column with P-Scores on right side of forest plot

#
forest(net3, xlim = c(-1.5, 1), ref = "plac",
xlab = "HbA1c difference",
rightcols = c("effect", "ci", "Pscore"),
just.addcols = "right")

# Add column with P-Scores on left side of forest plot

#
forest(net3, xlim = c(-1.5, 1), ref = "plac",
xlab = "HbA1c difference",
leftcols = c("studlab", "Pscore"),
just.addcols = "right")
38 forest.netsplit

# Sort forest plot by descending P-Score

#
forest(net3, xlim = c(-1.5, 1), ref = "plac",
xlab = "HbA1c difference",
rightcols = c("effect", "ci", "Pscore"),
just.addcols = "right",
sortvar = -Pscore)

# Drop reference group and sort by and print number of studies with
# direct treatment comparisons
#
forest(net3, xlim = c(-1.5, 1), ref = "plac",
xlab = "HbA1c difference",
leftcols = c("studlab", "k"),
leftlabs = c("Contrast\nto Placebo", "Direct\nComparisons"),
sortvar = -k,
drop = TRUE,
smlab = "Random Effects Model")

## End(Not run)

forest.netsplit Forest plot for direct and indirect evidence

Description
Forest plot to show direct and indirect evidence in network meta-analysis. Furthermore, estimates
from network meta-analysis as well as prediction intervals can be printed.

Usage
## S3 method for class 'netsplit'
forest(
x,
pooled = ifelse(x$x$random, "random", "common"),
show = "both",
subgroup = "comparison",
overall = TRUE,
direct = TRUE,
indirect = TRUE,
prediction = x$prediction,
only.reference = FALSE,
sortvar = NULL,
text.overall = "Network estimate",
text.direct = "Direct estimate",
text.indirect = "Indirect estimate",
text.predict = "Prediction interval",
forest.netsplit 39

type.overall,
type.direct,
type.indirect,
col.square = "gray",
col.square.lines = col.square,
col.inside = "white",
col.diamond = "gray",
col.diamond.lines = "black",
col.predict = "red",
col.predict.lines = "black",
equal.size = TRUE,
leftcols,
leftlabs,
rightcols = c("effect", "ci"),
rightlabs = NULL,
digits = gs("digits.forest"),
digits.prop = max(gs("digits.pval") - 2, 2),
backtransf = x$backtransf,
lab.NA = "",
smlab,
...
)

## S3 method for class 'netsplit'

plot(x, ...)

Arguments
x An object of class netsplit.
pooled A character string indicating whether results for the common ("common") or
random effects model ("random") should be plotted. Can be abbreviated.
show A character string indicating which comparisons should be printed (see Details).
subgroup A character string indicating which layout should be used in forest plot: sub-
groups by comparisons ("comparison") or subgroups by estimates ("estimate").
Can be abbreviated.
overall A logical indicating whether network meta-analysis estimates should be printed.
direct A logical indicating whether direct estimates should be printed.
indirect A logical indicating whether indirect estimates should be printed.
prediction A logical indicating whether prediction intervals should be printed.
only.reference A logical indicating whether only comparisons with the reference group should
be printed.
sortvar An optional vector used to sort comparisons (must be of same length as the total
number of comparisons).
text.overall A character string used in the plot to label the network estimates.
text.direct A character string used in the plot to label the direct estimates.
40 forest.netsplit

text.indirect A character string used in the plot to label the indirect estimates.
text.predict A character string used in the plot to label the prediction interval.
type.overall A character string specifying how to plot treatment effects and confidence inter-
vals for the overall network evidence.
type.direct A character string specifying how to plot treatment effects and confidence inter-
vals for the direct evidence.
type.indirect A character string specifying how to plot treatment effects and confidence inter-
vals for the indirect evidence.
col.square The colour for squares.
col.square.lines
The colour for the outer lines of squares.
col.inside The colour for results and confidence limits if confidence limits are completely
within squares squares.
col.diamond The colour of diamonds.
col.diamond.lines
The colour of the outer lines of diamonds.
col.predict Background colour of prediction intervals.
col.predict.lines
Colour of outer lines of prediction intervals.
equal.size A logical indicating whether all squares should be of equal size. Otherwise, the
square size is proportional to the precision of estimates.
leftcols A character vector specifying columns to be plotted on the left side of the forest
plot (see Details).
leftlabs A character vector specifying labels for columns on left side of the forest plot.
rightcols A character vector specifying columns to be plotted on the right side of the forest
plot (see Details).
rightlabs A character vector specifying labels for columns on right side of the forest plot.
digits Minimal number of significant digits for treatment effects and confidence inter-
vals, see print.default.
digits.prop Minimal number of significant digits for the direct evidence proportion.
backtransf A logical indicating whether results should be back transformed in forest plots.
If backtransf = TRUE, results for sm = "OR" are presented as odds ratios rather
than log odds ratios, for example.
lab.NA A character string to label missing values.
smlab A label printed at top of figure. By default, text indicating either common or
random effects model is printed.
... Additional arguments for forest.meta function.
forest.netsplit 41

Details
A forest plot, also called confidence interval plot, is drawn in the active graphics window.
The arguments leftcols and rightcols can be used to specify columns which are plotted on the
left and right side of the forest plot, respectively. If argument rightcols is FALSE, no columns will
be plotted on the right side.
If direct estimates are included in the forest plot (direct = TRUE, default), the following columns
will be printed on the left side of the forest plot: the comparisons (column "studlab" in forest.meta),
number of pairwise comparisons ("k"), direct evidence proportion ("k"), and I2 from pairwise com-
parison ("I2").
If direct estimates are not included in the forest plot (direct = FALSE), only the comparisons
("studlab") are printed on the left side of the forest plot.
For more information see help page of forest.meta function.
Argument show determines which comparisons are printed:

“all” All comparisons

“both” Only comparisons contributing both direct and indirect evidence
“with.direct” Comparisons providing direct evidence
“direct.only” Comparisons providing only direct evidence
“indirect.only” Comparisons providing only indirect evidence

Author(s)
Guido Schwarzer <[email protected]>

See Also
forest.meta

Examples
data(Senn2013)

# Only consider first five studies (to reduce runtime of example)

#
studies <- unique(Senn2013$studlab)
Senn2013.5 <- subset(Senn2013, studlab %in% studies[1:5])

net1 <- netmeta(TE, seTE, treat1.long, treat2.long,

studlab, data = Senn2013.5, common = FALSE, reference = "plac")
#
ns1 <- netsplit(net1)

# Forest plot showing comparisons contributing both direct and

# indirect evidence
#
forest(ns1, fontsize = 6, spacing = 0.5, addrow.subgroups = FALSE)

## Not run:
42 Franchini2012

# Forest plot showing comparisons contributing direct evidence

#
forest(ns1, fontsize = 6, spacing = 0.5, addrow.subgroups = FALSE,
show = "with.direct")

# Forest plot only showing network estimates compared to reference

# group and prediction intervals
#
forest(ns1, fontsize = 8, spacing = 0.75, show = "all",
only.reference = TRUE, prediction = TRUE,
direct = FALSE, indirect = FALSE)

## End(Not run)

Franchini2012 Network meta-analysis of treatments for Parkinson’s disease

Description
Network meta-analysis comparing the effects of a number of treatments for Parkinson’s disease.
The data are the mean lost work-time reduction in patients given dopamine agonists as adjunct
therapy in Parkinson’s disease (Franchini et al. 2012). The data are given as sample size, mean and
standard deviation in each trial arm. Treatments are placebo and four active drugs. These data are
used as an example in the supplemental material of Dias et al. (2013) where placebo is coded as 1
and the four active drugs as 2 to 5.

Format
A data frame with the following columns:

Study study label

Treatment1 treatment 1
y1 treatment effect arm 1
sd1 Standard deviation arm 1
n1 Sample size arm 1
Treatment2 treatment 2
y2 treatment effect arm 2
sd2 Standard deviation arm 2
n2 Sample size arm 2
Treatment3 treatment 3
y3 treatment effect arm 3
sd3 Standard deviation arm 3
n3 Sample size arm 3
funnel.netmeta 43

Source

Dias S, Sutton AJ, Ades AE and Welton NJ (2013): Evidence synthesis for decision making 2:
A generalized linear modeling framework for pairwise and network meta-analysis of randomized
controlled trials. Medical Decision Making, 33, 607–17
Franchini AJ, Dias S, Ades AE, Jansen JP, Welton NJ (2012): Accounting for correlation in network
meta-analysis with multi-arm trials. Research Synthesis Methods, 3, 142–60

See Also

pairwise, metacont, netmeta, netgraph.netmeta

Examples

data(Franchini2012)

# Transform data from arm-based format to contrast-based format

#
p1 <- pairwise(list(Treatment1, Treatment2, Treatment3),
n = list(n1, n2, n3),
mean = list(y1, y2, y3), sd = list(sd1, sd2, sd3),
data = Franchini2012, studlab = Study)
p1

# Conduct network meta-analysis

net1 <- netmeta(p1)
net1

# Draw network graphs

netgraph(net1, points = TRUE, cex.points = 3, cex = 1.5,
thickness = "se.common")
netgraph(net1, points = TRUE, cex.points = 3, cex = 1.5,
thickness = "se.common",
iterate = TRUE, plastic = TRUE)
netgraph(net1, points = TRUE, cex.points = 3, cex = 1.5,
thickness = "se.common",
iterate = TRUE, plastic = TRUE, start = "eigen")

funnel.netmeta ‘Comparison-adjusted’ funnel plot

Description

Draw a ‘comparison-adjusted’ funnel plot to assess funnel plot asymmetry in network meta-analysis.
44 funnel.netmeta

Usage
## S3 method for class 'netmeta'
funnel(
x,
order,
pooled = ifelse(x$random, "random", "common"),
xlab = NULL,
level = x$level,
pch,
col = "black",
legend = TRUE,
pos.legend = "topright",
pos.tests = "topleft",
lump.comparator = FALSE,
text.comparator = "comparator",
method.bias,
text.linreg = "(Egger)",
text.rank = "(Begg-Mazumdar)",
text.mm = "(Thompson-Sharp)",
sep.trts = x$sep.trts,
nchar.trts = x$nchar.trts,
backtransf = x$backtransf,
digits.pval = gs("digits.pval"),
warn.deprecated = gs("warn.deprecated"),
linreg = FALSE,
rank = FALSE,
mm = FALSE,
...
)

Arguments
x An object of class netmeta.
order A mandatory character or numerical vector specifying the order of treatments or
list of comparators (see Details).
pooled A character string indicating whether results for the common ("common") or
random effects model ("random") should be plotted. Can be abbreviated.
xlab A label for the x-axis.
level The confidence level utilised in the plot. For the funnel plot, confidence limits
are not drawn if yaxis = "size".
pch The plotting symbol(s) used for individual studies within direct comparisons.
col The colour(s) used for individual studies within direct comparisons.
legend A logical indicating whether a legend with information on direct comparisons
should be added to the plot.
pos.legend The position of the legend describing plotting symbols and colours for direct
comparisons.
funnel.netmeta 45

pos.tests The position of results for test(s) of funnel plot asymmetry.

lump.comparator
A logical indicating whether comparators should be lumped, e.g., to specify
inactive treatments. information on direct comparisons should be added to the
plot.
text.comparator
A character string used in the plot to label the comparator if lump.comparator
is TRUE.
method.bias A character vector indicating which test(s) for funnel plot asymmetry to use.
Admissible values are "Begg", "Egger", and "Thompson", can be abbreviated.
See function metabias.
text.linreg A character string used in the plot to label the Egger test for funnel plot asym-
metry.
text.rank A character string used in the plot to label the Begg test for funnel plot asym-
metry.
text.mm A character string used in the plot to label the Thompson-Sharp test for funnel
plot asymmetry.
sep.trts A character used in comparison names as separator between treatment labels.
nchar.trts A numeric defining the minimum number of characters used to create unique
treatment names (see netmeta).
backtransf A logical indicating whether results for relative summary measures (argument
sm equal to "OR", "RR", "HR", or "IRR") should be back transformed in funnel
plots. If backtransf = TRUE, results for sm = "OR" are printed as odds ratios
rather than log odds ratios, for example.
digits.pval Minimal number of significant digits for p-value of test(s) for funnel plot asym-
metry.
warn.deprecated
A logical indicating whether warnings should be printed if deprecated arguments
are used.
linreg Deprecated argument (replaced by method.bias).
rank Deprecated argument (replaced by method.bias).
mm Deprecated argument (replaced by method.bias).
... Additional graphical arguments passed as arguments to funnel.meta.

Details
A ‘comparison-adjusted’ funnel plot (Chaimani & Salanti, 2012) is drawn in the active graphics
window.
Argument order is mandatory to determine the order of treatments (Chaimani et al., 2013):
“Before using this plot, investigators should order the treatments in a meaningful way and make
assumptions about how small studies differ from large ones. For example, if they anticipate that
newer treatments are favored in small trials, then they could name the treatments from oldest to
newest so that all comparisons refer to ‘old versus new intervention’. Other possibilities include
46 funnel.netmeta

defining the comparisons so that all refer to an active treatment versus placebo or sponsored versus
non-sponsored intervention.”
Alternatively, it is possible to only provide a single or few treatment name(s) in argument order
to define the comparator(s). In this case only comparisons with this / these treatment(s) will be
considered. If argument lump.comparator is TRUE, all comparators will be lumped into a single
group. The text for this group can be specified with argument text.comparator.
In the funnel plot, if yaxis is "se", the standard error of the treatment estimates is plotted on the
y-axis which is likely to be the best choice (Sterne & Egger, 2001). Other possible choices for
yaxis are "invvar" (inverse of the variance), "invse" (inverse of the standard error), and "size"
(study size).

Value

A data frame with the following columns:

studlab Study label.

treat1 Label/Number for first treatment.
treat2 Label/Number for second treatment.
comparison Treatment comparison.
TE Estimate of treatment effect, e.g., log odds ratio.
TE.direct Pooled estimate from direct evidence.
TE.adj ‘Comparison-adjusted’ treatment effect (TE - TE.direct).
seTE Standard error of treatment estimate.
pch Plotting symbol(s).
col Colour of plotting symbol(s).

Author(s)

Guido Schwarzer <[email protected]>

References

Chaimani A & Salanti G (2012): Using network meta-analysis to evaluate the existence of small-
study effects in a network of interventions. Research Synthesis Methods, 3, 161–76
Chaimani A, Higgins JP, Mavridis D, Spyridonos P, Salanti G (2013): Graphical tools for network
meta-analysis in STATA. PLOS ONE, 8, e76654
Sterne JAC & Egger M (2001): Funnel plots for detecting bias in meta-analysis: Guidelines on
choice of axis. Journal of Clinical Epidemiology, 54, 1046–55

See Also

netmeta, funnel.meta, metabias

funnel.netmeta 47

Examples
## Not run:
data(Senn2013)

net1 <- netmeta(TE, seTE, treat1, treat2, studlab,

data = Senn2013, sm = "MD")

# 'Comparison-adjusted' funnel plot not created as argument 'order'

# is missing
#
try(funnel(net1))

# Only show comparisons with placebo

#
funnel(net1, order = "pl")

# Add result for Egger test of funnel plot asymmetry

#
funnel(net1, order = "pl", method.bias = "Egger",
digits.pval = 2)

# (Non-sensical) alphabetic order of treatments with placebo as

# last treatment
#
ord <- c("a", "b", "me", "mi", "pi", "r", "si", "su", "v", "pl")
funnel(net1, order = ord)

# Add results for tests of funnel plot asymmetry and use different
# plotting symbols and colours
#
funnel(net1, order = ord,
pch = rep(c(15:18, 1), 3), col = 1:3,
method.bias = c("Egger", "Begg", "Thompson"), digits.pval = 2)

# Same results for tests of funnel plot asymmetry using reversed

# order of treatments
#
funnel(net1, order = rev(ord),
pch = rep(c(15:18, 1), 3), col = 1:3,
method.bias = c("Egger", "Begg", "Thompson"), digits.pval = 2)

# Calculate tests for funnel plot asymmetry

#
f1 <- funnel(net1, order = ord)
#
metabias(metagen(TE.adj, seTE, data = f1))
metabias(metagen(TE.adj, seTE, data = f1), method = "Begg")
metabias(metagen(TE.adj, seTE, data = f1), method = "Thompson")

## End(Not run)
48 Gurusamy2011

Gurusamy2011 Network meta-analysis on blood loss during liver transplantation

Description
Network meta-analysis comparing the effects of a number of interventions for decreasing blood loss
and blood transfusion requirements during liver transplantation.

Format
A data frame with the following columns:

study study information (first author, year)

treatment treatment
death mortality at 60 days post-transplantation
n number of individuals in treatment arm

Source
Gurusamy KS, Pissanou T, Pikhart H, Vaughan J, Burroughs AK, Davidson BR (2011): Methods
to decrease blood loss and transfusion requirements for liver transplantation. Cochrane Database
of Systematic Reviews, CD009052

See Also
pairwise, metabin, netmetabin

Examples
data(Gurusamy2011)

# Only consider three studies (to reduce runtime of example)

#
studies <- c("Findlay 2001", "Garcia-Huete 1997", "Dalmau 2000")
three <- subset(Gurusamy2011, study %in% studies)

# Transform data from long arm-based format to contrast-based

# format. Argument 'sm' has to be used for odds ratio as summary
# measure; by default the risk ratio is used in the metabin
# function called internally.
#
p1 <- pairwise(treatment, death, n, studlab = study,
data = three, sm = "OR")

# Conduct Mantel-Haenszel network meta-analysis

#
netmetabin(p1, ref = "cont")

## Not run:
hasse 49

p2 <- pairwise(treatment, death, n, studlab = study,

data = Gurusamy2011, sm = "OR")

# Conduct Mantel-Haenszel network meta-analysis

netmetabin(p2, ref = "cont")

## End(Not run)

hasse Hasse diagram

Description
This function generates a Hasse diagram for a partial order of treatment ranks in a network meta-
analysis.

Usage
hasse(x, pooled = ifelse(x$random, "random", "common"), newpage = TRUE)

Arguments
x An object of class netposet (mandatory).
pooled A character string indicating whether Hasse diagram show be drawn for com-
mon ("common") or random effects model ("random"). Can be abbreviated.
newpage A logical value indicating whether a new figure should be printed in an existing
graphics window. Otherwise, the Hasse diagram is added to the existing figure.

Details
Generate a Hasse diagram (Carlsen & Bruggemann, 2014) for a partial order of treatment ranks in
a network meta-analysis (Rücker & Schwarzer, 2017).
This R function is a wrapper function for R function hasse in R package hasseDiagram (Krzysztof
Ciomek, https://github.com/kciomek/hasseDiagram), i.e., function hasse can only be used if
R package hasseDiagram is installed.

Author(s)
Gerta Rücker <[email protected]>, Guido Schwarzer <[email protected]

References
Carlsen L, Bruggemann R (2014): Partial order methodology: a valuable tool in chemometrics.
Journal of Chemometrics, 28, 226–34
Rücker G, Schwarzer G (2017): Resolve conflicting rankings of outcomes in network meta-analysis:
Partial ordering of treatments. Research Synthesis Methods, 8, 526–36
50 hasse

See Also

netmeta, netposet, netrank, plot.netrank

Examples
## Not run:
# Use depression dataset
#
data(Linde2015)

# Define order of treatments

#
trts <- c("TCA", "SSRI", "SNRI", "NRI",
"Low-dose SARI", "NaSSa", "rMAO-A", "Hypericum", "Placebo")

# Outcome labels
#
outcomes <- c("Early response", "Early remission")

# (1) Early response

#
p1 <- pairwise(treat = list(treatment1, treatment2, treatment3),
event = list(resp1, resp2, resp3),
n = list(n1, n2, n3),
studlab = id, data = Linde2015, sm = "OR")
#
net1 <- netmeta(p1, common = FALSE,
seq = trts, ref = "Placebo", small.values = "undesirable")

# (2) Early remission

#
p2 <- pairwise(treat = list(treatment1, treatment2, treatment3),
event = list(remi1, remi2, remi3),
n = list(n1, n2, n3),
studlab = id, data = Linde2015, sm = "OR")
#
net2 <- netmeta(p2, common = FALSE,
seq = trts, ref = "Placebo", small.values = "undesirable")

# Partial order of treatment rankings

#
po <- netposet(netrank(net1), netrank(net2), outcomes = outcomes)

# Hasse diagram
#
hasse(po)

## End(Not run)
hatmatrix 51

hatmatrix Derive hat matrix from network meta-analysis

Description
Auxiliary function to derive hat matrix from network meta-analysis

Usage
hatmatrix(
x,
method = "Ruecker",
type,
common = x$common,
random = x$random,
nchar.trts = x$nchar.trts,
nchar.studlab = x$nchar.studlab
)

## S3 method for class 'hatmatrix'

print(
x,
common = x$x$common,
random = x$x$random,
nchar.trts = x$x$nchar.trts,
nchar.studlab = x$x$nchar.studlab,
digits = gs("digits"),
legend = TRUE,
legend.studlab = TRUE,
...
)

Arguments
x A netmeta object.
method A character string indicating which method is used to derive the hat matrix.
Either "Ruecker", "Krahn" or "Davies" (can be abbreviated, see Details).
type A character string indicating which specific hat matrix should be derived (can
be abbreviated, see Details).
common A logical indicating whether a hat matrix should be printed for the common
effects network meta-analysis.
random A logical indicating whether a hat matrix should be printed for the random ef-
fects network meta-analysis.
nchar.trts A numeric defining the minimum number of characters used to create unique
treatment names.
52 hatmatrix

nchar.studlab A numeric defining the minimum number of characters used to create unique
study labels.
digits Minimal number of significant digits, see print.default.
legend A logical indicating whether a legend should be printed.
legend.studlab A logical indicating whether a legend should be printed for abbreviated study
labels.
... Additional arguments (ignored).

Details
This auxiliary function can be used to derive various hat matrices from a network meta-analysis
object.

Hat matrix by Rücker (2012):

This hat matrix is estimated if method = "Ruecker".
Let n be the number of different treatments (nodes, vertices) in a network and let m be the number
of existing comparisons (edges) between the treatments. If there are only two-arm studies, m
is equal to the number of studies, k. Let seTE.adj.common and seTE.adj.random be the vectors
of adjusted standard errors under the common and random effects model (see netmeta). Let W
be the m x m diagonal matrix that contains the inverse variance 1 / seTE.adj.common2 or 1 /
seTE.adj.random2 .
The given comparisons define the network structure. Therefrom an m x n design matrix X (edge-
vertex incidence matrix) is formed; for more precise information, see Rücker (2012). Moreover,
the n x n Laplacian matrix L and its Moore-Penrose pseudoinverse L+ are calculated (both matri-
ces play an important role in graph theory and electrical network theory). Using these matrices,
the variances based on both direct and indirect comparisons can be estimated. The hat matrix H
is estimated by H = XL+ XT W = X(XT W X)+ XT W.

Hat matrices by Krahn et al. (2013):

One of the following hat matrices is estimated if method = "Krahn".
Use of type = "design" (default) results in a hat matrix of dimension n(n-1)/2 x s, where s is the
sum of the number of independent comparisons from each design.
Use of type = "studies" results in a hat matrix of dimension n(n-1)/2 x l, where l is the number of
independent pairwise comparisons, i.e., a three-arm study contributes two pairwise comparisons.

Hat matrices by Davies et al. (2022):

One of three hat matrices is estimated if method = "Davies".
Here, we focus on the hat matrix of the aggregate (two-step) version of the graph theoretical
NMA model. In the first step, a pairwise meta-analysis is performed across each edge using
the adjusted weights (these account for correlations due to multi-arm trials). From this we obtain
direct treatment effect estimates (and corresponding aggregate weights) associated with each edge.
In step two, we combine these direct estimates in a network meta analysis to obtain the network
estimates. This is done using weighted least squares regression. The hat matrix associated with
this second step is called the aggregate hat matrix.
All three versions of the aggregate hat matrix contain the same information: the second two can
be derived directly from the first. They differ in their dimensionality.
hatmatrix 53

Each row of the hat matrix that represents a treatment comparison (ij) describes the flow of evi-
dence through each edge for that comparison. This defines a directed acyclic ’flow graph’ from
node i to node j.
(1) Use of type = "short" (default) results in a hat matrix of dimension e x e, where e is the
number of (unique) edges (direct comparisons) in the network. This is the aggregate hat matrix
described in Davies et al. (2022). Each row and column represents a pair of treatments for which
there is at least one direct comparison.
(2) Use of type = "long" results in a hat matrix of dimension n(n-1)/2 x e. There is a row for
every possible pair of treatments in the network - regardless of whether there is direct evidence
for this comparison. Each column represents a pair of treatments for which there is at least one
direct comparison. The extra rows can be calculated from the short hat matrix using consistency
equations.
(3) Use of type = "full" results in a hat matrix of dimension n(n-1)/2 x n(n-1)/2. In comparison
to the long hat matrix, columns of zeroes are added for comparisons that do not have any direct
evidence. Therefore, there is a row and column for every pair of treatments in the network. This
hat matrix is used to calculate the transition matrices for the random walk in netcontrib.

Value
A list with two hat matrices: common (common effects model) and random (random effects model).

Author(s)
Guido Schwarzer <[email protected]>

References
Davies AL, Papakonstantinou T, Nikolakopoulou A, Rücker G, Galla T (2022): Network meta-
analysis and random walks. Statistics in Medicine, 41, 2091–2114
Krahn U, Binder H, König J (2013): A graphical tool for locating inconsistency in network meta-
analyses. BMC Medical Research Methodology, 13, 35
Rücker G (2012): Network meta-analysis, electrical networks and graph theory. Research Synthesis
Methods, 3, 312–24

See Also
netmeta, netcontrib, netheat

Examples
data(Dong2013)
# Only consider first ten studies for concise output
first10 <- subset(Dong2013, id <= 10)
p1 <- pairwise(treatment, death, randomized, studlab = id,
data = first10, sm = "OR")
net1 <- netmeta(p1, common = FALSE)

hatmatrix(net1)
hatmatrix(net1, method = "k")
54 heatplot

hatmatrix(net1, method = "k", type = "studies")

hatmatrix(net1, method = "d")
hatmatrix(net1, method = "d", type = "long")
hatmatrix(net1, method = "d", type = "full")

heatplot Generic function for heat plots

Description
Generic function for heat plots

Usage
heatplot(x, ...)

Arguments
x An R object.
... Additional arguments.

Details
For more details, look at the following function to generate heat plots:

• heatplot.netmeta
• heatplot.crossnma (if installed)

Author(s)
Guido Schwarzer <[email protected] >

Examples
data(Senn2013)

# Only consider first five studies (to reduce runtime of example)

#
studies <- unique(Senn2013$studlab)
Senn2013.5 <- subset(Senn2013, studlab %in% studies[1:5])

# Conduct random effects network meta-analysis with

# placebo as reference treatment
#
net1 <- netmeta(TE, seTE, treat1.long, treat2.long, studlab,
data = Senn2013.5, sm = "MD", common = FALSE, reference = "plac")

# Generate a heat plot (with abbreviated treatment labels)

heatplot.netmeta 55

#
heatplot(net1, nchar.trts = 4)

heatplot.netmeta Heat Plot

Description
Produces a heat plot containing treatment estimates with confidence intervals for all possible pair-
wise comparisons.

Usage
## S3 method for class 'netmeta'
heatplot(
x,
pooled = ifelse(x$random, "random", "common"),
seq = x$seq,
nchar.trts = x$nchar.trts,
low.colour = "red",
mid.colour = "white",
high.colour = "springgreen4",
size = 6,
size.trt = 16,
size.axis = 12,
digits = gs("digits.forest"),
backtransf = x$backtransf,
...
)

Arguments
x An object of class netmeta.
pooled A character string indicating whether results for the common ("common") or
random effects model ("random") should be plotted. Can be abbreviated.
seq A character or numerical vector specifying the sequence of treatments in rows
and columns of the heat plot.
nchar.trts A numeric defining the minimum number of characters used to create unique
treatment names.
low.colour A string indicating the colour of low relative treatment effects for the heat plot
(e.g odds ratio of ~0.5)
mid.colour A string indicating the colour of null relative treatment effects for the heat plot
(e.g odds ratio of ~1.0).
high.colour A string indicating the colour of high relative treatment effects for the heat plot
(e.g odds ratio of ~2.0).
56 invmat

size The size of cell entries with the relative treatment effect and confidence intervals.
size.trt The size of treatment names placed on the top and left of the plot.
size.axis The size of labels on the top and left of the plot
digits Minimal number of significant digits for treatment effects and confidence inter-
vals, see print.default.
backtransf A logical indicating whether results should be back transformed in forest plots.
If backtransf = TRUE, results for sm = "OR" are presented as odds ratios rather
than log odds ratios, for example.
... Additional arguments.

Value
League heat plot, where a color scale is used to represent the values of relative treatment effects.

Examples
data(Senn2013)

# Only consider first five studies (to reduce runtime of example)

#
studies <- unique(Senn2013$studlab)
Senn2013.5 <- subset(Senn2013, studlab %in% studies[1:5])

# Conduct random effects network meta-analysis with

# placebo as reference treatment
#
net1 <- netmeta(TE, seTE, treat1.long, treat2.long, studlab,
data = Senn2013.5, sm = "MD", common = FALSE, reference = "plac")

# Generate a heat plot (with abbreviated treatment labels)

#
heatplot(net1, nchar.trts = 4)

invmat Moore-Penrose Pseudoinverse of a Matrix

Description
Calculates the Moore-Penrose pseudoinverse of a square matrix X.

Usage
invmat(X)

Arguments
X A square matrix.
invmat 57

Details

This function is used by default in R package netmeta to calculate the Moore-Penrose pseudoin-
verse L+ of the Laplacian matrix L (Rücker, 2012):
L+ = (X - J / n)−1 + J / n with identity matrix J of dimension nxn.

Value

The Moore-Penrose pseudoinverse for matrix X.

Author(s)

Gerta Rücker <[email protected]>, Guido Schwarzer <[email protected]

References

Rücker G (2012): Network meta-analysis, electrical networks and graph theory. Research Synthesis
Methods, 3, 312–24

See Also

netmeta, solve

Examples

data(smokingcessation)

p1 <- pairwise(list(treat1, treat2, treat3),

event = list(event1, event2, event3), n = list(n1, n2, n3),
data = smokingcessation, sm = "OR")
net1 <- netmeta(p1)

invmat(net1$L.matrix.common)

## Not run:
data(Senn2013)

net2 <- netmeta(TE, seTE, treat1.long, treat2.long, studlab,

data = Senn2013)
L1 <- net2$L.matrix.common
L2 <- invmat(net2$Lplus.matrix.common)
all.equal(round(L1, 10), round(L2, 10))

## End(Not run)
58 Linde2015

Linde2015 Network meta-analysis of treatments for depression

Description
Network meta-analysis of nine classes of antidepressants including placebo for the primary care
setting; partly shown in Linde et al. (2015), supplementary Table 2.

Format
A data frame with the following columns:

id Study ID
author First author
year Publication year
treatment1 First treatment
treatment2 Second treatment
treatment3 Third treatment
n1 Number of patients receiving first treatment
resp1 Number of early responder (treatment 1)
remi1 Number of early remissions (treatment 1)
loss1 Number of patients loss to follow-up (treatment 1)
loss.ae1 Number of patients loss to follow-up due to adverse events (treatment 1)
ae1 Number of patients with adverse events (treatment 1)
n2 Number of patients receiving second treatment
resp2 Number of early responder (treatment 2)
remi2 Number of early remissions (treatment 2)
loss2 Number of patients loss to follow-up (treatment 2)
loss.ae2 Number of patients loss to follow-up due to adverse events (treatment 2)
ae2 Number of patients with adverse events (treatment 2)
n3 Number of patients receiving third treatment
resp3 Number of early responder (treatment 3)
remi3 Number of early remissions (treatment 3)
loss3 Number of patients loss to follow-up (treatment 3)
loss.ae3 Number of patients loss to follow-up due to adverse events (treatment 3)
ae3 Number of patients with adverse events (treatment 3)

Source

Linde K, Kriston L, Rücker G, et al. (2015): Efficacy and acceptability of pharmacological treat-
ments for depressive disorders in primary care: Systematic review and network meta-analysis. An-
nals of Family Medicine, 13, 69–79

See Also

pairwise, metabin, netmeta, netposet

Linde2016 59

Examples
data(Linde2015)

# Transform data from arm-based format to contrast-based format

# Outcome: early response
p1 <- pairwise(list(treatment1, treatment2, treatment3),
event = list(resp1, resp2, resp3),
n = list(n1, n2, n3),
studlab = id, data = Linde2015, sm = "OR")
p1

## Not run:
# Define order of treatments
trts <- c("TCA", "SSRI", "SNRI", "NRI", "Low-dose SARI",
"NaSSa", "rMAO-A", "Hypericum", "Placebo")

# Conduct random effects network meta-analysis

net1 <- netmeta(p1, common = FALSE, reference = "Placebo", seq = trts)
print(net1, digits = 2)

## End(Not run)

Linde2016 Network meta-analysis of primary care depression treatments

Description
Network meta-analysis of 22 treatments (including placebo and usual care) for the primary care of
depression.

Format
A data frame with the following columns:

id Study ID
author First author
year Year of publication
treat1 First treatment (abbreviated)
treat2 Second treatment (abbreviated)
treat1.long First treatment
treat2.long Second treatment
lnOR Response after treatment (log odds ratio)
selnOR Standard error of log odds ratio
resp1 Responder (first treatment)
n1 Sample size (first treatment)
resp2 Responder (second treatment)
n2 Sample size (second treatment)
60 metabias.netmeta

Source
Linde K, Rücker G, Schneider A et al. (2016): Questionable assumptions hampered interpretation
of a network meta-analysis of primary care depression treatments. Journal of Clinical Epidemiol-
ogy, 71, 86–96

See Also
netmeta, netcomb

Examples
data(Linde2016)

# Only consider studies including Face-to-face PST (to reduce

# runtime of example)
#
face <- subset(Linde2016, id %in% c(16, 24, 49, 118))

# Conduct random effects network meta-analysis

#
net1 <- netmeta(lnOR, selnOR, treat1, treat2, id,
data = face, reference.group = "placebo",
sm = "OR", common = FALSE, nchar.trts = 6)
#
net1

## Not run:
# Conduct random effects network meta-analysis
#
net2 <- netmeta(lnOR, selnOR, treat1, treat2, id,
data = Linde2016, reference.group = "placebo",
sm = "OR", common = FALSE, nchar.trts = 6)
#
net2

## End(Not run)

metabias.netmeta Test of funnel plot asymmetry in network meta-analysis

Description
Test of funnel plot asymmetry in network meta-analysis

Usage
## S3 method for class 'netmeta'
metabias(
x,
metabias.netmeta 61

order,
pooled = ifelse(x$random, "random", "common"),
method.bias = "Egger",
lump.comparator = FALSE,
...
)

Arguments
x An object of class netmeta.
order A mandatory character or numerical vector specifying the order of treatments or
list of comparators (see Details).
pooled A character string indicating whether results for the common ("common") or ran-
dom effects model ("random") should be used in test of funnel plot asymmetry.
Can be abbreviated.
method.bias A character vector indicating which test(s) for funnel plot asymmatrx to use.
Admissible values are "Begg", "Egger", and "Thompson", can be abbreviated.
See function metabias.meta.
lump.comparator
A logical indicating whether comparators should be lumped, e.g., to specify
inactive treatments. information on direct comparisons should be added to the
plot.
... Additional arguments (passed on to metabias.meta).

Details
Test of funnel plot asymmetry in network meta-analysis
Argument order is mandatory to determine the order of treatments (Chaimani et al., 2013):
“[...] investigators should order the treatments in a meaningful way and make assumptions about
how small studies differ from large ones. For example, if they anticipate that newer treatments
are favored in small trials, then they could name the treatments from oldest to newest so that all
comparisons refer to ‘old versus new intervention’. Other possibilities include defining the com-
parisons so that all refer to an active treatment versus placebo or sponsored versus non-sponsored
intervention.”
Alternatively, it is possible to only provide a single or few treatment name(s) in argument order
to define the comparator(s). In this case only comparisons with this / these treatment(s) will be
considered. If argument lump.comparator is TRUE, all comparators will be lumped into a single
group.

Value
A list with class metabias containing the following components if a test for funnel plot asymmetry
is conducted:

statistic Test statistic.

df The degrees of freedom of the test statistic in the case that it follows a t distri-
bution.
62 metabias.netmeta

pval The p-value for the test.

estimate Estimates used to calculate test statisic.
method A character string indicating what type of test was used.
title Title of Cochrane review.
complab Comparison label.
outclab Outcome label.
var.model A character string indicating whether none, multiplicative, or additive residual
heterogeneity variance was assumed.
method.bias As defined above.
x Network meta-analysis object.
version Version of R package meta used to create object.
version.netmeta
Version of R package netmeta used to create object.
Or a list with the following elements if test is not conducted due to the number of studies:
k Number of comparisons.
k.min Minimum number of comparisons to perform test for funnel plot asymmetry.
version Version of R package meta used to create object.
version.netmeta
Version of R package netmeta used to create object.

Author(s)
Guido Schwarzer <[email protected]>

References
Chaimani A & Salanti G (2012): Using network meta-analysis to evaluate the existence of small-
study effects in a network of interventions. Research Synthesis Methods, 3, 161–76
Chaimani A, Higgins JP, Mavridis D, Spyridonos P, Salanti G (2013): Graphical tools for network
meta-analysis in STATA. PLOS ONE, 8, e76654

See Also
netmeta, funnel.netmeta, metabias

Examples
## Not run:
data(Senn2013)

net1 <- netmeta(TE, seTE, treat1, treat2, studlab,

data = Senn2013, sm = "MD")

# Test for asymmetry in 'comparison-adjusted' funnel plot not

# conducted as argument 'order' is missing
netbind 63

#
try(metabias(net1))

# Test for funnel plot asymmetry comparing active treatments with

# placebo
metabias(net1, order = "pl")

# Rank test
#
metabias(net1, order = "pl", method.bias = "Begg")

# Test for funnel plot asymmetry based on (non-sensical) alphabetic

# order of treatments with placebo as last treatment
#
ord <- c("a", "b", "me", "mi", "pi", "r", "si", "su", "v", "pl")
metabias(net1, order = ord)

## End(Not run)

netbind Combine network meta-analysis objects

Description
This function can be used to combine network meta-analysis objects which is especially useful to
generate a forest plot with results of several network meta-analyses.

Usage
netbind(
...,
name,
common,
random,
col.study = "black",
col.inside = "white",
col.square = "gray",
col.square.lines = col.square,
backtransf,
reference.group,
baseline.reference,
warn.deprecated = gs("warn.deprecated"),
fixed,
comb.fixed,
comb.random
)
64 netbind

Arguments
... Any number of network meta-analysis objects or a single list with network meta-
analyses.
name An optional character vector providing descriptive names for network meta-
analysis objects.
common A logical indicating whether results for the common effects model should be
reported.
random A logical indicating whether results for the random effects model should be
reported.
col.study The colour for network estimates and confidence limits.
col.inside The colour for network estimates and confidence limits if confidence limits are
completely within squares.
col.square The colour for squares.
col.square.lines
The colour for the outer lines of squares.
backtransf A logical indicating whether results should be back transformed. If backtransf
= TRUE (default), results for sm = "OR" are printed as odds ratios rather than log
odds ratios, for example.
reference.group
Reference treatment.
baseline.reference
A logical indicating whether results should be expressed as comparisons of other
treatments versus the reference treatment (default) or vice versa. This argument
is only considered if reference.group has been specified.
warn.deprecated
A logical indicating whether warnings should be printed if deprecated arguments
are used.
fixed Deprecated argument; replaced by common.
comb.fixed Deprecated argument; replaced by common.
comb.random Deprecated argument; replaced by random.

Value
An object of class "netbind" with corresponding forest function. The object is a list containing
the following components:

common A data frame with results for the common effects model.
random A data frame with results for the random effects model.
sm Summary measure used in network meta-analyses.
level.ma Level for confidence intervals.
reference.group, baseline.reference
As defined above.
netcomb 65

Author(s)
Guido Schwarzer <[email protected]>

See Also
netmeta, netcomb, discomb, forest.netbind

Examples
data(Linde2016)

# Only consider studies including Face-to-face PST (to reduce

# runtime of example)
#
face <- subset(Linde2016, id %in% c(16, 24, 49, 118))

# Standard random effects NMA model (with placebo as reference

# treatment)
#
net1 <- netmeta(lnOR, selnOR, treat1, treat2, id,
data = face, reference.group = "placebo",
sm = "OR", common = FALSE)

# Additive CNMA model with placebo as inactive component and

# reference
#
nc1 <- netcomb(net1, inactive = "placebo")

# Combine results of standard NMA and CNMA

#
nb1 <- netbind(nc1, net1,
name = c("Additive CNMA", "Standard NMA"),
col.study = c("red", "black"), col.square = c("red", "black"))
forest(nb1,
col.by = "black", addrow.subgroups = FALSE,
fontsize = 10, spacing = 0.7, squaresize = 0.9,
label.left = "Favours Placebo",
label.right = "Favours other")

netcomb Additive network meta-analysis for combinations of treatments

Description
Some treatments in a network meta-analysis may be combinations of other treatments or have com-
mon components. The influence of individual components can be evaluated in an additive network
meta-analysis model assuming that the effect of treatment combinations is the sum of the effects of
its components. This function implements this additive model in a frequentist way.
66 netcomb

Usage
netcomb(
x,
inactive = NULL,
sep.comps = "+",
C.matrix,
common = x$common,
random = x$random | !is.null(tau.preset),
tau.preset = NULL,
details.chkident = FALSE,
nchar.comps = x$nchar.trts,
func.inverse = invmat,
backtransf = x$backtransf,
na.unident = TRUE,
warn.deprecated = gs("warn.deprecated"),
...
)

Arguments
x An object of class netmeta.
inactive A character string defining the inactive treatment component (see Details).
sep.comps A single character to define separator between treatment components.
C.matrix C matrix (see Details).
common A logical indicating whether a common effects network meta-analysis should be
conducted.
random A logical indicating whether a random effects network meta-analysis should be
conducted.
tau.preset An optional value for the square-root of the between-study variance τ 2 .
details.chkident
A logical indicating whether details on unidentifiable components should be
printed.
nchar.comps A numeric defining the minimum number of characters used to create unique
names for components (see Details).
func.inverse R function used to calculate the pseudoinverse of the Laplacian matrix L (see
netmeta).
backtransf A logical indicating whether results should be back transformed in printouts and
forest plots.
na.unident A logical indicating whether unidentifiable components and combinations should
be set to missing values.
warn.deprecated
A logical indicating whether warnings should be printed if deprecated arguments
are used.
... Additional arguments (to catch deprecated arguments).
netcomb 67

Details
Treatments in network meta-analysis (NMA) can be complex interventions. Some treatments may
be combinations of others or have common components. The standard analysis provided by netmeta
is a NMA where all existing (single or combined) treatments are considered as different nodes in
the network. Exploiting the fact that some treatments are combinations of common components, an
additive component network meta-analysis (CNMA) model can be used to evaluate the influence of
individual components. This model assumes that the effect of a treatment combination is the sum of
the effects of its components which implies that common components cancel out in comparisons.
The additive CNMA model has been implemented using Bayesian methods (Mills et al., 2012;
Welton et al., 2013). This function implements the additive model in a frequentist way (Rücker et
al., 2020).
The underlying multivariate model is given by

δ = Bθ, θ = Cβ

with

δ vector of true treatment effects (differences) from individual studies,

B design matrix describing the structure of the network,
θ parameter vector that represents the existing combined treatments,
C matrix describing how the treatments are composed,
β parameter vector representing the treatment components.

All parameters are estimated using weighted least squares regression.

Argument inactive can be used to specify a single component that does not have any therapeutic
value. Accordingly, it is assumed that the treatment effect of the combination of this component
with an additional treatment component is equal to the treatment effect of the additional component
alone.
Argument sep.comps can be used to specify the separator between individual components. By
default, the matrix C is calculated internally from treatment names. However, it is possible to
specify a different matrix using argument C.matrix.
By default, component names are not abbreviated in printouts. However, in order to get more
concise printouts, argument nchar.comps can be used to define the minimum number of characters
for abbreviated component names (see abbreviate, argument minlength). R function treats is
utilised internally to create abbreviated component names.

Value
An object of class netcomb with corresponding print, summary, and forest functions. The object
is a list containing the following components:

studlab Study labels.

treat1 Label/Number for first treatment.
treat2 Label/Number for second treatment.
TE Estimate of treatment effect, i.e. difference between first and second treatment.
68 netcomb

seTE Standard error of treatment estimate.

seTE.adj.common, seTE.adj.random
Standard error of treatment estimate, adjusted for multi-arm studies.
design Design of study providing pairwise comparison.
event1 Number of events in first treatment group.
event2 Number of events in second treatment group.
n1 Number of observations in first treatment group.
n2 Number of observations in second treatment group.
k Total number of studies.
m Total number of pairwise comparisons.
n Total number of treatments.
d Total number of designs (corresponding to the unique set of treatments com-
pared within studies).
c Total number of components.
trts Treatments included in network meta-analysis.
k.trts Number of studies evaluating a treatment.
n.trts Number of observations receiving a treatment (if arguments n1 and n2 are pro-
vided).
events.trts Number of events observed for a treatment (if arguments event1 and event2
are provided).
studies Study labels coerced into a factor with its levels sorted alphabetically.
narms Number of arms for each study.
designs Unique list of designs present in the network. A design corresponds to the set of
treatments compared within a study.
comps Unique list of components present in the network.
TE.nma.common, TE.nma.random
A vector of length m of consistent treatment effects estimated by network meta-
analysis (nma) (common and random effects model).
seTE.nma.common, seTE.nma.random
A vector of length m of effective standard errors estimated by network meta-
analysis (common and random effects model).
lower.nma.common, lower.nma.random
A vector of length m of lower confidence interval limits for consistent treat-
ment effects estimated by network meta-analysis (common and random effects
model).
upper.nma.common, upper.nma.random
A vector of length m of upper confidence interval limits for the consistent treat-
ment effects estimated by network meta-analysis (common and random effects
model).
statistic.nma.common, statistic.nma.random
A vector of length m of z-values for test of treatment effect for individual com-
parisons (common and random effects model).
netcomb 69

pval.nma.common, pval.nma.random
A vector of length m of p-values for test of treatment effect for individual com-
parisons (common and random effects model).
TE.cnma.common, TE.cnma.random
A vector of length m of consistent treatment effects estimated by the additive
(common and random effects) model.
seTE.cnma.common, seTE.cnma.random
A vector of length m with standard errors estimated by the additive (common
and random effects) model.
lower.cnma.common, lower.cnma.random
A vector of length m of lower confidence interval limits for consistent treatment
effects estimated by the additive (common and random effects) model.
upper.cnma.common, upper.cnma.random
A vector of length m of upper confidence interval limits for consistent treatment
effects estimated by the additive (common and random effects) model.
statistic.cnma.common, statistic.cnma.random
A vector of length m of z-values for the test of an overall effect estimated by the
additive (common and random effects) model.
pval.cnma.common, pval.cnma.random
A vector of length m of p-values for the test of an overall effect estimated by the
additive (common and random effects) model.
TE.common, TE.random
nxn matrix with overall treatment effects estimated by the additive (common
and random effects) model.
seTE.common, seTE.random
nxn matrix with standard errors estimated by the additive (common and random
effects) model.
lower.common, upper.common, lower.random, upper.random
nxn matrices with lower and upper confidence interval limits estimated by the
additive (common and random effects) model.
statistic.common, pval.common, statistic.random, pval.random
nxn matrices with z-values and p-values for test of overall effect estimated by
the additive (common and random effects) model.
Comp.common, Comp.random
A vector of component effects (common and random effects model).
seComp.common, seComp.random
A vector with corresponding standard errors (common and random effects model).
lower.Comp.common, lower.Comp.random
A vector with lower confidence limits for components (common and random
effects model).
upper.Comp.common, upper.Comp.random
A vector with upper confidence limits for components (common and random
effects model).
statistic.Comp.common, statistic.Comp.random
A vector with z-values for the overall effect of components (common and ran-
dom effects model).
70 netcomb

pval.Comp.common, pval.Comp.random
A vector with p-values for the overall effect of components (common and ran-
dom effects model).
Comb.common, Comb.random
A vector of combination effects (common and random effects model).
seComb.common, seComb.random
A vector with corresponding standard errors (common and random effects model).
lower.Comb.common, lower.Comb.random
A vector with lower confidence limits for combinations (common and random
effects model).
upper.Comb.common, upper.Comb.random
A vector with upper confidence limits for combinations (common and random
effects model).
statistic.Comb.common, statistic.Comb.random
A vector with z-values for the overall effect of combinations (common and ran-
dom effects model).
pval.Comb.common, pval.Comb.random
A vector with p-values for the overall effect of combinations (common and ran-
dom effects model).
Q.additive Overall heterogeneity / inconsistency statistic (additive model).
df.Q.additive Degrees of freedom for test of heterogeneity / inconsistency (additive model).
pval.Q.additive
P-value for test of heterogeneity / inconsistency (additive model).
tau Square-root of between-study variance (additive model).
I2, lower.I2, upper.I2
I-squared, lower and upper confidence limits.
Q.standard Overall heterogeneity / inconsistency statistic (standard model).
df.Q.standard Degrees of freedom for test of heterogeneity / inconsistency (standard model).
pval.Q.standard
P-value for test of heterogeneity / inconsistency (standard model).
Q.diff Test statistic for difference in goodness of fit between standard and additive
model.
df.Q.diff Degrees of freedom for difference in goodness of fit between standard and addi-
tive model.
pval.Q.diff P-value for difference in goodness of fit between standard and additive model.
A.matrix Adjacency matrix (nxn).
B.matrix Edge-vertex incidence matrix (mxn).
C.matrix As defined above.
sm Summary measure.
level.ma Level for confidence intervals.
common, random, tau.preset
As defined above.
sep.trts A character used in comparison names as separator between treatment labels.
netcomb 71

nchar.comps A numeric defining the minimum number of characters used to create unique
component names.
inactive, sep.comps
As defined above.
backtransf A logical indicating whether results should be back transformed in printouts and
forest plots.
title Title of meta-analysis / systematic review.
x As defined above.
call Function call.
version Version of R package netmeta used to create object.

Note
This function calculates effects for individual components and complex interventions present in the
network.
R function netcomplex can be used to calculate the effect for arbitrary complex interventions in
a component network meta-analysis. Furthermore, R function netcomparison can be used to cal-
culate the effect for comparisons of two arbitrary complex intervention in a component network
meta-analysis.

Author(s)
Gerta Rücker <[email protected]>, Guido Schwarzer <[email protected]

References
König J, Krahn U, Binder H (2013): Visualizing the flow of evidence in network meta-analysis and
characterizing mixed treatment comparisons. Statistics in Medicine, 32, 5414–29
Mills EJ, Thorlund K, Ioannidis JP (2012): Calculating additive treatment effects from multiple
randomized trials provides useful estimates of combination therapies. Journal of Clinical Epidemi-
ology, 65, 1282–8
Rücker G, Petropoulou M, Schwarzer G (2020): Network meta-analysis of multicomponent inter-
ventions. Biometrical Journal, 62, 808–21
Welton NJ, Caldwell DM, Adamopoulos E, Vedhara K (2009): Mixed treatment comparison meta-
analysis of complex interventions: psychological interventions in coronary heart disease. American
Journal of Epidemiology, 169: 1158–65

See Also
discomb, netmeta, forest.netcomb, print.netcomb, netcomplex, netcomparison

Examples
data(Linde2016)

# Only consider studies including Face-to-face PST (to reduce

# runtime of example)
72 netcomb

#
face <- subset(Linde2016, id %in% c(16, 24, 49, 118))

# Conduct random effects network meta-analysis

#
net1 <- netmeta(lnOR, selnOR, treat1, treat2, id,
data = face, ref = "placebo", sm = "OR", common = FALSE)
net1
forest(net1, xlim = c(0.2, 50))

# Additive model for treatment components (with placebo as inactive

# treatment)
#
nc1 <- netcomb(net1, inactive = "placebo")
nc1
forest(nc1, xlim = c(0.2, 50))

## Not run:
# Specify, order of treatments
#
trts <- c("TCA", "SSRI", "SNRI", "NRI", "Low-dose SARI", "NaSSa",
"rMAO-A", "Ind drug", "Hypericum", "Face-to-face CBT",
"Face-to-face PST", "Face-to-face interpsy", "Face-to-face psychodyn",
"Other face-to-face", "Remote CBT", "Self-help CBT", "No contact CBT",
"Face-to-face CBT + SSRI", "Face-to-face interpsy + SSRI",
"Face-to-face PST + SSRI", "UC", "Placebo")
#
# Note, three treatments are actually combinations of 'SSRI' with
# other components:
# "Face-to-face CBT + SSRI",
# "Face-to-face interpsy + SSRI",
# "Face-to-face PST + SSRI"

# Conduct random effects network meta-analysis

#
net2 <- netmeta(lnOR, selnOR, treat1, treat2, id,
data = Linde2016, ref = "placebo",
seq = trts, sm = "OR", common = FALSE)
net2
forest(net2, xlim = c(0.2, 50))

# Additive model for treatment components (with placebo as inactive

# treatment)
#
nc2 <- netcomb(net2, inactive = "placebo")
nc2
forest(nc2, xlim = c(0.2, 50))

## End(Not run)
netcomparison 73

netcomparison Calculate comparison effects of two arbitrary complex interventions

in component network meta-analysis

Description
Calculate comparison effects of two arbitrary complex interventions (i.e., combinations of several
components) in component network meta-analysis.

Usage
netcomparison(
x,
treat1,
treat2,
common = x$common,
random = x$random,
level = x$level.ma,
nchar.comps = x$nchar.comps,
backtransf = x$backtransf,
warn.deprecated = gs("warn.deprecated"),
...
)

## S3 method for class 'netcomparison'

print(
x,
common = x$common,
random = x$random,
backtransf = x$backtransf,
nchar.comps = x$nchar.comps,
digits = gs("digits"),
digits.stat = gs("digits.stat"),
digits.pval = gs("digits.pval"),
scientific.pval = gs("scientific.pval"),
zero.pval = gs("zero.pval"),
JAMA.pval = gs("JAMA.pval"),
big.mark = gs("big.mark"),
legend = TRUE,
warn.deprecated = gs("warn.deprecated"),
...
)

Arguments
x An object of class netcomb or netcomparison (print function).
treat1 A character vector defining the first complex intervention(s).
74 netcomparison

treat2 A character vector defining the second complex intervention(s).

common A logical indicating whether results for common effects model should be con-
ducted.
random A logical indicating whether results for random effects model should be con-
ducted.
level The level used to calculate confidence intervals for combinations of components.
nchar.comps A numeric defining the minimum number of characters used to create unique
names for components (see Details).
backtransf A logical indicating whether printed results should be back transformed. If
backtransf=TRUE, results for sm="OR" are printed as odds ratios rather than
log odds ratios.
warn.deprecated
A logical indicating whether warnings should be printed if deprecated arguments
are used.
... Additional arguments (to catch deprecated arguments).
digits Minimal number of significant digits, see print.default.
digits.stat Minimal number of significant digits for z-value of test for overall effect, see
print.default.
digits.pval Minimal number of significant digits for p-values, see print.default.
scientific.pval
A logical specifying whether p-values should be printed in scientific notation,
e.g., 1.2345e-01 instead of 0.12345.
zero.pval A logical specifying whether p-values should be printed with a leading zero.
JAMA.pval A logical specifying whether p-values for test of combination effect should be
printed according to JAMA reporting standards.
big.mark A character used as thousands separator.
legend A logical indicating whether a legend should be printed.

Details
R functions netcomb and discomb calculate effects for individual components and complex inter-
ventions present in the component network meta-analysis (CNMA). This function can be used to
calculate the effect for comparisons of two arbitrary complex interventions defined by arguments
treat1 and treat2.
All complex interventions occuring in the network are considered for the first complex intervention
if argument treat1 is missing. The reference group defined in the (C)NMA is used as second
complex intervention if argument treat2 is missing. The first complex intervention in the (C)NMA
is used if the reference group is not defined.
The following matrices are needed to calculate comparison effects of arbitrary complex interven-
tions, (Rücker et al., 2020, Section 3.2):

• B matrix describing how comparisons are composed by complex intervetions,

• C matrix describing how the complex interventions are composed by the components.
netcomparison 75

Internally, both matrices are constructed based on arguments x, treat1 and treat2.
By default, component names are not abbreviated in printouts. However, in order to get more
concise printouts, argument nchar.comps can be used to define the minimum number of characters
for abbreviated component names (see abbreviate, argument minlength). R function treats is
utilised internally to create abbreviated component names.

Value
A list is returned by the function netcomparison with the following elements:

comparison Comparison.
TE.common, TE.random
A vector of comparison effects (common and random effects model).
seTE.common, seTE.random
A vector with corresponding standard errors (common and random effects model).
lower.common, lower.random
A vector with lower confidence limits for comparisons (common and random
effects model).
upper.common, upper.random
A vector with upper confidence limits for comparisons (common and random
effects model).
statistic.common, statistic.random
A vector with z-values for the overall effect of comparisons (common and ran-
dom effects model).
pval.common, pval.random
A vector with p-values for the overall effect of comparisons (common and ran-
dom effects model).
trts Treatments included in comparisons.
comps Components included in comparisons.
treat1, treat2 A defined above.
common, random A defined above.
level, nchar.comps, backtransf, x
A defined above.
B.matrix B matrix.
C.matrix C matrix.

Note
R function netcomplex can be used to calculate the effect for arbitrary complex interventions in a
component network meta-analysis.

Author(s)
Guido Schwarzer <[email protected]>
76 netcomparison

References
Rücker G, Petropoulou M, Schwarzer G (2020): Network meta-analysis of multicomponent inter-
ventions. Biometrical Journal, 62, 808–21

See Also
netcomb, discomb, netcomplex

Examples
data(Linde2016)

# Only consider studies including Face-to-face PST (to reduce

# runtime of example)
#
face <- subset(Linde2016, id %in% c(16, 24, 49, 118))

# Conduct random effects network meta-analysis

#
net1 <- netmeta(lnOR, selnOR, treat1, treat2, id,
data = face, ref = "placebo", sm = "OR", common = FALSE)

# Additive model for treatment components (with placebo as inactive

# treatment)
#
nc1 <- netcomb(net1, inactive = "placebo")

# Result for comparison Face-to-face PST vs TCA

netcomparison(nc1, "Face-to-face PST", "TCA", nchar.comps = 4)
netcomparison(nc1, "F", "T", nchar.comps = 4)

# Result for comparison Face-to-face PST vs TCA + Placebo

netcomparison(nc1, "Face-to-face PST", "TCA + Plac", nchar.comps = 4)

## Not run:
# Artificial example
t1 <- rep("A", 3)
t2 <- c("B+C", "A+C", "C+D")
TE <- c(0, 1, 0)
seTE <- rep(1, 3)
# Conduct (C)NMA
net2 <- netmeta(TE, seTE, t1, t2, random = FALSE)
nc2 <- netcomb(net2)

# Result for comparison A vs B + D

netcomparison(nc2, "A", "B + D")
# Same results
netcomparison(nc2, "A", "B+D")
netcomparison(nc2, "A", "D+B")
netcomparison(nc2, "a", "d+b")

# Generated B matrix
netcomplex 77

netcomparison(nc2, "A", "B + D")$C.matrix

# Generated B matrix
netcomparison(nc2, "A", "B + D")$B.matrix

## End(Not run)

netcomplex Calculate effect of arbitrary complex interventions in component net-

work meta-analysis

Description
Calculate effect of arbitrary complex interventions (i.e., combinations of several components) in
component network meta-analysis.

Usage
netcomplex(
x,
complex,
common = x$common,
random = x$random,
level = x$level.ma,
nchar.comps = x$nchar.trts,
backtransf = x$backtransf,
warn.deprecated = gs("warn.deprecated"),
...
)

## S3 method for class 'netcomplex'

print(
x,
common = x$common,
random = x$random,
backtransf = x$backtransf,
nchar.comps = x$nchar.comps,
digits = gs("digits"),
digits.stat = gs("digits.stat"),
digits.pval = gs("digits.pval"),
scientific.pval = gs("scientific.pval"),
zero.pval = gs("zero.pval"),
JAMA.pval = gs("JAMA.pval"),
big.mark = gs("big.mark"),
legend = TRUE,
warn.deprecated = gs("warn.deprecated"),
...
)
78 netcomplex

Arguments
x An object of class netcomb or netcomplex (print function).
complex A matrix, vector or single numeric defining the complex intervention(s) (see
Details).
common A logical indicating whether results for common effects model should be con-
ducted.
random A logical indicating whether results for random effects model should be con-
ducted.
level The level used to calculate confidence intervals for combinations of components.
nchar.comps A numeric defining the minimum number of characters used to create unique
names for components (see Details).
backtransf A logical indicating whether printed results should be back transformed. If
backtransf=TRUE, results for sm="OR" are printed as odds ratios rather than
log odds ratios.
warn.deprecated
A logical indicating whether warnings should be printed if deprecated arguments
are used.
... Additional arguments (to catch deprecated arguments).
digits Minimal number of significant digits, see print.default.
digits.stat Minimal number of significant digits for z-value of test for overall effect, see
print.default.
digits.pval Minimal number of significant digits for p-values, see print.default.
scientific.pval
A logical specifying whether p-values should be printed in scientific notation,
e.g., 1.2345e-01 instead of 0.12345.
zero.pval A logical specifying whether p-values should be printed with a leading zero.
JAMA.pval A logical specifying whether p-values for test of combination effect should be
printed according to JAMA reporting standards.
big.mark A character used as thousands separator.
legend A logical indicating whether a legend should be printed.

Details
R functions netcomb and discomb only report results for complex interventions present in the net-
work. This function can be used to calculate the effect for arbitrary complex interventions.
Complex interventions can be specified using argument complex:

• a character vector with definition of complex interventions,

• a single numeric defining the number of components to combine in a complex intervention,
• a dedicated C matrix.
netcomplex 79

In order to calculate effects of arbitrary complex interventions, a C matrix is needed which describes
how the complex interventions are composed by the components (Rücker et al., 2020, Section
3.2). The C matrix is constructed internally if not provided by argument complex. All complex
interventions occuring in the network are considered if argument complex is missing.
By default, component names are not abbreviated in printouts. However, in order to get more
concise printouts, argument nchar.comps can be used to define the minimum number of characters
for abbreviated component names (see abbreviate, argument minlength). R function treats is
utilised internally to create abbreviated component names.

Value
A list is returned by the function netcomplex with the following elements:
complex Complex intervention(s).
Comb.common, Comb.random
A vector of combination effects (common and random effects model).
seComb.common, seComb.random
A vector with corresponding standard errors (common and random effects model).
lower.Comb.common, lower.Comb.random
A vector with lower confidence limits for combinations (common and random
effects model).
upper.Comb.common, upper.Comb.random
A vector with upper confidence limits for combinations (common and random
effects model).
statistic.Comb.common, statistic.Comb.random
A vector with z-values for the overall effect of combinations (common and ran-
dom effects model).
pval.Comb.common, pval.Comb.random
A vector with p-values for the overall effect of combinations (common and ran-
dom effects model).
common, random A defined above.
level, nchar.comps, backtransf, x
A defined above.
C.matrix C matrix.

Note
R function netcomparison can be used to calculate the effect for comparisons of two arbitrary
complex intervention in a component network meta-analysis.

Author(s)
Guido Schwarzer <[email protected]>

References
Rücker G, Petropoulou M, Schwarzer G (2020): Network meta-analysis of multicomponent inter-
ventions. Biometrical Journal, 62, 808–21
80 netcomplex

See Also
netcomb, discomb, netcomparison

Examples
data(Linde2016)

# Only consider studies including Face-to-face PST (to reduce

# runtime of example)
#
face <- subset(Linde2016, id %in% c(16, 24, 49, 118))

# Conduct random effects network meta-analysis

#
net1 <- netmeta(lnOR, selnOR, treat1, treat2, id,
data = face, ref = "placebo", sm = "OR", common = FALSE)

# Additive model for treatment components (with placebo as inactive

# treatment)
#
nc1 <- netcomb(net1, inactive = "placebo")

# Result for combination Face-to-face PST + SSRI

netcomplex(nc1, "Face-to-face PST + SSRI", nchar.comps = 4)
netcomplex(nc1, "F + S", nchar.comps = 4)

# Result for combination Face-to-face PST + SSRI + Placebo

netcomplex(nc1, "Face-to-face PST + SSRI + Plac", nchar.comps = 4)

## Not run:
# Artificial example
t1 <- rep("A", 3)
t2 <- c("B+C", "A+C", "C+D")
TE <- c(0, 1, 0)
seTE <- rep(1, 3)
# Conduct (C)NMA
net2 <- netmeta(TE, seTE, t1, t2, random = FALSE)
nc2 <- netcomb(net2)

# Result for combination A + B + C

netcomplex(nc2, "A + B + C")
# Same results
netcomplex(nc2, "A+B+C")
netcomplex(nc2, "B+C+A")
netcomplex(nc2, "C+B+A")
netcomplex(nc2, "c+b+a")

# Generated C matrix
netcomplex(nc2, c(LETTERS[1:4], "A+B+C"))$C.matrix

# Results for all possible combinations of two components

netcomplex(nc2, 2)
netconnection.default 81

# Results for all possible combinations of three components

netcomplex(nc2, 3)

## End(Not run)

netconnection.default Get information on network connectivity (number of subnetworks, dis-

tance matrix)

Description
To determine the network structure and to test whether a given network is fully connected. Network
information is provided as a triple of vectors treat1, treat2, and studlab where each row corre-
sponds to an existing pairwise treatment comparison (treat1, treat2) in a study (studlab). The
function calculates the number of subnetworks (connectivity components; value of 1 corresponds
to a fully connected network) and the distance matrix (in block-diagonal form in the case of sub-
networks). If some treatments are combinations of other treatments or have common components,
an analysis based on the additive network meta-analysis model might be possible, see discomb
function.

Usage
## Default S3 method:
netconnection(
data = NULL,
treat1,
treat2,
studlab = NULL,
subset = NULL,
sep.trts = ":",
nchar.trts = 666,
title = "",
details.disconnected = FALSE,
warn = FALSE,
...
)

## S3 method for class 'pairwise'

netconnection(
data,
sep.trts = ":",
nchar.trts = 666,
title = "",
details.disconnected = FALSE,
warn = FALSE,
...
82 netconnection.default

## S3 method for class 'netconnection'

print(
x,
digits = max(4, .Options$digits - 3),
nchar.trts = x$nchar.trts,
details = FALSE,
details.disconnected = x$details.disconnected,
...
)

netconnection(data, ...)

Arguments
data An optional data frame containing the study information.
treat1 Label / number for first treatment or a data frame created with pairwise.
treat2 Label / number for second treatment.
studlab An optional - but important! - vector with study labels (see Details).
subset An optional vector specifying a subset of studies to be used.
sep.trts A character used in comparison names as separator between treatment labels.
nchar.trts A numeric defining the minimum number of characters used to create unique
treatment names.
title Title of meta-analysis / systematic review.
details.disconnected
A logical indicating whether to print more details for disconnected networks.
warn A logical indicating whether warnings should be printed.
... Additional arguments (ignored at the moment)
x An object of class netconnection.
digits Minimal number of significant digits, see print.default.
details A logical indicating whether to print the distance matrix.

Value
An object of class netconnection with corresponding print function. The object is a list contain-
ing the following components:
treat1, treat2, studlab, title, warn, nchar.trts
As defined above.
k Total number of studies.
m Total number of pairwise comparisons.
n Total number of treatments.
n.subnets Number of subnetworks; equal to 1 for a fully connected network.
netconnection.default 83

D.matrix Distance matrix.

A.matrix Adjacency matrix.
L.matrix Laplace matrix.
call Function call.
version Version of R package netmeta used to create object.

Author(s)
Gerta Rücker <[email protected]>, Guido Schwarzer <[email protected]

See Also
netmeta, netdistance, discomb

Examples
data(Senn2013)

nc1 <- netconnection(treat1, treat2, studlab, data = Senn2013)

nc1

# Extract number of (sub)networks

#
nc1$n.subnets

# Extract distance matrix

#
nc1$D.matrix

## Not run:
# Conduct network meta-analysis (results not shown)
#
net1 <- netmeta(TE, seTE, treat1, treat2, studlab, data = Senn2013)

# Artificial example with two subnetworks

#
t1 <- c("G", "B", "B", "D", "A", "F")
t2 <- c("B", "C", "E", "E", "H", "A")
#
nc2 <- netconnection(t1, t2)
print(nc2, details = TRUE)

# Number of subnetworks
#
nc2$n.subnets

# Extract distance matrix

#
nc2$D.matrix

# Conduct network meta-analysis (results in an error message due to

84 netcontrib

# unconnected network)
try(net2 <- netmeta(1:6, 1:6, t1, t2, 1:6))

# Conduct network meta-analysis on first subnetwork

#
net2.1 <- netmeta(1:6, 1:6, t1, t2, 1:6, subset = nc2$subnet == 1)

# Conduct network meta-analysis on second subnetwork

#
net2.2 <- netmeta(1:6, 1:6, t1, t2, 1:6, subset = nc2$subnet == 2)

net2.1
net2.2

## End(Not run)

netcontrib Contribution matrix in network meta-analysis

Description
This function generates the contribution of direct comparisons to every network treatment compar-
ison. The output is a matrix where rows represent network treatment effects and columns represent
the contribution of direct treatment effects.

Usage
netcontrib(
x,
method = "shortestpath",
hatmatrix.F1000 = FALSE,
common = x$common,
random = x$random,
nchar.trts = x$nchar.trts,
warn.deprecated = gs("warn.deprecated"),
verbose = FALSE,
...
)

## S3 method for class 'netcontrib'

print(
x,
common = x$x$common,
random = x$x$random,
digits = 4,
nchar.trts = x$nchar.trts,
legend = TRUE,
netcontrib 85

warn.deprecated = gs("warn.deprecated"),
...
)

Arguments
x An object of class netmeta or netcontrib.
method A character string indicating which method is to calculate the contribution ma-
trix. Either "randomwalk" or "shortestpath", can be abbreviated.
hatmatrix.F1000
A logical indicating whether hat matrix given in F1000 article should be used
for method = "shortestpath".
common A logical indicating whether a contribution matrix should be printed for the
common effects network meta-analysis.
random A logical indicating whether a contribution matrix should be printed for the
random effects network meta-analysis.
nchar.trts A numeric defining the minimum number of characters used to create unique
treatment names (see Details).
warn.deprecated
A logical indicating whether warnings should be printed if deprecated arguments
are used.
verbose A logical indicating whether progress information should be printed.
... Additional arguments.
digits Minimal number of significant digits, see print.default.
legend A logical indicating whether a legend should be printed.

Details
In network meta-analysis (NMA), it is important to assess the influence of limitations or other
characteristics of individual studies on the estimates obtained from the network. To this end, the
contribution matrix shows how much each direct treatment effect contributes to each treatment
effect estimate from network meta-analysis.
We use ideas from graph theory to derive the proportion that is contributed by each direct treatment
effect. We start with the ’projection’ matrix in a two-step network meta-analysis model, called the H
matrix, which is analogous to the hat matrix in a linear regression model. H entries are translated to
proportion contributions based on the observation that the rows of H can be interpreted as flow net-
works. A stream is defined as the composition of a path and its associated flow (Papakonstantinou
et al., 2018).
To account for multi-arm trials, we use the H matrix from a two-step (aggregate) version of the graph
theoretical NMA model (Davies et al., 2022). This H matrix can be obtained from hatmatrix with
argument method = "davies".
Two methods are implemented to estimate the streams and as a result, the proportion contributions:
(1) If argument method = "randomwalk", an analytical random-walk (RW) approach is used (Davies
et al., 2022). Here, the "full" version of the aggregate H matrix (hatmatrix with arguments method
86 netcontrib

= "davies" and type = "full") is used to define RW transition matrices. For each pair of treat-
ments (ij) in the network, the elements in the corresponding row of H-full define a transition matrix
from node i to node j. We use the igraph package to find every (directed) path from node i to node
j. The flow through each path is then equal to the probability that a walker takes that path. This is
simply the product of the transition probabilities associated with each edge along the path.
(2) If argument method = "shortestpath", an iterative algorithm is used (Papakonstantinou et al.,
2018). Broadly speaking, each iteration of the algorithm consists of the following steps: (i) A path
in the evidence flow network is selected. (ii) The minimum flow through the edges making up the
path is identified. This is assigned as the flow associated with the path. (iii) The flow of the path
is subtracted from the values of flow in the edges that make up that path. This means that the edge
corresponding to the minimum flow in that path is removed from the graph. (iv) A new path is then
selected from the remaining graph. The process repeats until all the evidence flow in the edges has
been assigned to a path.
In the original F1000 paper (Papakonstantinou et al., 2018), the hat matrix used did not account for
correlations due to multi-arm trials. For reproducibility the result of this version can be obtained
by specifying hatmatrix.F1000 = TRUE for method = "shortestpath". For other purposes, this
method is not recommended.
Once the streams have been identified (either by method (1) or (2)), the proportion contribution of
each direct comparison is equal to the sum over the flow of evidence in each path containing that
edge divided by the number of edges that make up that path.
By default, treatment names are not abbreviated in printouts. However, in order to get more concise
printouts, argument nchar.trts can be used to define the minimum number of characters for ab-
breviated treatment names (see abbreviate, argument minlength). R function treats is utilised
internally to create abbreviated treatment names.
Calculation of network contributions can be compute-intensive for the random-walk approach in
large networks. Crude information on the computation progress is printed if argument verbose is
TRUE. In addition, computation times are printed if R package tictoc is installed.

Value
An object of class netcontrib with corresponding print function. The object is a list containing
the following components:

common Numeric matrix of percentage contributions of direct comparisons for each net-
work comparison for the common effects model.
random Numeric matrix of percentage contributions of direct comparisons for each net-
work comparison for the random effects model.
x As defined above.
tictoc.common Computation times under common effects model (if R package tictoc is in-
stalled).
tictoc.random Computation times under random effects model (if R package tictoc is installed).

with the contribution matrices for common and random NMA. Each matrix has the percentage
contributions of each direct comparison as columns for each network comparison, direct or indirect
as rows.
netdistance 87

Author(s)
Theodoros Papakonstantinou <[email protected]>, Annabel Davies <[email protected]>

References
Davies AL, Papakonstantinou T, Nikolakopoulou A, Rücker G, Galla T (2022): Network meta-
analysis and random walks. Statistics in Medicine, 41, 2091–2114
Papakonstantinou, T., Nikolakopoulou, A., Rücker, G., Chaimani, A., Schwarzer, G., Egger, M.,
Salanti, G. (2018): Estimating the contribution of studies in network meta-analysis: paths, flows
and streams. F1000Research

See Also
netmeta

Examples
# Use the Woods dataset
#
data("Woods2010")
p1 <- pairwise(treatment, event = r, n = N,
studlab = author, data = Woods2010, sm = "OR")

net1 <- netmeta(p1)

cm <- netcontrib(net1)
cm

netcontrib(net1, method = "r")

netdistance Calculate distance matrix for an adjacency matrix

Description
Calculate distance matrix for an adjacency matrix based on distance algorithm by Müller et al.
(1987).

Usage
netdistance(x)

Arguments
x Either a netmeta object or an adjacency matrix.

Author(s)
Gerta Rücker <[email protected]>
88 netgraph

References
Müller WR, Szymanski K, Knop JV, and Trinajstic N (1987): An algorithm for construction of the
molecular distance matrix. Journal of Computational Chemistry, 8, 170–73

See Also
netmeta, netconnection

Examples
data(smokingcessation)

p1 <- pairwise(list(treat1, treat2, treat3),

event = list(event1, event2, event3), n = list(n1, n2, n3),
data = smokingcessation, sm = "OR")
net1 <- netmeta(p1, common = FALSE)

netdistance(net1)

## Not run:
data(Senn2013)

net1 <- netmeta(TE, seTE, treat1, treat2, studlab,

data = Senn2013, sm = "MD")

netdistance(net1)
netdistance(net1$A.matrix)

## End(Not run)

netgraph Generic function for network graphs

Description
Generic function for network graphs

Usage
netgraph(x, ...)

Arguments
x An R object.
... Additional arguments.
netgraph 89

Details
For more details, look at the following functions to generate network graphs:
• netgraph.netmeta
• netgraph.netimpact
• netgraph.netconnection
• netgraph.netcomb
• netgraph.discomb

Author(s)
Guido Schwarzer <[email protected] >

Examples
data(smokingcessation)

# Transform data from arm-based format to contrast-based format

#
p1 <- pairwise(list(treat1, treat2, treat3),
event = list(event1, event2, event3), n = list(n1, n2, n3),
data = smokingcessation, sm = "OR")

# Conduct random effects network meta-analysis

#
net1 <- netmeta(p1, common = FALSE)

# Network graph with default settings

#
netgraph(net1)

## Not run:
data(Senn2013)

# Generation of an object of class 'netmeta' with reference

# treatment 'plac'
#
net2 <- netmeta(TE, seTE, treat1, treat2, studlab,
data = Senn2013, sm = "MD", reference = "plac")

# Network graph with default settings

#
netgraph(net2)

data(Woods2010)
p3 <- pairwise(treatment, event = r, n = N,
studlab = author, data = Woods2010, sm = "OR")
net3 <- netmeta(p3)

# Network graph with default settings

#
90 netgraph.discomb

netgraph(net3)

# Network graph with

# - number of studies for each pairwise comparison and
# - number of participants for each treatment arm
#
netgraph(net3, number.of.studies = TRUE,
labels = paste0(trts, " (n=", n.trts, ")"))

## End(Not run)

netgraph.discomb Network graph for objects of class discomb

Description

This function generates a graph of the evidence network.

Usage

## S3 method for class 'discomb'

netgraph(x, plastic = FALSE, ...)

Arguments

x An object of class discomb.

plastic A logical indicating whether the appearance of the comparisons should be in
’3D look’.
... Additional arguments passed on to netgraph.netmeta (see Details).

Details

The arguments seq and iterate are used internally and cannot be specified by the user.

Author(s)

Guido Schwarzer <[email protected]>, Gerta Rücker <[email protected]

See Also

discomb, netgraph.netmeta
netgraph.netcomb 91

Examples
# Artificial dataset
#
t1 <- c("A + B", "A + C", "A" , "A" , "D", "D", "E")
t2 <- c("C" , "B" , "B + C", "A + D", "E", "F", "F")
#
mean <- c(4.1, 2.05, 0, 0, 0.1, 0.1, 0.05)
se.mean <- rep(0.1, 7)
#
study <- paste("study", c(1:4, 5, 5, 5))
#
dat <- data.frame(mean, se.mean, t1, t2, study,
stringsAsFactors = FALSE)
#
trts <- c("A", "A + B", "A + C", "A + D",
"B", "B + C", "C", "D", "E", "F")
#
comps <- LETTERS[1:6]

# Use netconnection() to display network information

#
netconnection(t1, t2, study)

dc1 <- discomb(mean, se.mean, t1, t2, study, seq = trts)

netgraph(dc1)

netgraph.netcomb Network graph for objects of class netcomb

Description
This function generates a graph of the evidence network.

Usage
## S3 method for class 'netcomb'
netgraph(x, ...)

Arguments
x An object of class netcomb.
... Additional arguments passed on to netgraph.netmeta.

Author(s)
Guido Schwarzer <[email protected]>, Gerta Rücker <[email protected]
92 netgraph.netconnection

See Also

netcomb, netgraph.netmeta

Examples
data(Linde2016)

# Only consider studies including Face-to-face PST (to reduce

# runtime of example)
#
face <- subset(Linde2016, id %in% c(16, 24, 49, 118))

# Conduct random effects network meta-analysis

#
net1 <- netmeta(lnOR, selnOR, treat1, treat2, id,
data = face, ref = "placebo", sm = "OR", common = FALSE)

# Additive model for treatment components (with placebo as inactive

# treatment)
#
nc1 <- netcomb(net1, inactive = "placebo")

netgraph(nc1)

netgraph.netconnection
Network graph for objects of class netconnection

Description

This function generates a graph of the evidence network.

Usage

## S3 method for class 'netconnection'

netgraph(
x,
seq,
col = seq_len(x$n.subnets),
reference.group = NULL,
plastic = FALSE,
...
)
netgraph.netconnection 93

Arguments

x An object of class netconnection.

seq A character or numerical vector specifying the sequence of treatments arrange-
ment (anticlockwise if start.layout = "circle").
col A single color (or vector of colors) for lines connecting treatments (edges) if
argument plastic = FALSE (see Details).
reference.group
Reference treatment (only relevant for disconnected networks).
plastic A logical indicating whether the appearance of the comparisons should be in
’3D look’.
... Additional arguments passed on to netgraph.netmeta (see Details).

Details

Argument col can be a single color for all edges, a vector of length equal to the number of edges,
or a vector of length equal to the number of subnetworks. Argument reference.group is only
considered in disconnected networks, i.e., if more than one (sub)network exists, and if argument
col provides colors for subnetworks. In this case, the first color provided in argument col defines
the color for the subnetwork with the reference treatment.

Author(s)

Guido Schwarzer <[email protected]>, Gerta Rücker <[email protected]

See Also

netconnection, netgraph.netmeta

Examples
# Artificial example with two subnetworks
#
t1 <- c("G", "B", "B", "D", "A", "F")
t2 <- c("B", "C", "E", "E", "H", "A")
#
nc1 <- netconnection(t1, t2)
print(nc1, details = TRUE)

netgraph(nc1, points = TRUE, adj = 0.5, bg.points = "lightgray")

netgraph(nc1, points = TRUE, adj = 0.5, bg.points = "lightgray",
plastic = TRUE)
94 netgraph.netimpact

netgraph.netimpact Network graph for objects of class netimpact

Description
This function generates a graph of the evidence network.

Usage
## S3 method for class 'netimpact'
netgraph(
x,
col.ignore = "red",
number.of.studies = TRUE,
main,
sub,
multiarm = FALSE,
col.multiarm = NULL,
alpha.transparency = 0.5,
col.ignore.multiarm = "transparent",
col = "black",
plastic = FALSE,
...
)

Arguments
x An object of class netimpact.
col.ignore A character string indicating color for comparisons removed from network, ei-
ther "transparent" or any color defined in colours.
number.of.studies
A logical indicating whether number of studies should be added to network
graph.
main Main title.
sub Subtitle.
multiarm A logical indicating whether multi-arm studies should be marked in plot.
col.multiarm Either a function from R package colorspace or grDevice to define colors for
multi-arm studies or a character vector with colors to highlight multi-arm stud-
ies.
alpha.transparency
The alpha transparency of colors used to highlight multi-arm studies (0 means
transparent and 1 means opaque).
col.ignore.multiarm
A character string indicating color to mark multi-arm studies removed from net-
work, either "transparent" or any color defined in colours.
netgraph.netimpact 95

col A single color (or vector of colors) for lines connecting treatments (edges) if
argument plastic = FALSE. Length of the vector must be equal to the number
of edges.
plastic A logical indicating whether the appearance of the comparisons should be in
’3D look’.
... Additional arguments passed on to netgraph.netmeta.

Author(s)

Guido Schwarzer <[email protected]>, Gerta Rücker <[email protected]

See Also

netimpact, netgraph.netmeta

Examples
data(Franchini2012)

# Only consider first two studies (to reduce runtime of example)

#
studies <- unique(Franchini2012$Study)
p1 <- pairwise(list(Treatment1, Treatment2, Treatment3),
n = list(n1, n2, n3),
mean = list(y1, y2, y3), sd = list(sd1, sd2, sd3),
data = subset(Franchini2012, Study %in% studies[1:2]),
studlab = Study)

net1 <- netmeta(p1)

ni1 <- netimpact(net1, verbose = TRUE)
netgraph(ni1)
netgraph(ni1, plastic = TRUE)

## Not run:
p2 <- pairwise(list(Treatment1, Treatment2, Treatment3),
n = list(n1, n2, n3),
mean = list(y1, y2, y3), sd = list(sd1, sd2, sd3),
data = Franchini2012,
studlab = Study)

net2 <- netmeta(p2)

ni2 <- netimpact(net2, verbose = TRUE)
netgraph(ni2)
netgraph(ni2, plastic = TRUE)

## End(Not run)
96 netgraph.netmeta

netgraph.netmeta Network graph

Description
This function generates a graph of the evidence network.

Usage
## S3 method for class 'netmeta'
netgraph(
x,
seq = x$seq,
labels = x$trts,
cex = 1,
adj = NULL,
srt.labels = 0,
offset = if (!is.null(adj) && all(unique(adj) == 0.5)) 0 else 0.0175,
scale = 1.1,
col = if (iterate) "slateblue" else "black",
plastic = !(iterate & allfigures),
thickness = "number.of.studies",
lwd = 5,
lwd.min = lwd/2.5,
lwd.max,
rescale.thickness,
dim = "2d",
rotate = 0,
highlight = NULL,
col.highlight = "red2",
scale.highlight = 1,
multiarm = FALSE,
col.multiarm = NULL,
alpha.transparency = 0.5,
points = !missing(cex.points),
cex.points = 1,
pch.points = 20,
col.points = if (length(pch.points) == 1 && pch.points == 21) "black" else "red",
bg.points = "red",
points.min,
points.max,
rescale.pointsize,
number.of.studies = FALSE,
cex.number.of.studies = cex,
col.number.of.studies = "white",
bg.number.of.studies = "black",
pos.number.of.studies = 0.5,
netgraph.netmeta 97

start.layout = ifelse(dim == "2d", "circle", "eigen"),

eig1 = 2,
eig2 = 3,
eig3 = 4,
iterate = FALSE,
tol = 1e-04,
maxit = 500,
allfigures = FALSE,
A.matrix = x$A.matrix,
N.matrix = sign(A.matrix),
D.matrix = netdistance(N.matrix),
xpos = NULL,
ypos = NULL,
zpos = NULL,
figure = TRUE,
...
)

Arguments
x An object of class netmeta (mandatory).
seq A character or numerical vector specifying the sequence of treatments arrange-
ment (anticlockwise if start.layout = "circle").
labels An optional vector with treatment labels.
cex The magnification to be used for treatment labels.
adj One, two, or three values in [0, 1] (or a vector / matrix with length / number of
rows equal to the number of treatments) specifying the x (and optionally y and
z) adjustment for treatment labels.
srt.labels The character string "orthogonal" (can be abbreviated), a single numeric or
numerical vector with value(s) between -180 and 180 specifying the angle to
rotate treatment labels (see Details).
offset Distance between edges (i.e. treatments) in graph and treatment labels for 2-D
plots (value of 0.0175 corresponds to a difference of 1.75% of the range on x-
and y-axis).
scale Additional space added outside of edges (i.e. treatments). Increase this value
for larger treatment labels (value of 1.10 corresponds to an additional space of
10% around the network graph).
col A single color (or vector of colors) for lines connecting treatments (edges) if
argument plastic = FALSE. Length of the vector must be equal to the number
of edges (see list element ’comparisons’ in netmeta).
plastic A logical indicating whether the appearance of the comparisons should be in
’3D look’ (not to be confused with argument dim).
thickness Either a character variable to determine the method to plot line widths (see De-
tails) or a matrix of the same dimension and row and column names as argument
A.matrix with information on line width.
lwd A numeric for scaling the line width of comparisons.
98 netgraph.netmeta

lwd.min Minimum line width in network graph. All connections with line widths below
this values will be set to lwd.min.
lwd.max Maximum line width in network graph. The connection with the largest value
according to argument thickness will be set to this value.
rescale.thickness
A logical value or R function to scale the thickness of lines (see Details).
dim A character string indicating whether a 2- or 3-dimensional plot should be pro-
duced, either "2d" or "3d".
rotate A single numeric with value between -180 and 180 specifying the angle to rotate
nodes in a circular network.
highlight A character vector identifying comparisons that should be marked in the network
graph, e.g. highlight = "treat1:treat2".
col.highlight Color(s) to highlight the comparisons given by highlight.
scale.highlight
Scaling factor(s) for the line width(s) to highlight the comparisons given by
highlight.
multiarm A logical indicating whether multi-arm studies should be marked in plot.
col.multiarm Either a function from R package colorspace or grDevice to define colors for
multi-arm studies or a character vector with colors to highlight multi-arm stud-
ies.
alpha.transparency
The alpha transparency of colors used to highlight multi-arm studies (0 means
transparent and 1 means opaque).
points A logical indicating whether points should be printed at nodes (i.e. treatments)
of the network graph.
cex.points, pch.points, col.points, bg.points
Corresponding size, type, color, and background color for points. Can be a
vector with length equal to the number of treatments.
points.min Minimum point size. All points with size below this values will be set to
points.min.
points.max Maximum point size in network graph. The node with the largest value accord-
ing to argument cex.points will be set to this value.
rescale.pointsize
A logical value or R function to scale the point size (see Details).
number.of.studies
A logical indicating whether number of studies should be added to network
graph.
cex.number.of.studies
The magnification to be used for number of studies.
col.number.of.studies
Color for number of studies.
bg.number.of.studies
Color for shadow around number of studies.
netgraph.netmeta 99

pos.number.of.studies
A single value (or vector of values) in [0, 1] specifying the position of the num-
ber of studies on the lines connecting treatments (edges). Length of the vector
must be equal to the number of edges.
start.layout A character string indicating which starting layout is used if iterate = TRUE.
If "circle" (default), the iteration starts with a circular ordering of the vertices;
if "eigen", eigenvectors of the Laplacian matrix are used, calculated via generic
function eigen (spectral decomposition); if "prcomp", eigenvectors of the Lapla-
cian matrix are calculated via generic function prcomp (principal component
analysis); if "random", a random layout is used, drawn from a bivariate normal.
eig1 A numeric indicating which eigenvector is used as x coordinate if start =
"eigen" or "prcomp" and iterate = TRUE. Default is 2, the eigenvector to the
second-smallest eigenvalue of the Laplacian matrix.
eig2 A numeric indicating which eigenvector is used as y-coordinate if start = "eigen"
or "prcomp" and iterate = TRUE. Default is 3, the eigenvector to the third-
smallest eigenvalue of the Laplacian matrix.
eig3 A numeric indicating which eigenvector is used as z-coordinate if start = "eigen"
or "prcomp" and iterate = TRUE. Default is 4, the eigenvector to the fourth-
smallest eigenvalue of the Laplacian matrix.
iterate A logical indicating whether the stress majorization algorithm is carried out for
optimization of the layout.
tol A numeric for the tolerance for convergence if iterate = TRUE.
maxit An integer defining the maximum number of iteration steps if iterate = TRUE.
allfigures A logical indicating whether all iteration steps are shown if iterate = TRUE.
May slow down computations if set to TRUE (especially if plastic = TRUE).
A.matrix Adjacency matrix (nxn) characterizing the structure of the network graph. Row
and column names must be the same set of values as provided by argument seq.
N.matrix Neighborhood matrix (nxn) replacing A.matrix if neighborhood is to be speci-
fied differently from node adjacency in the network graph, for example content-
based. Row and column names must be the same set of values as provided by
argument seq.
D.matrix Distance matrix (nxn) replacing A.matrix and N.matrix if distances should be
provided directly. Row and column names must be the same set of values as
provided by argument seq.
xpos Vector (n) of x coordinates.
ypos Vector (n) of y coordinates.
zpos Vector (n) of z coordinates.
figure A logical indicating whether network graph should be shown.
... Additional graphical arguments.

Details
This function generates a network graph for an R object created with netmeta.
100 netgraph.netmeta

Layout of network graph: The network is laid out in the plane, where the nodes in the graph
layout correspond to the treatments and edges display the observed treatment comparisons. For
the default setting, nodes are placed on a circle. Other starting layouts are "eigen", "prcomp",
and "random" (Rücker & Schwarzer 2015). If iterate = TRUE, the layout is further optimized
using the stress majorization algorithm. This algorithm specifies an ’ideal’ distance (e.g., the
graph distance) between two nodes in the plane. In the optimal layout, these distances are best
approximated in the sense of least squares. Starting from an initial layout, the optimum is approx-
imated in an iterative process called stress majorization (Kamada and Kawai 1989, Michailidis
and de Leeuw 2001, Hu 2012). The starting layout can be chosen as a circle or coming from
eigenvectors of the Laplacian matrix (corresponding to Hall’s algorithm, Hall 1970), calculated
in different ways, or random. Moreover, it can be chosen whether the iteration steps are shown
(argument allfigures = TRUE).
An optimized circular presentation which typically has a reduced (sometimes minimal) number
of crossings can be achieved by using argument seq = "optimal" in combination with argument
start.layout. Note, is is not possible of prespecify the best value for argument start.layout
for any situation as the result depends on the network structure.

Definition of line widths: Argument thickness providing the line width of edges (comparisons)
can be a matrix of the same dimension as argument A.matrix or any of the following character
strings (which can be abbreviated):
• Proportional to number of studies comparing two treatments (thickness = "number.of.studies",
default)
• Proportional to inverse standard error of common effects model comparing two treatments
(thickness = "se.common")
• Proportional to inverse standard error of random effects model comparing two treatments
(thickness = "se.random")
• Weight from common effects model comparing two treatments (thickness = "w.common")
• Weight from random effects model comparing two treatments (thickness = "w.random")
• Same line width for all comparisons (thickness = "equal")
Only evidence from direct treatment comparisons is considered to determine the line width if
argument thickness is equal to any but the last method.
Line widths are determined by argument lwd if all lines have the same width. This is possible if
either argument thickness = "equal", all pairwise comparisons have the same number of studies
for thickness = "number.of.studies" or all direct comparisons are equally precise.
Otherwise, the line width of the thickest line is equal to the value of argument lwd.max and all
lines with a thickness below the value of argument lwd.min are set to this value. Default for
argument lwd.max is 4 * lwd.
Argument rescale.thickness can be used to provide a function to specify the relative line
width of edges (comparisons). By default, the square root function sqrt is used in order to lessen
differences in line widths. Argument rescale.thickness = FALSE or rescale.thickness = I,
i.e., the identity function I, can be used to not rescale line widths.

Definition of point sizes: Points are printed at nodes (treatments) if argument points = TRUE or
argument cex.points is provided.
Point sizes are equal to the value of argument cex.points if all points are of equal size.
netgraph.netmeta 101

Otherwise, the point size of the largest point is equal to the value of argument points.max and
all points smaller than the value of argument points.min are set to this value. The default for ar-
gument points.max is equal to the largest value provided in argument cex.points if this largest
value is below or equal to 25. Otherwise the default is points.max = 8.
Argument rescale.pointsize can be used to provide a function to specify relative point sizes.
Point sizes are not rescaled at all if they are all equal or the largest cex.points value is below or
equal to 25. Otherwise, the square root function sqrt is used in order to lessen the differences in
point sizes. Argument rescale.pointsize = FALSE or rescale.pointsize = I, i.e., the identity
function I, can be used to not rescale point sizes.

Other settings: Argument srt.labels can be used to specific the rotation (in degrees) of the
treatment labels. If srt.labels is equal to "orthogonal", treatment labels are orthogonal to the
circle. If srt.labels is a single numeric, all labels are rotated by this degree. If srt.labels is
a numeric vector, it must be of the same length as the number of treatments and labels are rotated
counter-clockwise starting on the right side. Finally, if srt.labels is a named numeric vector,
it must be of the same length as the number of treatments and the names must be equal to the
treatment names (and treatment labels are rotated according to the specified values).
Further, a couple of graphical parameters can be specified, such as color and appearance of the
edges (treatments) and the nodes (comparisons), whether special comparisons should be high-
lighted and whether multi-arm studies should be indicated as colored polygons. By default, if
R package colorspace is available the sequential_hcl function is used to highlight multi-arm
studies; otherwise the rainbow is used.
In order to generate 3-D plots (argument dim = "3d"), R package rgl is necessary. Note, under
macOS the X.Org X Window System must be available (see https://www.xquartz.org).

Value
A list containing two data frames with information on nodes and edges.
List element ’nodes’

trts Treatment names.

labels Treatment labels.
seq Sequence of treatment labels.
srt String rotation.
xpos Position of treatment / edge on x-axis.
ypos Position of treatment / edge on y-axis.
zpos Position of treatment / edge on z-axis (for 3-D plots).
xpos.labels Position of treatment labels on x-axis (for 2-D plots).
ypos.labels Position of treatment labels on y-axis (for 2-D plots).
offset.x Offset of treatment labels on x-axis (for 2-D plots).
offset.y Offset of treatment labels on y-axis (for 2-D plots).
cex Point size of treatments / edges.
col Color for points.
pch Point type.
102 netgraph.netmeta

bg Background color for points.

adj.x Adjustment for treatment label on x-axis.
adj.y Adjustment for treatment label on y-axis.
adj.z Adjustment for treatment label on z-axis (for 3-D plots).

List element ’edges’

treat1 Name of first treatment.

treat2 Name of second treatment.
n.stud Number of studies directly comparing treatments.
xpos Position of number of studies on x-axis.
ypos Position of number of studies on y-axis.
adj Adjustment of number of studies.
pos.number.of.studies
Position of number of studies on edge.
col Color for edges.

Author(s)

Gerta Rücker <[email protected]>, Ulrike Krahn <[email protected]>,

Jochem König <[email protected]>, Guido Schwarzer <[email protected]>

References

Hall KM (1970): An r-dimensional quadratic placement algorithm. Management Science, 17, 219–
29
Hu Y (2012): Combinatorial Scientific Computing, Chapter Algorithms for Visualizing Large Net-
works, pages 525–49. Chapman and Hall / CRC, Computational Science.
Kamada T, Kawai S (1989): An algorithm for drawing general undirected graphs. Information
Processing Letters, 31, 7–15
Krahn U, Binder H, König J (2013): A graphical tool for locating inconsistency in network meta-
analyses. BMC Medical Research Methodology, 13, 35
Michailidis G, de Leeuw J (2001): Data visualization through graph drawing. Computational Statis-
tics, 16, 435–50
Rücker G, Schwarzer G (2016): Automated drawing of network plots in network meta-analysis.
Research Synthesis Methods, 7, 94–107

See Also

netmeta
netgraph.netmeta 103

Examples

data(smokingcessation)

# Transform data from arm-based format to contrast-based format

#
p1 <- pairwise(list(treat1, treat2, treat3),
event = list(event1, event2, event3), n = list(n1, n2, n3),
data = smokingcessation, sm = "OR")

# Conduct random effects network meta-analysis

#
net1 <- netmeta(p1, common = FALSE)

# Network graph with default settings

#
netgraph(net1)

## Not run:
data(Senn2013)

# Generation of an object of class 'netmeta' with reference

# treatment 'plac'
#
net2 <- netmeta(TE, seTE, treat1, treat2, studlab,
data = Senn2013, sm = "MD", reference = "plac")

# Network graph with default settings

#
netgraph(net2)

# Network graph with specified order of the treatments and one

# highlighted comparison
#
trts <- c("plac", "benf", "migl", "acar", "sulf",
"metf", "rosi", "piog", "sita", "vild")
netgraph(net2, highlight = "rosi:plac", seq = trts)

# Same network graph using argument 'seq' in netmeta function

#
net3 <- netmeta(TE, seTE, treat1, treat2, studlab,
data = Senn2013, sm = "MD", reference = "plac", seq = trts)
netgraph(net3, highlight = "rosi:plac")

# Network graph optimized, starting from a circle, with multi-arm

# study colored
#
netgraph(net2, start = "circle", iterate = TRUE,
multiarm = TRUE, col.multiarm = "purple")

# Network graph optimized, starting from a circle, with multi-arm

# study colored and all intermediate iteration steps visible
#
104 netheat

netgraph(net2, start = "circle", iterate = TRUE,

multiarm = TRUE, col.multiarm = "purple",
allfigures = TRUE)

# Network graph optimized, starting from Laplacian eigenvectors,

# with multi-arm study colored
#
netgraph(net2, start = "eigen",
multiarm = TRUE, col.multiarm = "purple")

# Network graph optimized, starting from different Laplacian

# eigenvectors, with multi-arm study colored
#
netgraph(net2, start = "prcomp",
multiarm = TRUE, col.multiarm = "purple")

# Network graph optimized, starting from random initial layout,

# with multi-arm study colored
#
netgraph(net2, start = "random",
multiarm = TRUE, col.multiarm = "purple")

# Network graph without plastic look and one highlighted comparison

#
netgraph(net2, plastic = FALSE, highlight = "rosi:plac")

# Network graph with same thickness for all comparisons

#
netgraph(net2, thickness = "equal")

# Network graph with changed labels and specified order of the

# treatments
#
netgraph(net2, seq = c(1, 3, 5, 2, 9, 4, 7, 6, 8, 10),
labels = LETTERS[1:10])

# Rotate treatment labels (orthogonal to circle)

#
netgraph(net2, srt.labels = "o")

# Network graph in 3-D (opens a new device, where you may rotate and
# zoom the plot using the mouse / the mouse wheel).
# The rgl package must be installed for 3-D plots.
#
netgraph(net2, dim = "3d")

## End(Not run)

netheat Net heat plot

netheat 105

Description
This function creates a net heat plot, a graphical tool for locating inconsistency in network meta-
analyses.

Usage
netheat(
x,
random = FALSE,
tau.preset = NULL,
showall = TRUE,
nchar.trts = x$nchar.trts,
...
)

Arguments
x An object of class netmeta.
random A logical indicating whether the net heat plot should be based on a random
effects model.
tau.preset An optional value for the square-root of the between-study variance τ 2 for a
random effects model on which the net heat plot will be based.
showall A logical indicating whether results should be shown for all designs or only a
sensible subset (see Details).
nchar.trts A numeric defining the minimum number of characters used to create unique
treatment names.
... Additional arguments.

Details
The net heat plot is a matrix visualization proposed by Krahn et al. (2013) that highlights hot spots
of inconsistency between specific direct evidence in the whole network and renders transparent
possible drivers.
In this plot, the area of a gray square displays the contribution of the direct estimate of one design
in the column to a network estimate in a row. In combination, the colors show the detailed change
in inconsistency when relaxing the assumption of consistency for the effects of single designs.
The colors on the diagonal represent the inconsistency contribution of the corresponding design.
The colors on the off-diagonal are associated with the change in inconsistency between direct and
indirect evidence in a network estimate in the row after relaxing the consistency assumption for the
effect of one design in the column. Cool colors indicate an increase and warm colors a decrease:
the stronger the intensity of the color, the greater the difference between the inconsistency before
and after the detachment. So, a blue colored element indicates that the evidence of the design in
the column supports the evidence in the row. A clustering procedure is applied to the heat matrix
in order to find warm colored hot spots of inconsistency. In the case that the colors of a column
corresponding to design d are identical to the colors on the diagonal, the detaching of the effect of
design d dissolves the total inconsistency in the network.
106 netheat

The pairwise contrasts corresponding to designs of three- or multi-arm studies are marked by ’_’
following the treatments of the design.
Designs where only one treatment is involved in other designs of the network or where the removal
of corresponding studies would lead to a splitting of the network do not contribute to the incon-
sistency assessment. By default (showall = TRUE), these designs are not incorporated into the net
heat plot. If showall = FALSE, additional designs with minimal contribution to the inconsistency Q
statistic are not incorporated (i.e., designs with abs(Q.inc.design) <= .Machine$double.eps^0.5).).
In the case of random = TRUE, the net heat plot is based on a random effects model generalised for
multivariate meta-analysis in which the between-study variance τ 2 is estimated by the method of
moments (see Jackson et al., 2012) and embedded in a full design-by-treatment interaction model
(see Higgins et al., 2012).

Author(s)
Ulrike Krahn <[email protected]>

References
Krahn U, Binder H, König J (2013): A graphical tool for locating inconsistency in network meta-
analyses. BMC Medical Research Methodology, 13, 35
Jackson D, White IR and Riley RD (2012): Quantifying the impact of between-study heterogeneity
in multivariate meta-analyses. Statistics in Medicine, 31, 3805–20
Higgins JPT, Jackson D, Barrett JK, Lu G, Ades AE, White IR (2012): Consistency and inconsis-
tency in network meta-analysis: concepts and models for multi-arm studies. Research Synthesis
Methods, 3, 98–110

See Also
netmeta

Examples
data(Senn2013)

# Only consider first five studies (to reduce runtime of example)

#
studies <- unique(Senn2013$studlab)
Senn2013.5 <- subset(Senn2013, studlab %in% studies[1:5])

# Conduct network meta-analysis with placebo as reference treatment

#
net1 <- netmeta(TE, seTE, treat1, treat2, studlab,
data = Senn2013.5, sm = "MD", reference = "plac")

# Generate a net heat plot based on a common effects model

#
netheat(net1)

## Not run:
# Generate a net heat plot based on a random effects model
netimpact 107

#
netheat(net1, random = TRUE)

## End(Not run)

netimpact Determine the importance of individual studies in network meta-

analysis

Description
This function measures the importance of individual studies in network meta-analysis by the reduc-
tion of the precision if the study is removed / ignored from the network (Rücker et al., 2020).

Usage
netimpact(
x,
seTE.ignore = 100 * max(x$seTE, na.rm = TRUE),
event.ignore = 0.01,
verbose = FALSE
)

Arguments
x An object of class netmeta.
seTE.ignore Assumed (large) standard error in order to mimicking the removal of individual
studies from the network meta-analysis (ignored for netmetabin objects).
event.ignore Assumed event number mimicking the removal of individual studies from the
network meta-analysis (considered for netmetabin objects).
verbose A logical indicating whether information on the estimation progress should be
printed.

Value
An object of class "netimpact" with corresponding netgraph and print function. The object is a
list containing the following components:
impact.common A matrix with contributions of individual studies (columns) to comparisons
(rows) under the common effects model.
impact.random A matrix with contributions of individual studies (columns) to comparisons
(rows) under the random effects model.
ignored.comparisons
List with comparisons of ignored study.
seTE.ignore, event.ignore, x
As defined above.
nets List of all network meta-analyses (removing a single study).
version Version of R package netmeta used to create object.
108 netleague

Author(s)
Guido Schwarzer <[email protected]>, Gerta Rücker <[email protected]

References
Rücker G, Nikolakopoulou A, Papakonstantinou T, Salanti G, Riley RD, Schwarzer G (2020): The
statistical importance of a study for a network meta-analysis estimate. BMC Medical Research
Methodology, 20, 190

See Also
netmeta, netmetabin, netgraph.netimpact, print.netimpact

Examples
data(Franchini2012)

# Only consider first two studies (to reduce runtime of example)

#
studies <- unique(Franchini2012$Study)
p1 <- pairwise(list(Treatment1, Treatment2, Treatment3),
n = list(n1, n2, n3),
mean = list(y1, y2, y3), sd = list(sd1, sd2, sd3),
data = subset(Franchini2012, Study %in% studies[1:2]),
studlab = Study)

net1 <- netmeta(p1)

ni1 <- netimpact(net1, verbose = TRUE)
ni1

netgraph(ni1)

netleague Create league table with network meta-analysis results

Description
A league table is a square matrix showing all pairwise comparisons in a network meta-analysis.
Typically, both treatment estimates and confidence intervals are shown.

Usage
netleague(
x,
y,
common = x$common,
random = x$random,
netleague 109

seq = x$seq,
ci = TRUE,
backtransf = TRUE,
direct = FALSE,
digits = gs("digits"),
big.mark = gs("big.mark"),
text.NA = ".",
bracket = gs("CIbracket"),
separator = gs("CIseparator"),
lower.blank = gs("CIlower.blank"),
upper.blank = gs("CIupper.blank"),
writexl = !missing(path),
path = "leaguetable.xlsx",
overwrite = FALSE,
warn.deprecated = gs("warn.deprecated"),
...
)

## S3 method for class 'netleague'

print(
x,
common = x$x$common,
random = x$x$random,
warn.deprecated = gs("warn.deprecated"),
...
)

Arguments
x An object of class netmeta or netleague (mandatory).
y An object of class netmeta (optional).
common A logical indicating whether a league table should be printed for the common
effects network meta-analysis.
random A logical indicating whether a league table should be printed for the random
effects network meta-analysis.
seq A character or numerical vector specifying the sequence of treatments in rows
and columns of a league table.
ci A logical indicating whether confidence intervals should be shown.
backtransf A logical indicating whether printed results should be back transformed. If
backtransf = TRUE, results for sm = "OR" are printed as odds ratios rather than
log odds ratios, for example.
direct A logical indicating whether league table with network estimates (default) or es-
timates from direct comparisons should be generated if argument y is not miss-
ing.
digits Minimal number of significant digits, see print.default.
big.mark A character used as thousands separator.
110 netleague

text.NA A character string to label missing values.

bracket A character with bracket symbol to print lower confidence interval: "[", "(", "{",
"".
separator A character string with information on separator between lower and upper con-
fidence interval.
lower.blank A logical indicating whether blanks between left bracket and lower confidence
limit should be printed.
upper.blank A logical indicating whether blanks between separator and upper confidence
limit should be printed.
writexl A logical indicating whether an Excel file should be created (R package writexl
must be available).
path A character string specifying the filename of the Excel file.
overwrite A logical indicating whether an existing Excel file should be overwritten.
warn.deprecated
A logical indicating whether warnings should be printed if deprecated arguments
are used.
... Additional arguments (passed on to write_xlsx to create Excel file).

Details
A league table is a square matrix showing all pairwise comparisons in a network meta-analysis
(Hutton et al., 2015). Typically, both treatment estimates and confidence intervals are shown.
If argument y is not provided, the league table contains the network estimates from network meta-
analysis object x in the lower triangle and the direct treatment estimates from pairwise comparisons
in the upper triangle. Note, for the random-effects model, the direct treatment estimates are based
on the common between-study variance τ 2 from the network meta-analysis, i.e. the square of list
element x$tau.
If argument y is provided, the league table contains information on treatment comparisons from
network meta-analysis object x in the lower triangle and from network meta-analysis object y in the
upper triangle. This is, for example, useful to print information on efficacy and safety in the same
league table.
By default, an R object with the league tables is generated. Alternatively, an Excel file is created if
argument writexl = TRUE.
This implementation reports pairwise comparisons of the treatment in the column versus the treat-
ment in the row in the lower triangle and row versus column in the upper triangle. This is a common
presentation for network meta-analyses which allows to easily compare direction and magnitude of
treatment effects. For example, given treatments A, B, and C, the results reported in the first row
and second column as well as second row and first column are from the pairwise comparison A
versus B. Note, this presentation is different from the printout of a network meta-analysis object
which reports opposite pairwise comparisons in the lower and upper triangle, e.g., A versus B in
the first row and second column and B versus A in the second row and first column.
If the same network meta-analysis object is used for arguments x and y, reciprocal treatment esti-
mates will be shown in the upper triangle (see examples), e.g., the comparison B versus A.
R function netrank can be used to change the order of rows and columns in the league table (see
examples).
netleague 111

Value
An object of class netleague with corresponding print function if writexl = FALSE. The object is
a list containing the league tables in list elements ’common’ and ’random’. An Excel file is created
if writexl = TRUE. In this case, NULL is returned in R.

Author(s)
Guido Schwarzer <[email protected]>, Gerta Rücker <[email protected]

References
Hutton B, Salanti G, Caldwell DM, et al. (2015): The PRISMA Extension Statement for Reporting
of Systematic Reviews Incorporating Network Meta-analyses of Health Care Interventions: Check-
list and Explanations. Annals of Internal Medicine, 162, 777

See Also
netmeta, netposet, netrank

Examples
# Network meta-analysis of count mortality statistics
#
data(Woods2010)

p0 <- pairwise(treatment, event = r, n = N,

studlab = author, data = Woods2010, sm = "OR")
net0 <- netmeta(p0)

oldopts <- options(width = 100)

# League table for common and random effects model with

# - network estimates in lower triangle
# - direct estimates in upper triangle
#
netleague(net0, digits = 2, bracket = "(", separator = " - ")

# League table for common effects model

#
netleague(net0, random = FALSE, digits = 2)

# Change order of treatments according to treatment ranking (random

# effects model)
#
netleague(net0, common = FALSE, digits = 2, seq = netrank(net0))
#
print(netrank(net0), common = FALSE)

## Not run:
# Create a CSV file with league table for random effects model
#
112 netleague

league0 <- netleague(net0, digits = 2, bracket = "(", separator = " to ")

#
write.table(league0$random, file = "league0-random.csv",
row.names = FALSE, col.names = FALSE, sep = ",")
#
# Create Excel files with league tables
# (if R package writexl is available)
#
netleague(net0, digits = 2, bracket = "(", separator = " to ",
path = tempfile(fileext = ".xlsx"))

## End(Not run)

# Use depression dataset

#
data(Linde2015)

# Define order of treatments

#
trts <- c("TCA", "SSRI", "SNRI", "NRI",
"Low-dose SARI", "NaSSa", "rMAO-A", "Hypericum", "Placebo")

# Outcome labels
#
outcomes <- c("Early response", "Early remission")

# (1) Early response

#
p1 <- pairwise(treat = list(treatment1, treatment2, treatment3),
event = list(resp1, resp2, resp3), n = list(n1, n2, n3),
studlab = id, data = Linde2015, sm = "OR")
#
net1 <- netmeta(p1, common = FALSE,
seq = trts, ref = "Placebo", small = "undesirable")

# (2) Early remission

#
p2 <- pairwise(treat = list(treatment1, treatment2, treatment3),
event = list(remi1, remi2, remi3), n = list(n1, n2, n3),
studlab = id, data = Linde2015, sm = "OR")
#
net2 <- netmeta(p2, common = FALSE,
seq = trts, ref = "Placebo", small = "undesirable")

options(width = 200)
netleague(net1, digits = 2)

netleague(net1, digits = 2, ci = FALSE)

netleague(net2, digits = 2, ci = FALSE)

# League table for two outcomes with

# - network estimates of first outcome in lower triangle
netmatrix 113

# - network estimates of second outcome in upper triangle

#
netleague(net1, net2, digits = 2, ci = FALSE)

netleague(net1, net2, seq = netrank(net1), ci = FALSE)

netleague(net1, net2, seq = netrank(net2), ci = FALSE)

print(netrank(net1))
print(netrank(net2))

# Report results for network meta-analysis twice

#
netleague(net1, net1, seq = netrank(net1), ci = FALSE,
backtransf = FALSE)
netleague(net1, net1, seq = netrank(net1), ci = FALSE,
backtransf = FALSE, direct = TRUE)

options(oldopts)

## Not run:
# Generate a partial order of treatment rankings
#
np <- netposet(net1, net2, outcomes = outcomes)

# Requires R package 'hasse'

#
hasse(np)
plot(np)

## End(Not run)

netmatrix Create a matrix with additional information for pairwise comparisons

Description
Auxiliary function to create a matrix with additional information for pairwise comparisons

Usage
netmatrix(
x,
var,
levels,
labels = levels,
func = "mode",
ties.method = "random"
)
114 netmatrix

Arguments
x A netmeta object.
var Variable with additional information.
levels An optional vector of the values that var might have taken (see factor).
labels An optional vector with labels for var (see factor).
func A character string with the function name to summarize values within pairwise
comparisons; see Details.
ties.method A character string describing how ties are handled if func = "mode"; see Details.

Details
For each pairwise comparison, unique values will be calculated for the variable var based on the
argument func: "mode" (most common value), "min" (minimum value), "max", "mean", "median",
and "sum". In order to determine the most common value, the argument ties.method can be used
in the case of ties with "first" meaning that the first / smallest value will be selected; similar for
"last" (last / largest value) and "random" (random selection).

Value
A matrix with the same row and column names as the adjacency matrix x$A.matrix.

Author(s)
Guido Schwarzer <[email protected]>

See Also
netmeta, netgraph.netmeta

Examples
data(smokingcessation)
# Add variable with (fictious) risk of bias values
# with 1 = "low risk" and 2 = "high risk"
#
smokingcessation$rob <- rep(1:2, 12)

p1 <- pairwise(list(treat1, treat2, treat3),

event = list(event1, event2, event3), n = list(n1, n2, n3),
data = smokingcessation, sm = "OR")
net1 <- netmeta(p1, common = FALSE, ref = "A")

# Generate network graph with information on risk of bias

#
col.rob <- netmatrix(net1, rob, ties.method = "last",
levels = 1:2, labels = c("green", "yellow"))
#
netgraph(net1, plastic = FALSE, col = col.rob,
cex.points = 5, bg.points = "gray", adj = 0.5)
netmeasures 115

netgraph(net1, plastic = FALSE, col = col.rob,

cex.points = n.trts, bg.points = "blue",
labels = paste0(trts, " (n=", n.trts, ")"),
offset = c(0.05, 0.035, 0.05, 0.025))

netmeasures Measures for characterizing a network meta-analysis

Description

This function provides measures for quantifying the direct evidence proportion, the mean path
length and the minimal parallelism (the latter on aggregated and study level) of mixed treatment
comparisons (network estimates) as well as the evidence flow per design, see König et al. (2013).
These measures support the critical evaluation of the network meta-analysis results by rendering
transparent the process of data pooling.

Usage

netmeasures(
x,
random = x$random | !missing(tau.preset),
tau.preset = x$tau.preset,
warn = TRUE,
warn.deprecated = gs("warn.deprecated"),
...
)

Arguments

x An object of class netmeta.

random A logical indicating whether random effects model should be used to calculate
network measures.
tau.preset An optional value for the square-root of the between-study variance τ 2 .
warn A logical indicating whether warnings should be printed.
warn.deprecated
A logical indicating whether warnings should be printed if deprecated arguments
are used.
... Additional arguments (to catch deprecated arguments).
116 netmeasures

Details
The direct evidence proportion gives the absolute contribution of direct effect estimates combined
for two-arm and multi-arm studies to one network estimate.
Concerning indirectness, comparisons with a mean path length beyond two should be interpreted
with particular caution, as more than two direct comparisons have to be combined serially on aver-
age.
Large indices of parallelism, either on study-level or on aggregated level, can be considered as
supporting the validity of a network meta-analysis if there is only a small amount of heterogeneity.
The network estimates for two treatments are linear combinations of direct effect estimates compar-
ing these or other treatments. The linear coefficients can be seen as the generalization of weights
known from classical meta-analysis. These coefficients are given in the projection matrix H of the
underlying model. For multi-arm studies, the coefficients depend on the choice of the study-specific
baseline treatment, but the absolute flow of evidence can be made explicit for each design as shown
in König et al. (2013) and is given in H.tilde.
All measures are calculated based on the common effects meta-analysis by default. In the case that
in function netmeta the argument random = TRUE, all measures are calculated for a random effects
model. The value of the square-root of the between-study variance τ 2 can also be prespecified by
argument tau.preset in function netmeta.

Value
A list containing the following components:
random, tau.preset
As defined above.
proportion A named vector of the direct evidence proportion of each network estimate.
meanpath A named vector of the mean path length of each network estimate.
minpar A named vector of the minimal parallelism on aggregated level of each network
estimate.
minpar.study A named vector of the minimal parallelism on study level of each network esti-
mate.
H.tilde Design-based hat matrix with information on absolute evidence flow per design.
The number of rows is equal to the number of possible pairwise treatment com-
parisons and the number of columns is equal to the number of designs.

Author(s)
Ulrike Krahn <[email protected]>, Jochem König <[email protected]>

References
König J, Krahn U, Binder H (2013): Visualizing the flow of evidence in network meta-analysis and
characterizing mixed treatment comparisons. Statistics in Medicine, 32, 5414–29

See Also
netmeta
netmeasures 117

Examples

data(smokingcessation)

# Transform data from arm-based format to contrast-based format

#
p1 <- pairwise(list(treat1, treat2, treat3),
event = list(event1, event2, event3), n = list(n1, n2, n3),
data = smokingcessation, sm = "OR")

# Conduct network meta-analysis

#
net1 <- netmeta(p1)

# Calculate measures based on a common effects model

#
nm1 <- netmeasures(net1)

# Plot of minimal parallelism versus mean path length

#
plot(nm1$meanpath, nm1$minpar, type = "n",
xlab = "Mean path length", ylab = "Minimal parallelism")
text(nm1$meanpath, nm1$minpar, names(nm1$meanpath), cex = 0.8)

## Not run:
data(Senn2013)

# Conduct common effects network meta-analysis with reference

# treatment 'plac', i.e. placebo
#
net2 <- netmeta(TE, seTE, treat1, treat2, studlab,
data = Senn2013, sm = "MD", reference = "plac", random = FALSE)

# Calculate measures based on a common effects model

#
nm2 <- netmeasures(net2)

# Plot of minimal parallelism versus mean path length

#
plot(nm2$meanpath, nm2$minpar, type = "n",
xlab = "Mean path length", ylab = "Minimal parallelism")
text(nm2$meanpath, nm2$minpar, names(nm2$meanpath), cex = 0.8)

# Conduct random effects network meta-analysis with reference

# treatment 'plac', i.e. placebo
#
net3 <- netmeta(TE, seTE, treat1, treat2, studlab,
data = Senn2013, sm = "MD", reference = "plac", common = FALSE)

# Calculate measures based on a random effects model

#
nm3 <- netmeasures(net3)
118 netmeta

## End(Not run)

netmeta Network meta-analysis using graph-theoretical method

Description
Network meta-analysis is a generalisation of pairwise meta-analysis that compares all pairs of treat-
ments within a number of treatments for the same condition. The graph-theoretical approach for
network meta-analysis uses methods that were originally developed in electrical network theory. It
has been found to be equivalent to the frequentist approach to network meta-analysis which is based
on weighted least squares regression (Rücker, 2012).
Print method for objects of class netmeta.

Usage
netmeta(
TE,
seTE,
treat1,
treat2,
studlab,
data = NULL,
subset = NULL,
sm,
level = gs("level"),
level.ma = gs("level.ma"),
common = gs("common"),
random = gs("random") | !is.null(tau.preset),
prediction = FALSE,
level.predict = gs("level.predict"),
reference.group,
baseline.reference = TRUE,
small.values = "desirable",
all.treatments = NULL,
seq = NULL,
method.tau = "DL",
tau.preset = NULL,
tol.multiarm = 0.001,
tol.multiarm.se = NULL,
details.chkmultiarm = FALSE,
sep.trts = ":",
nchar.trts = 666,
nchar.studlab = 666,
func.inverse = invmat,
n1 = NULL,
netmeta 119

n2 = NULL,
event1 = NULL,
event2 = NULL,
incr = NULL,
sd1 = NULL,
sd2 = NULL,
time1 = NULL,
time2 = NULL,
backtransf = gs("backtransf"),
title = "",
keepdata = gs("keepdata"),
control = NULL,
warn = TRUE,
warn.deprecated = gs("warn.deprecated"),
nchar = nchar.trts,
...
)

## S3 method for class 'netmeta'

print(
x,
common = x$common,
random = x$random,
prediction = x$prediction,
reference.group = x$reference.group,
baseline.reference = x$baseline.reference,
all.treatments = x$all.treatments,
backtransf = x$backtransf,
nchar.trts = x$nchar.trts,
header = TRUE,
digits = gs("digits"),
digits.stat = gs("digits.stat"),
digits.pval = max(gs("digits.pval"), 2),
digits.pval.Q = max(gs("digits.pval.Q"), 2),
digits.Q = gs("digits.Q"),
digits.tau2 = gs("digits.tau2"),
digits.tau = gs("digits.tau"),
digits.I2 = gs("digits.I2"),
scientific.pval = gs("scientific.pval"),
big.mark = gs("big.mark"),
text.tau2 = gs("text.tau2"),
text.tau = gs("text.tau"),
text.I2 = gs("text.I2"),
legend = TRUE,
warn.deprecated = gs("warn.deprecated"),
...
)
120 netmeta

Arguments
TE Estimate of treatment effect, i.e. difference between first and second treatment
(e.g. log odds ratio, mean difference, or log hazard ratio). Or an R object created
with pairwise.
seTE Standard error of treatment estimate.
treat1 Label/Number for first treatment.
treat2 Label/Number for second treatment.
studlab An optional - but important! - vector with study labels (see Details).
data An optional data frame containing the study information.
subset An optional vector specifying a subset of studies to be used.
sm A character string indicating underlying summary measure, e.g., "RD", "RR",
"OR", "ASD", "HR", "MD", "SMD", or "ROM".
level The level used to calculate confidence intervals for individual comparisons.
level.ma The level used to calculate confidence intervals for network estimates.
common A logical indicating whether results for the common effects model should be
printed.
random A logical indicating whether results for the random effects model should be
printed.
prediction A logical indicating whether prediction intervals should be printed.
level.predict The level used to calculate prediction intervals for a new study.
reference.group
Reference treatment.
baseline.reference
A logical indicating whether results should be expressed as comparisons of other
treatments versus the reference treatment (default) or vice versa. This argument
is only considered if reference.group has been specified.
small.values A character string specifying whether small treatment effects indicate a benefi-
cial ("desirable") or harmful ("undesirable") effect (passed on to netrank,
can be abbreviated.
all.treatments A logical or "NULL". If TRUE, matrices with all treatment effects, and confidence
limits will be printed.
seq A character or numerical vector specifying the sequence of treatments in print-
outs.
method.tau A character string indicating which method is used to estimate the between-
study variance τ 2 and its square root τ . Either "DL", "REML", or "ML", can be
abbreviated.
tau.preset An optional value for manually setting the square-root of the between-study
variance τ 2 .
tol.multiarm A numeric for the tolerance for consistency of treatment estimates in multi-arm
studies which are consistent by design.
netmeta 121

tol.multiarm.se
A numeric for the tolerance for consistency of standard errors in multi-arm stud-
ies which are consistent by design. This check is not conducted if the argument
is NULL.
details.chkmultiarm
A logical indicating whether treatment estimates and / or variances of multi-
arm studies with inconsistent results or negative multi-arm variances should be
printed.
sep.trts A character used in comparison names as separator between treatment labels.
nchar.trts A numeric defining the minimum number of characters used to create unique
treatment names.
nchar.studlab A numeric defining the minimum number of characters used to create unique
study labels.
func.inverse R function used to calculate the pseudoinverse of the Laplacian matrix L (see
Details).
n1 Number of observations in first treatment group.
n2 Number of observations in second treatment group.
event1 Number of events in first treatment group.
event2 Number of events in second treatment group.
incr Numerical value added to cell frequencies (for details, see pairwise).
sd1 Standard deviation in first treatment group.
sd2 Standard deviation in second treatment group.
time1 Person time at risk in first treatment group.
time2 Person time at risk in second treatment group.
backtransf A logical indicating whether results should be back transformed in printouts and
forest plots. If backtransf = TRUE, results for sm = "OR" are presented as odds
ratios rather than log odds ratios, for example.
title Title of meta-analysis / systematic review.
keepdata A logical indicating whether original data (set) should be kept in netmeta object.
control An optional list to control the iterative process to estimate the between-study
variance τ 2 . This argument is passed on to rma.mv.
warn A logical indicating whether warnings should be printed (e.g., if studies are
excluded from meta-analysis due to zero standard errors).
warn.deprecated
A logical indicating whether warnings should be printed if deprecated arguments
are used.
nchar Deprecated argument (replaced by nchar.trts).
... Additional arguments.
x An object of class netmeta.
header A logical indicating whether information on title of meta-analysis, comparison
and outcome should be printed at the beginning of the printout.
122 netmeta

digits Minimal number of significant digits, see print.default.

digits.stat Minimal number of significant digits for tests of overall effect, see print.default.
digits.pval Minimal number of significant digits for p-value of overall effects, see print.default.
digits.pval.Q Minimal number of significant digits for p-value of heterogeneity tests, see
print.default.
digits.Q Minimal number of significant digits for heterogeneity statistics, see print.default.
digits.tau2 Minimal number of significant digits for between-study variance, see print.default.
digits.tau Minimal number of significant digits for square root of between-study variance,
see print.default.
digits.I2 Minimal number of significant digits for I-squared statistic, see print.default.
scientific.pval
A logical specifying whether p-values should be printed in scientific notation,
e.g., 1.2345e-01 instead of 0.12345.
big.mark A character used as thousands separator.
text.tau2 Text printed to identify between-study variance τ 2 .
text.tau Text printed to identify τ , the square root of the between-study variance τ 2 .
text.I2 Text printed to identify heterogeneity statistic I2 .
legend A logical indicating whether a legend should be printed.

Details
Network meta-analysis using R package netmeta is described in detail in Schwarzer et al. (2015),
Chapter 8.
Let n be the number of different treatments (nodes, vertices) in a network and let m be the number
of existing comparisons (edges) between the treatments. If there are only two-arm studies, m is the
number of studies. Let TE and seTE be the vectors of observed effects and their standard errors.
Let W be the mxm diagonal matrix that contains the inverse variance 1 / seTE^2.
The given comparisons define the network structure. Therefrom an mxn design matrix X (edge-
vertex incidence matrix) is formed; for more precise information, see Rücker (2012). Moreover,
the nxn Laplacian matrix L and its Moore-Penrose pseudoinverse L+ are calculated (both matrices
play an important role in graph theory and electrical network theory). Using these matrices, the
variances based on both direct and indirect comparisons can be estimated. Moreover, the hat matrix
H can be estimated by H = XL+X^tW = X(X^t W X)^+X^tW and finally consistent treatment
effects can be estimated by applying the hat matrix to the observed (potentially inconsistent) effects.
H is a projection matrix which maps the observed effects onto the consistent (n-1)-dimensional
subspace. This is the Aitken estimator (Senn et al., 2013). As in pairwise meta-analysis, the Q
statistic measures the deviation from consistency. Q can be separated into parts for each pairwise
meta-analysis and a part for remaining inconsistency between comparisons.
Often multi-arm studies are included in a network meta-analysis. In multi-arm studies, the treatment
effects on different comparisons are not independent, but correlated. This is accounted for by
reweighting all comparisons of each multi-arm study. The method is described in Rücker (2012)
and Rücker and Schwarzer (2014).
Comparisons belonging to multi-arm studies are identified by identical study labels (argument
studlab). It is therefore important to use identical study labels for all comparisons belonging to the
netmeta 123

same multi-arm study, e.g., study label "Willms1999" for the three-arm study in the data example
(Senn et al., 2013). The function netmeta then automatically accounts for within-study correlation
by reweighting all comparisons of each multi-arm study.

Data entry for this function is in contrast-based format, that is, data are given as contrasts (differ-
ences) between two treatments (argument TE) with standard error (argument seTE). In principle,
meta-analysis functions from R package meta, e.g. metabin for binary outcomes or metacont for
continuous outcomes, can be used to calculate treatment effects separately for each treatment com-
parison which is a rather tedious enterprise. If data are provided in arm-based format, that is, data
are given for each treatment arm separately (e.g. number of events and participants for binary out-
comes), a much more convenient way to transform data into contrast-based form is available. Func-
tion pairwise can automatically transform data with binary outcomes (using the metabin function
from R package meta), continuous outcomes (metacont function), incidence rates (metainc func-
tion), and generic outcomes (metagen function). Additional arguments of these functions can be
provided (see help page of function pairwise).

Note, all pairwise comparisons must be provided for a multi-arm study. Consider a multi-arm study
of p treatments with known variances. For this study, treatment effects and standard errors must be
provided for each of p(p - 1) / 2 possible comparisons. For instance, a three-arm study contributes
three pairwise comparisons, a four-arm study even six pairwise comparisons. Function pairwise
automatically calculates all pairwise comparisons for multi-arm studies.

A simple random effects model assuming that a constant heterogeneity variance is added to each
comparison of the network can be defined via a generalised methods of moments estimate of the
between-studies variance τ 2 (Jackson et al., 2012). This is added to the observed sampling variance
seTE^2 of each comparison in the network (before appropriate adjustment for multi-arm studies).
Then, as in standard pairwise meta-analysis, the procedure is repeated with the resulting enlarged
standard errors.

For the random-effects model, the direct treatment estimates are based on the common between-
study variance τ 2 from the network meta-analysis.

Internally, both common and random effects models are calculated regardless of values choosen for
arguments common and random. Accordingly, the network estimates for the random effects model
can be extracted from component TE.random of an object of class "netmeta" even if argument
random = FALSE. However, all functions in R package netmeta will adequately consider the values
for common and random. E.g. function print.summary.netmeta will not print results for the
random effects model if random = FALSE.

By default, treatment names are not abbreviated in printouts. However, in order to get more concise
printouts, argument nchar.trts can be used to define the minimum number of characters for ab-
breviated treatment names (see abbreviate, argument minlength). R function treats is utilised
internally to create abbreviated treatment names.

Names of treatment comparisons are created by concatenating treatment labels of pairwise compar-
isons using sep.trts as separator (see paste). These comparison names are used in the covariance
matrices Cov.common and Cov.random and in some R functions, e.g, decomp.design. By default,
a colon is used as the separator. If any treatment label contains a colon the following characters
are used as separator (in consecutive order): "-", "_", "/", "+", ".", "|", and "*". If all of these
characters are used in treatment labels, a corresponding error message is printed asking the user to
specify a different separator.
124 netmeta

Value
An object of class netmeta with corresponding print, summary, forest, and netrank functions.
The object is a list containing the following components:
studlab, treat1, treat2, TE, seTE
As defined above.
seTE.adj.common, seTE.adj.random
Standard error of treatment estimate, adjusted for multi-arm studies.
design Design of study providing pairwise comparison.
n1, n2, event1, event2, incr
As defined above.
mean1, mean2, sd1, sd2, time1, time2
As defined above.
sd1, sd2, time1, time2
As defined above.
k Total number of studies.
m Total number of pairwise comparisons.
n Total number of treatments.
d Total number of designs (corresponding to the unique set of treatments com-
pared within studies).
trts Treatments included in network meta-analysis.
k.trts Number of studies evaluating a treatment.
n.trts Number of observations receiving a treatment (if arguments n1 and n2 are pro-
vided).
events.trts Number of events observed for a treatment (if arguments event1 and event2
are provided).
multiarm Logical vector to identify pairwise comparisons from multi-arm studies.
n.arms Number of treatment arms in study providing pairwise comparison.
studies Vector with unique study labels.
narms Number of arms for each study.
designs Vector with unique designs present in the network. A design corresponds to the
set of treatments compared within a study.
designs Vector with unique direct comparisons present in the network.
TE.nma.common, TE.nma.random
A vector of length m of consistent treatment effects estimated by network meta-
analysis (nma) (common / random effects model).
seTE.nma.common, seTE.nma.random
A vector of length m of effective standard errors estimated by network meta-
analysis (common / random effects model).
lower.nma.common, lower.nma.random
A vector of length m of lower confidence interval limits for consistent treatment
effects estimated by network meta-analysis (common effects / random effects
model).
netmeta 125

upper.nma.common, upper.nma.random
A vector of length m of upper confidence interval limits for the consistent treat-
ment effects estimated by network meta-analysis (common effects / random ef-
fects model).
statistic.nma.common, statistic.nma.random
A vector of length m of z-values for test of treatment effect for individual com-
parisons (common / random effects model).
pval.nma.common, pval.nma.random
A vector of length m of p-values for test of treatment effect for individual com-
parisons (common / random effects model).
leverage.common
A vector of length m of leverages, interpretable as factors by which variances
are reduced using information from the whole network.
w.common, w.random
A vector of length m of weights of individual studies (common / random effects
model).
Q.common A vector of length m of contributions to total heterogeneity / inconsistency statis-
tic.
TE.common, TE.random
nxn matrix with estimated overall treatment effects (common / random effects
model).
seTE.common, seTE.random
nxn matrix with standard errors (common / random effects model).
lower.common, upper.common, lower.random, upper.random
nxn matrices with lower and upper confidence interval limits (common / random
effects model).
statistic.common, pval.common, statistic.random, pval.random
nxn matrices with z-value and p-value for test of overall treatment effect (com-
mon / random effects model).
seTE.predict nxn matrix with standard errors for prediction intervals.
lower.predict, upper.predict
nxn matrices with lower and upper prediction interval limits.
prop.direct.common, prop.direct.random
A named vector of the direct evidence proportion of each network estimate.
(common effects / random effects model).
TE.direct.common, TE.direct.random
nxn matrix with estimated treatment effects from direct evidence (common ef-
fects / random effects model).
seTE.direct.common, seTE.direct.random
nxn matrix with estimated standard errors from direct evidence (common effects
/ random effects model).
lower.direct.common, upper.direct.common, lower.direct.random,
nxn matrices with lower and upper confidence interval limits from direct evi-
dence (common / random effects model).
upper.direct.random
nxn matrices with lower and upper confidence interval limits from direct evi-
dence (common effects / random effects model).
126 netmeta

statistic.direct.common, pval.direct.common, statistic.direct.random,

nxn matrices with z-value and p-value for test of overall treatment effect from
direct evidence (common / random effects model).
pval.direct.random
nxn matrices with z-value and p-value for test of overall treatment effect from
direct evidence (common / random effects model).
TE.indirect.common, TE.indirect.random
nxn matrix with estimated treatment effects from indirect evidence (common /
random effects model).
seTE.indirect.common, seTE.indirect.random
nxn matrix with estimated standard errors from indirect evidence (common /
random effects model).
lower.indirect.common, upper.indirect.common, lower.indirect.random,
nxn matrices with lower and upper confidence interval limits from indirect evi-
dence (common / random effects model).
upper.indirect.random
nxn matrices with lower and upper confidence interval limits from indirect evi-
dence (common / random effects model).
statistic.indirect.common, pval.indirect.common, statistic.indirect.random,
nxn matrices with z-value and p-value for test of overall treatment effect from
indirect evidence (common / random effects model).
pval.indirect.random
nxn matrices with z-value and p-value for test of overall treatment effect from
indirect evidence (common / random effects model).
Q Overall heterogeneity / inconsistency statistic.
df.Q Degrees of freedom for test of heterogeneity / inconsistency.
pval.Q P-value for test of heterogeneity / inconsistency.
I2, lower.I2, upper.I2
I-squared, lower and upper confidence limits.
tau Square-root of between-study variance.
Q.heterogeneity
Overall heterogeneity statistic.
df.Q.heterogeneity
Degrees of freedom for test of overall heterogeneity.
pval.Q.heterogeneity
P-value for test of overall heterogeneity.
Q.inconsistency
Overall inconsistency statistic.
df.Q.inconsistency
Degrees of freedom for test of overall inconsistency.
pval.Q.inconsistency
P-value for test of overall inconsistency.
Q.decomp Data frame with columns ’treat1’, ’treat2’, ’Q’, ’df’ and ’pval.Q’, providing
heterogeneity statistics for each pairwise meta-analysis of direct comparisons.
netmeta 127

A.matrix Adjacency matrix (nxn).

X.matrix Design matrix (mxn).
B.matrix Edge-vertex incidence matrix (mxn).
L.matrix.common, L.matrix.random
Laplacian matrix (nxn).
Lplus.matrix.common, Lplus.matrix.random
Moore-Penrose pseudoinverse of the Laplacian matrix (nxn).
Q.matrix Matrix of heterogeneity statistics for pairwise meta-analyses, where direct com-
parisons exist (nxn).
G.matrix Matrix with variances and covariances of comparisons (mxm). G is defined as
BL+B^t.
H.matrix.common, H.matrix.random
Hat matrix (mxm), defined as H = GW = BL+B^tW.
n.matrix nxn matrix with number of observations in direct comparisons (if arguments n1
and n2 are provided).
events.matrix nxn matrix with number of events in direct comparisons (if arguments event1
and event2 are provided).
P.common, P.random
nxn matrix with direct evidence proportions (common / random effects model).
Cov.common Variance-covariance matrix (common effects model)
Cov.random Variance-covariance matrix (random effects model)
sm, level, level.ma
As defined above.
common, random As defined above.
prediction, level.predict
As defined above.
reference.group, baseline.reference, small.values, all.treatments
As defined above.
seq, tau.preset, tol.multiarm, tol.multiarm.se
As defined above.
details.chkmultiarm, sep.trts, nchar.trts
As defined above.
backtransf, title, warn, warn.deprecated
As defined above.
call Function call.
version Version of R package netmeta used to create object.

Note
R function rma.mv from R package metafor (Viechtbauer 2010) is called internally to estimate
the between-study variance τ 2 for the (restricted) maximum likelihood method. For binary out-
comes, incidence rates, and the mean difference, the variance-covariance matrix is calculated if
arguments event1, event2, n1, and n2 (binary outcomes); event1, event2, time1, and time2 (in-
cidence rates); n1, n2, sd1, and sd2 (mean difference) are provided. For data sets preprocessed with
pairwise the respective variables are selected automatically.
128 netmeta

Author(s)
Gerta Rücker <[email protected]>, Guido Schwarzer <[email protected]

References
Jackson D, White IR, Riley RD (2012): Quantifying the impact of between-study heterogeneity in
multivariate meta-analyses. Statistics in Medicine, 31, 3805–20
Rücker G (2012): Network meta-analysis, electrical networks and graph theory. Research Synthesis
Methods, 3, 312–24
Rücker G, Schwarzer G (2014): Reduce dimension or reduce weights? Comparing two approaches
to multi-arm studies in network meta-analysis. Statistics in Medicine, 33, 4353–69
Schwarzer G, Carpenter JR, Rücker G (2015): Meta-Analysis with R (Use R!). Springer Interna-
tional Publishing, Switzerland
Senn S, Gavini F, Magrez D, Scheen A (2013): Issues in performing a network meta-analysis.
Statistical Methods in Medical Research, 22, 169–89
Viechtbauer W (2010): Conducting Meta-Analyses in R with the metafor Package. Journal of
Statistical Software, 36, 1–48

See Also
pairwise, forest.netmeta, netrank, metagen

Examples
data(smokingcessation)

# Transform data from arm-based format to contrast-based format

#
p1 <- pairwise(list(treat1, treat2, treat3),
event = list(event1, event2, event3), n = list(n1, n2, n3),
data = smokingcessation, sm = "OR")

# Conduct random effects network meta-analysis

#
net1 <- netmeta(p1, common = FALSE)
net1

## Not run:
data(Senn2013)

# Conduct common effects network meta-analysis

#
net2 <- netmeta(TE, seTE, treat1, treat2, studlab,
data = Senn2013, sm = "MD", random = FALSE)
net2
net2$Q.decomp

# Comparison with reference group

#
netmetabin 129

print(net2, reference = "plac")

# Conduct random effects network meta-analysis

#
net3 <- netmeta(TE, seTE, treat1, treat2, studlab,
data = Senn2013, sm = "MD", common = FALSE)
net3

# Change printing order of treatments with placebo last and use

# long treatment names
#
trts <- c("acar", "benf", "metf", "migl", "piog",
"rosi", "sita", "sulf", "vild", "plac")
net4 <- netmeta(TE, seTE, treat1.long, treat2.long, studlab,
data = Senn2013, sm = "MD", common = FALSE,
seq = trts, reference = "Placebo")
print(net4, digits = 2)

## End(Not run)

netmetabin Network meta-analysis of binary outcome data

Description
Provides three models for the network meta-analysis of binary data (Mantel-Haenszel method,
based on the non-central hypergeometric distribution, and the inverse variance method).

Usage
netmetabin(
event1,
n1,
event2,
n2,
treat1,
treat2,
studlab,
data = NULL,
subset = NULL,
sm,
method = "MH",
cc.pooled = FALSE,
incr,
allincr,
addincr,
allstudies,
level = gs("level"),
130 netmetabin

level.ma = gs("level.ma"),
common = gs("common"),
random = method == "Inverse" & (gs("random") | !is.null(tau.preset)),
prediction = FALSE,
level.predict = gs("level.predict"),
reference.group = "",
baseline.reference = TRUE,
all.treatments = NULL,
seq = NULL,
tau.preset = NULL,
tol.multiarm = 0.001,
tol.multiarm.se = NULL,
details.chkmultiarm = FALSE,
details.chkdata = TRUE,
sep.trts = ":",
nchar.trts = 666,
func.inverse = invmat,
backtransf = gs("backtransf"),
title = "",
keepdata = gs("keepdata"),
warn = TRUE,
warn.deprecated = gs("warn.deprecated"),
...
)

Arguments
event1 Number of events (first treatment).
n1 Number of observations (first treatment).
event2 Number of events (second treatment).
n2 Number of observations (second treatment)
treat1 Label/Number for first treatment.
treat2 Label/Number for second treatment.
studlab An optional - but important! - vector with study labels (see Details).
data An optional data frame containing the study information.
subset An optional vector specifying a subset of studies to be used.
sm A character string indicating underlying summary measure, i.e., "RD", "RR",
"OR", "ASD".
method A character string indicating which method is to be used for pooling of studies.
One of "Inverse", "MH", or "NCH", can be abbreviated.
cc.pooled A logical indicating whether incr should be used as a continuity correction,
when calculating the network meta-analysis estimates.
incr A numerical value which is added to each cell count, i.e., to the numbers of
events and non-events, of all treatment arms in studies with zero events or non-
events in any of the treatment arms ("continuity correction").
netmetabin 131

allincr A logical indicating whether incr should be added to each cell count of all stud-
ies if a continuity correction was used for at least one study (only considered if
method = "Inverse"). If FALSE (default), incr is used as continuity correc-
tion only for studies with zero events or zero non-events in any of the treatment
arms.
addincr A logical indicating whether incr should be added to each cell count of all stud-
ies, irrespective of zero cell counts (only considered if method = "Inverse").
allstudies A logical indicating whether studies with zero events or non-events in all treat-
ment arms should be included in an inverse variance meta-analysis (applies only
if method = "Inverse" and sm is equal to either "RR" or "OR").
level The level used to calculate confidence intervals for individual studies.
level.ma The level used to calculate confidence intervals for network estimates.
common A logical indicating whether a common effects network meta-analysis should be
conducted.
random A logical indicating whether a random effects network meta-analysis should be
conducted.
prediction A logical indicating whether a prediction interval should be printed (only con-
sidered if method = "Inverse").
level.predict The level used to calculate prediction interval for a new study (only considered
if method = "Inverse").
reference.group
Reference treatment.
baseline.reference
A logical indicating whether results should be expressed as comparisons of other
treatments versus the reference treatment (default) or vice versa. This argument
is only considered if reference.group has been specified.
all.treatments A logical or "NULL". If TRUE, matrices with all treatment effects, and confidence
limits will be printed.
seq A character or numerical vector specifying the sequence of treatments in print-
outs.
tau.preset An optional value for manually setting the square-root of the between-study
variance τ 2 (only considered if method = "Inverse").
tol.multiarm A numeric for the tolerance for consistency of treatment estimates in multi-arm
studies which are consistent by design (only considered if method = "Inverse").
tol.multiarm.se
A numeric for the tolerance for consistency of standard errors in multi-arm stud-
ies which are consistent by design (only considered if the argument is not NULL
and method = "Inverse").
details.chkmultiarm
A logical indicating whether treatment estimates and / or variances of multi-
arm studies with inconsistent results or negative multi-arm variances should be
printed (only considered if method = "Inverse").
details.chkdata
A logical indicating whether number of events and participants of studies with
inconsistent data should be printed.
132 netmetabin

sep.trts A character used in comparison names as separator between treatment labels.

nchar.trts A numeric defining the minimum number of characters used to create unique
treatment names (see Details).
func.inverse R function used to calculate the pseudoinverse of the Laplacian matrix L (see
netmeta).
backtransf A logical indicating whether results should be back transformed in printouts and
forest plots. If backtransf = TRUE, results for sm = "OR" are presented as odds
ratios rather than log odds ratios, for example.
title Title of meta-analysis / systematic review.
keepdata A logical indicating whether original data (set) should be kept in netmeta object.
warn A logical indicating whether warnings should be printed (e.g., if studies are
excluded from meta-analysis due to zero standard errors).
warn.deprecated
A logical indicating whether warnings should be printed if deprecated arguments
are used.
... Additional arguments (to catch deprecated arguments).

Details
This function implements three models for the network meta-analysis of binary data:

• The Mantel-Haenszel network meta-analysis model, as described in Efthimiou et al. (2019)

(method = "MH");
• a network meta-analysis model using the non-central hypergeometric distribution with the
Breslow approximation, as described in Stijnen et al. (2010) (method = "NCH");
• the inverse variance method for network meta-analysis (method = "Inverse"), also provided
by netmeta.

Comparisons belonging to multi-arm studies are identified by identical study labels (argument
studlab). It is therefore important to use identical study labels for all comparisons belonging
to the same multi-arm study.
Data entry for this function is in contrast-based format, that is, each line of the data corresponds
to a single pairwise comparison between two treatments (arguments treat1, treat2, event1, n1,
event2, and n2). If data are provided in arm-based format, that is, number of events and participants
are given for each treatment arm separately, function pairwise can be used to transform the data to
contrast-based format (see help page of function pairwise).
Note, all pairwise comparisons must be provided for a multi-arm study. Consider a multi-arm study
of p treatments with known variances. For this study, the number of events and observations must
be provided for each treatment, for each of p(p - 1) / 2 possible comparisons in separate lines in the
data. For instance, a three-arm study contributes three pairwise comparisons, a four-arm study even
six pairwise comparisons. Function pairwise automatically calculates all pairwise comparisons
for multi-arm studies.
For method = "Inverse", both common and random effects models are calculated regardless of
values choosen for arguments common and random. Accordingly, the network estimates for the
random effects model can be extracted from component TE.random of an object of class "netmeta"
netmetabin 133

even if argument random = FALSE. However, all functions in R package netmeta will adequately
consider the values for common and random. E.g. function print.summary.netmeta will not print
results for the random effects model if random = FALSE.
For the random-effects model, the direct treatment estimates are based on the common between-
study variance τ 2 from the network meta-analysis.
For method = "MH" and method = "NCH", only a common effects model is available.
By default, treatment names are not abbreviated in printouts. However, in order to get more concise
printouts, argument nchar.trts can be used to define the minimum number of characters for ab-
breviated treatment names (see abbreviate, argument minlength). R function treats is utilised
internally to create abbreviated treatment names.
Names of treatment comparisons are created by concatenating treatment labels of pairwise compar-
isons using sep.trts as separator (see paste). These comparison names are used in the covariance
matrices Cov.common and Cov.random and in some R functions, e.g, decomp.design. By default,
a colon is used as the separator. If any treatment label contains a colon the following characters
are used as separator (in consecutive order): "-", "_", "/", "+", ".", "|", and "*". If all of these
characters are used in treatment labels, a corresponding error message is printed asking the user to
specify a different separator.

Value
An object of class netmetabin and netmeta with corresponding print, summary, forest, and
netrank functions. The object is a list containing the following components:
studlab, treat1, treat2
As defined above.
n1, n2, event1, event2
As defined above.
TE Estimate of treatment effect, i.e. difference between first and second treatment
(e.g. log odds ratio).
seTE Standard error of treatment estimate.
k Total number of studies.
m Total number of pairwise comparisons.
n Total number of treatments.
d Total number of designs (corresponding to the unique set of treatments com-
pared within studies).
trts Treatments included in network meta-analysis.
k.trts Number of studies evaluating a treatment.
n.trts Number of observations receiving a treatment.
events.trts Number of events observed for a treatment.
studies Study labels coerced into a factor with its levels sorted alphabetically.
narms Number of arms for each study.
designs Unique list of designs present in the network. A design corresponds to the set of
treatments compared within a study.
134 netmetabin

TE.common, seTE.common
nxn matrix with estimated overall treatment effects and standard errors for com-
mon effects model.
lower.common, upper.common
nxn matrices with lower and upper confidence interval limits for common effects
model.
statistic.common, pval.common
nxn matrices with z-value and p-value for test of overall treatment effect under
common effects model.
TE.random, seTE.random
nxn matrix with estimated overall treatment effects and standard errors for ran-
dom effects model (only available if method = "Inverse").
lower.random, upper.random
nxn matrices with lower and upper confidence interval limits for random effects
model (only available if method = "Inverse").
statistic.random, pval.random
nxn matrices with z-value and p-value for test of overall treatment effect under
random effects model (only available if method = "Inverse").
TE.direct.common, seTE.direct.common
nxn matrix with estimated treatment effects and standard errors from direct evi-
dence under common effects model.
lower.direct.common, upper.direct.common
nxn matrices with lower and upper confidence interval limits from direct evi-
dence under common effects model.
statistic.direct.common, pval.direct.common
nxn matrices with z-value and p-value for test of overall treatment effect from
direct evidence under common effects model.
TE.direct.random, seTE.direct.random
nxn matrix with estimated treatment effects and standard errors from direct evi-
dence under random effects model (only available if method = "Inverse").
lower.direct.random, upper.direct.random
nxn matrices with lower and upper confidence interval limits from direct evi-
dence under random effects model (only available if method = "Inverse").
statistic.direct.random, pval.direct.random
nxn matrices with z-value and p-value for test of overall treatment effect from di-
rect evidence under random effects model (only available if method = "Inverse").
Q Overall heterogeneity / inconsistency statistic. (only available if method = "Inverse")
df.Q Degrees of freedom for test of heterogeneity / inconsistency.
pval.Q P-value for test of heterogeneity / inconsistency.
I2, lower.I2, upper.I2
I-squared, lower and upper confidence limits (only available if method = "Inverse").
tau Square-root of between-study variance (only available if method = "Inverse").
Q.heterogeneity
Overall heterogeneity statistic. (only available if method = "Inverse")
df.Q.heterogeneity
Degrees of freedom for test of overall heterogeneity.
netmetabin 135

pval.Q.heterogeneity
P-value for test of overall heterogeneity.
Q.inconsistency
Overall inconsistency statistic.
df.Q.inconsistency
Degrees of freedom for test of overall inconsistency.
pval.Q.inconsistency
P-value for test of overall inconsistency.
A.matrix Adjacency matrix (nxn).
H.matrix Hat matrix (mxm)
n.matrix nxn matrix with number of observations in direct comparisons.
events.matrix nxn matrix with number of events in direct comparisons.
sm, method, level, level.ma
As defined above.
incr, allincr, addincr, allstudies, cc.pooled
As defined above.
common, random As defined above.
prediction, level.predict
As defined above.
reference.group, baseline.reference, all.treatments
As defined above.
seq, tau.preset, tol.multiarm, tol.multiarm.se
As defined above.
details.chkmultiarm, details.chkdata
As defined above.
sep.trts, nchar.trts
As defined above.
backtransf, title, warn, warn.deprecated
As defined above.
data Data set (in contrast-based format).
data.design List with data in arm-based format (each list element corresponds to a single
design).
call Function call.
version Version of R package netmeta used to create object.

Author(s)
Orestis Efthimiou <[email protected]>, Guido Schwarzer <[email protected]>

References
Efthimiou O, Rücker G, Schwarzer G, Higgins J, Egger M, Salanti G (2019): A Mantel-Haenszel
model for network meta-analysis of rare events. Statistics in Medicine, 38, 2992–3012
Senn S, Gavini F, Magrez D, Scheen A (2013): Issues in performing a network meta-analysis.
Statistical Methods in Medical Research, 22, 169–89
136 netmetabin

Stijnen T, Hamza TH, Ozdemir P (2010): Random effects meta-analysis of event outcome in the
framework of the generalized linear mixed model with applications in sparse data. Statistics in
Medicine, 29, 3046–67

See Also
pairwise, netmeta

Examples
data(Dong2013)

# Only consider first ten studies (to reduce runtime of example)

#
first10 <- subset(Dong2013, id <= 10)

# Transform data from long arm-based format to contrast-based

# format. Argument 'sm' has to be used for odds ratio as summary
# measure; by default the risk ratio is used in the metabin
# function called internally.
#
p1 <- pairwise(treatment, death, randomized, studlab = id,
data = first10, sm = "OR")

# Conduct Mantel-Haenszel network meta-analysis (without continuity

# correction)
#
nb1 <- netmetabin(p1, ref = "plac")
nb1

# Obtain the league table

#
netleague(nb1)

## Not run:
# Conduct Mantel-Haenszel network meta-analysis for the whole
# dataset
#
p2 <- pairwise(treatment, death, randomized, studlab = id,
data = Dong2013, sm = "OR")
netmetabin(p2, ref = "plac")

# Conduct network meta-analysis using the non-central

# hypergeometric model (without continuity correction)
#
netmetabin(p2, ref = "plac", method = "NCH")

# Conduct Mantel-Haenszel network meta-analysis (with continuity

# correction of 0.5; include all studies)
#
netmetabin(p2, ref = "plac", cc.pooled = TRUE)
netpairwise 137

data(Gurusamy2011)

p3 <- pairwise(treatment, death, n, studlab = study,

data = Gurusamy2011, sm = "OR")

# Conduct Mantel-Haenszel network meta-analysis (without continuity

# correction)
#
netmetabin(p3, ref = "cont")

## End(Not run)

netpairwise Conduct pairwise meta-analyses for all comparisons with direct evi-
dence in a network meta-analysis

Description
Conduct pairwise meta-analyses for all comparisons with direct evidence in a network meta-analysis.

Usage
netpairwise(
x,
separate = FALSE,
common = x$common,
random = x$random,
level = x$level,
level.ma = x$level.ma,
prediction = x$prediction,
level.predict = x$level.predict,
reference.group = if (missing(order)) x$reference.group else "",
baseline.reference = x$baseline.reference,
method.tau = x$method.tau,
order = NULL,
sep.trts = x$sep.trts,
nchar.trts = x$nchar.trts,
backtransf = x$backtransf,
warn.deprecated = gs("warn.deprecated"),
...
)

## S3 method for class 'netpairwise'

print(x, ...)

## S3 method for class 'netpairwise'

summary(object, ...)
138 netpairwise

## S3 method for class 'summary.netpairwise'

print(x, ...)

## S3 method for class 'netpairwise'

forest(x, ...)

## S3 method for class 'netpairwise'

plot(x, ...)

## S3 method for class 'netpairwise'

funnel(x, k.min = 3, ...)

## S3 method for class 'netpairwise'

radial(x, k.min = 3, ...)

## S3 method for class 'netpairwise'

baujat(x, k.min = 3, ...)

## S3 method for class 'netpairwise'

metabias(x, k.min = 10, ...)

## S3 method for class 'metabias.netpairwise'

print(x, ...)

## S3 method for class 'netpairwise'

trimfill(x, k.min = 3, ...)

## S3 method for class 'trimfill.netpairwise'

print(x, ...)

## S3 method for class 'netpairwise'

metainf(x, k.min = 2, ...)

## S3 method for class 'metainf.netpairwise'

print(x, ...)

## S3 method for class 'netpairwise'

metacum(x, k.min = 2, ...)

## S3 method for class 'metacum.netpairwise'

print(x, ...)

## S3 method for class 'netpairwise'

metareg(x, ..., k.min = 2)

## S3 method for class 'metareg.netpairwise'

print(x, ...)
netpairwise 139

Arguments
x An object of class netmeta or netpairwise.
separate A logical indicating whether results for pairwise comparisons should be printed
as separate meta-analyses or as subgroups which is more concise.
common A logical indicating whether a common effects network meta-analysis should be
conducted.
random A logical indicating whether a random effects network meta-analysis should be
conducted.
level The level used to calculate confidence intervals for individual comparisons.
level.ma The level used to calculate confidence intervals for pooled estimates.
prediction A logical indicating whether prediction intervals should be printed.
level.predict The level used to calculate prediction intervals for a new study.
reference.group
Reference treatment.
baseline.reference
A logical indicating whether results should be expressed as comparisons of other
treatments versus the reference treatment (default) or vice versa. This argument
is only considered if reference.group has been specified.
method.tau A character string indicating which method is used to estimate the between-
study variance τ 2 and its square root τ . Either "DL", "REML", or "ML", can be
abbreviated.
order An optional character or numerical vector specifying the order of treatments.
sep.trts A character used in comparison names as separator between treatment labels.
nchar.trts A numeric defining the minimum number of characters used to create unique
treatment names (see Details).
backtransf A logical indicating whether results should be back transformed in printouts and
forest plots. If backtransf = TRUE, results for sm = "OR" are presented as odds
ratios rather than log odds ratios, for example.
warn.deprecated
A logical indicating whether warnings should be printed if deprecated arguments
are used.
... Additional arguments (passed on to metagen or print functions and to catch
deprecated arguments).
object An object of class netpairwise.
k.min Minimum number of studies in pairwise comparison to show funnel plot, radial
plot or conduct test for funnel plot asymmetry.

Details
Conduct pairwise meta-analyses for all comparisons with direct evidence in a network meta-analysis.
In contrast to netmeta and netsplit, unadjusted standard errors are used in the calculations and
the between-study heterogeneity variance is allowed to differ between comparisons.
The R function metagen is called internally.
140 netpairwise

Value
Either a single metagen object with pairwise comparisons as subgroups or a list with metagen
objects for each direct pairwise comparison.

Note
This function must not be confused with pairwise which can be used as a pre-processing step
to convert data from arm-based to contrast-based format by calculating all pairwise comparisons
within a study.

Author(s)
Guido Schwarzer <[email protected]>

See Also
netmeta, netsplit, pairwise

Examples
oldsets <- settings.meta(digits = 2, digits.tau2 = 2, digits.tau = 2)

data(smokingcessation)

# Transform data from arm-based format to contrast-based format

#
p1 <- pairwise(list(treat1, treat2, treat3),
event = list(event1, event2, event3), n = list(n1, n2, n3),
data = smokingcessation, sm = "OR")

# Conduct random effects network meta-analysis

#
net1 <- netmeta(p1, common = FALSE)

# Calculate and print concise results for all pairwise

# meta-analyses
#
np1 <- netpairwise(net1)
np1
print(np1, details.method = FALSE)

## Not run:
data(Senn2013)

# Random effects model

#
net2 <- netmeta(TE, seTE, treat1.long, treat2.long, studlab,
data = Senn2013, sm = "MD", common = FALSE, reference = "plac")

# Calculate and print concise results for all pairwise

# meta-analyses
netposet 141

#
np2 <- netpairwise(net2)
np2
print(np2, details.method = FALSE)

forest(np2)

# Print detailed information for each pairwise comparison

#
np3 <- netpairwise(net2, separate = TRUE)
forest(np3)
funnel(np3)
radial(np3)
funnel(np3, k.min = 1)

## End(Not run)

settings.meta(oldsets)

netposet Partial order of treatments in network meta-analysis

Description

Partial order of treatments in network meta-analysis. The set of treatments in a network is called
a partially ordered set (in short, a poset), if different outcomes provide different treatment ranking
lists.

Usage

netposet(
...,
outcomes,
treatments,
small.values,
common,
random,
fixed,
comb.fixed,
comb.random
)

## S3 method for class 'netposet'

print(x, pooled = ifelse(x$random, "random", "common"), ...)
142 netposet

Arguments

... See details.

outcomes A character vector with outcome names.
treatments A character vector with treatment names.
small.values See details.
common A logical indicating whether to show results for the common effects model.
random A logical indicating whether to show results for the random effects model.
fixed Ignored deprecated argument (replaced by common).
comb.fixed Ignored deprecated argument (replaced by common).
comb.random Ignored deprecated argument (replaced by random).
x An object of class netposet.
pooled A character string indicating whether Hasse diagram should be drawn for com-
mon ("common") or random effects model ("random"). Can be abbreviated.

Details

In network meta-analysis, frequently different outcomes are considered which may each provide a
different ordering of treatments. The concept of a partially ordered set (in short, a poset, Carlsen &
Bruggemann, 2014) of treatments can be used to gain further insights in situations with apparently
conflicting orderings. This implementation for rankings in network meta-analyis is described in
Rücker & Schwarzer (2017).
In function netposet, argument ...{} can be any of the following:

• arbitrary number of netrank objects providing P-scores;

• arbitrary number of netmeta objects;
• single ranking matrix with each column providing P-scores (Rücker & Schwarzer 2015) or
SUCRA values (Salanti et al. 2011) for an outcome and rows corresponding to treatments.

Note, albeit in general a ranking matrix is not constrained to have values between 0 and 1, netposet
stops with an error in this case as this function expects a matrix with P-scores or SUCRA values.
Argument outcomes can be used to label outcomes. If argument outcomes is missing,

• column names of the ranking matrix are used as outcome labels (if first argument is a ranking
matrix and column names are available);
• capital letters ’A’, ’B’, . . . are used as outcome labels and a corresponding warning is printed.

Argument treatments can be used to provide treatment labels if the first argument is a ranking
matrix. If argument treatment is missing,

• row names of the ranking matrix are used as treatment labels (if available);
• letters ’a’, ’b’, . . . are used as treatment labels and a corresponding warning is printed.
netposet 143

If argument ...{} consists of netmeta objects, netrank is called internally to calculate P-scores.
In this case, argument small.values can be used to specify for each outcome whether small values
are beneficial ("desirable") or harmfull ("undesirable"); see netrank. This argument is ignored
for a ranking matrix and netrank objects.
Arguments common and random can be used to define whether results should be printed and plotted
for common and random effects model. If netmeta and netrank objects are provided in argument
...{}, values for common and random within these objects are considered; if these values are not
unique, argument common or random are set to TRUE.
In function print.netposet, argument ...{} is passed on to the printing function.

Value
An object of class netposet with corresponding print, plot, and hasse functions. The object is
a list containing the following components:
P.common Ranking matrix with rows corresponding to treatments and columns correspond-
ing to outcomes (common effects model).
M0.common Hasse matrix skipping unnecessary paths (common effects model).
M.common "Full" Hasse matrix (common effects model).
O.common Matrix with information about partial ordering (common effects model).
P.random Ranking matrix with rows corresponding to treatments and columns correspond-
ing to outcomes (random effects model).
M0.random Hasse matrix skipping unnecessary paths (random effects model).
M.random "Full" Hasse matrix (random effects model).
O.random Matrix with information about partial ordering (random effects model).
small.values, common, random
As.defined above.
call Function call.
version Version of R package netmeta used to create object.

Author(s)
Gerta Rücker <[email protected]>, Guido Schwarzer <[email protected]

References
Carlsen L, Bruggemann R (2014): Partial order methodology: a valuable tool in chemometrics.
Journal of Chemometrics, 28, 226–34
Rücker G, Schwarzer G (2015): Ranking treatments in frequentist network meta-analysis works
without resampling methods. BMC Medical Research Methodology, 15, 58
Rücker G, Schwarzer G (2017): Resolve conflicting rankings of outcomes in network meta-analysis:
Partial ordering of treatments. Research Synthesis Methods, 8, 526–36
Salanti G, Ades AE, Ioannidis JP (2011): Graphical methods and numerical summaries for present-
ing results from multiple-treatment meta-analysis: an overview and tutorial. Journal of Clinical
Epidemiology, 64, 163–71
144 netposet

See Also
netmeta, netrank, plot.netrank, hasse, plot.netposet

Examples
## Not run:
# Use depression dataset
#
data(Linde2015)

# Define order of treatments

#
trts <- c("TCA", "SSRI", "SNRI", "NRI",
"Low-dose SARI", "NaSSa", "rMAO-A", "Hypericum", "Placebo")

# Outcome labels
#
outcomes <- c("Early response", "Early remission")

# (1) Early response

#
p1 <- pairwise(treat = list(treatment1, treatment2, treatment3),
event = list(resp1, resp2, resp3), n = list(n1, n2, n3),
studlab = id, data = Linde2015, sm = "OR")
#
net1 <- netmeta(p1, common = FALSE,
seq = trts, ref = "Placebo", small.values = "undesirable")

# (2) Early remission

#
p2 <- pairwise(treat = list(treatment1, treatment2, treatment3),
event = list(remi1, remi2, remi3), n = list(n1, n2, n3),
studlab = id, data = Linde2015, sm = "OR")
#
net2 <- netmeta(p2, common = FALSE,
seq = trts, ref = "Placebo", small.values = "undesirable")

# Partial order of treatment rankings (two outcomes)

#
po <- netposet(netrank(net1), netrank(net2), outcomes = outcomes)

# Hasse diagram
#
hasse(po)

#
# Outcome labels
#
outcomes <- c("Early response", "Early remission",
"Lost to follow-up", "Lost to follow-up due to AEs",
"Adverse events (AEs)")
netposet 145

# (3) Loss to follow-up

#
p3 <- pairwise(treat = list(treatment1, treatment2, treatment3),
event = list(loss1, loss2, loss3), n = list(n1, n2, n3),
studlab = id, data = Linde2015, sm = "OR")
#
net3 <- netmeta(p3, common = FALSE,
seq = trts, ref = "Placebo", small.values = "desirable")

# (4) Loss to follow-up due to adverse events

#
p4 <- pairwise(treat = list(treatment1, treatment2, treatment3),
event = list(loss.ae1, loss.ae2, loss.ae3), n = list(n1, n2, n3),
studlab = id, data = subset(Linde2015, id != 55), sm = "OR")
#
net4 <- netmeta(p4, common = FALSE,
seq = trts, ref = "Placebo", small.values = "desirable")

# (5) Adverse events

#
p5 <- pairwise(treat = list(treatment1, treatment2, treatment3),
event = list(ae1, ae2, ae3), n = list(n1, n2, n3),
studlab = id, data = Linde2015, sm = "OR")
#
net5 <- netmeta(p5, common = FALSE,
seq = trts, ref = "Placebo", small.values = "desirable")

# Partial order of treatment rankings (all five outcomes)

#
po.ranks <- netposet(netrank(net1), netrank(net2),
netrank(net3), netrank(net4), netrank(net5), outcomes = outcomes)

# Same result
#
po.nets <- netposet(net1, net2, net3, net4, net5,
outcomes = outcomes)
#
all.equal(po.ranks, po.nets)

# Print matrix with P-scores (random effects model)

#
po.nets$P.random

# Hasse diagram for all outcomes (random effects model)

#
hasse(po.ranks)

# Hasse diagram for outcomes early response and early remission

#
po12 <- netposet(netrank(net1), netrank(net2),
outcomes = outcomes[1:2])
hasse(po12)
146 netrank

# Scatter plot
#
oldpar <- par(pty = "s")
plot(po12)
par(oldpar)

## End(Not run)

# Example using ranking matrix with P-scores

#
# Ribassin-Majed L, Marguet S, Lee A.W., et al. (2017):
# What is the best treatment of locally advanced nasopharyngeal
# carcinoma? An individual patient data network meta-analysis.
# Journal of Clinical Oncology, 35, 498-505
#
outcomes <- c("OS", "PFS", "LC", "DC")
treatments <- c("RT", "IC-RT", "IC-CRT", "CRT",
"CRT-AC", "RT-AC", "IC-RT-AC")
#
# P-scores (from Table 1)
#
pscore.os <- c(15, 33, 63, 70, 96, 28, 45) / 100
pscore.pfs <- c( 4, 46, 79, 52, 94, 36, 39) / 100
pscore.lc <- c( 9, 27, 47, 37, 82, 58, 90) / 100
pscore.dc <- c(16, 76, 95, 48, 72, 32, 10) / 100
#
pscore.matrix <- data.frame(pscore.os, pscore.pfs, pscore.lc, pscore.dc)
rownames(pscore.matrix) <- treatments
colnames(pscore.matrix) <- outcomes
pscore.matrix
#
po <- netposet(pscore.matrix)
po12 <- netposet(pscore.matrix[, 1:2])
po
po12
#
hasse(po)
hasse(po12)
#
oldpar <- par(pty = "s")
plot(po12)
par(oldpar)

netrank Frequentist method to rank treatments in network

Description
Ranking treatments in frequentist network meta-analysis with and without resampling methods.
netrank 147

Usage
netrank(
x,
small.values = x$small.values,
method,
nsim,
common = x$common,
random = x$random,
warn.deprecated = gs("warn.deprecated"),
...
)

## S3 method for class 'netrank'

print(
x,
common = x$common,
random = x$random,
sort = TRUE,
digits = gs("digits.prop"),
warn.deprecated = gs("warn.deprecated"),
...
)

Arguments
x An object of class netmeta or rankogram.
small.values A character string specifying whether small treatment effects indicate a benefi-
cial ("desirable") or harmful ("undesirable") effect, can be abbreviated.
method A character string specifying whether the "P-score" or "SUCRA" ranking metric
will be calculated.
nsim Number of simulations to calculate SUCRAs.
common A logical indicating whether to print P-scores or SUCRAs for the common ef-
fects model.
random A logical indicating whether to print P-scores or SUCRAs for the random effects
model.
warn.deprecated
A logical indicating whether warnings should be printed if deprecated arguments
are used.
... Additional arguments passed on to print.data.frame function (used inter-
nally).
sort A logical indicating whether printout should be sorted by decreasing P-score.
digits Minimal number of significant digits, see print.default.

Details
Treatments are ranked based on a network meta-analysis. Ranking is performed by a ranking metric:
P-score or SUCRA.
148 netrank

P-scores are based solely on the point estimates and standard errors of the network estimates. They
measure the extent of certainty that a treatment is better than another treatment, averaged over all
competing treatments (Rücker and Schwarzer 2015).
The Surface Under the Cumulative RAnking curve (SUCRA) is the rank of treatment i within
the range of treatments, measured on a scale from 0 (worst) to 1 (best) (Salanti et al. 2011). A
resampling method is used to calculate SUCRAs for frequentist network meta-analysis. The number
of simulations is determine by argument nsim.
The interpretation of P-scores and SUCRAs is comparable.
The P-score of treatment i is defined as the mean of all 1 - P[j] where P[j] denotes the one-sided
P-value of accepting the alternative hypothesis that treatment i is better than one of the competing
treatments j. Thus, if treatment i is better than many other treatments, many of these P-values will
be small and the P-score will be large. Vice versa, if treatment i is worse than most other treatments,
the P-score is small.
The P-score of treatment i can be interpreted as the mean extent of certainty that treatment i is better
than another treatment.

Value
An object of class netrank with corresponding print function. The object is a list containing the
following components:
ranking.common A named numeric vector with P-scores or SUCRAs for the common effects
model.
Pmatrix.common Numeric matrix based on pairwise one-sided p-values for the common effects
model.
ranking.random A named numeric vector with P-scores or SUCRAs for the random effects model.
Pmatrix.random Numeric matrix based on pairwise one-sided p-values of the random effects
model.
small.values, method, x
As defined above.
version Version of R package netmeta used to create object.

Author(s)
Gerta Rücker <[email protected]>, Guido Schwarzer <[email protected]
Theodoros Papakonstantinou <[email protected]>

References
Rücker G, Schwarzer G (2017): Resolve conflicting rankings of outcomes in network meta-analysis:
Partial ordering of treatments. Research Synthesis Methods, 8, 526–36
Salanti G, Ades AE, Ioannidis JP (2011): Graphical methods and numerical summaries for present-
ing results from multiple-treatment meta-analysis: an overview and tutorial. Journal of Clinical
Epidemiology, 64, 163–71

See Also
netmeta, rankogram, plot.rankogram
netsplit 149

Examples

data(smokingcessation)

p1 <- pairwise(list(treat1, treat2, treat3),

event = list(event1, event2, event3), n = list(n1, n2, n3),
data = smokingcessation, sm = "OR")
net1 <- netmeta(p1)

netrank(net1)

## Not run:
data(Senn2013)

net2 <- netmeta(TE, seTE, treat1, treat2, studlab,

data = Senn2013, sm = "MD", random = FALSE)

nr2 <- netrank(net2)

nr2
print(nr2, sort = FALSE)

net3 <- netmeta(TE, seTE, treat1, treat2, studlab,

data = Senn2013, sm = "MD")

nr3 <- netrank(net3)

nr3
print(nr3, sort = "common")
print(nr3, sort = FALSE)

net4 <- netmeta(TE, seTE, treat1, treat2, studlab,

data = Senn2013, sm = "MD")

nr4 <- netrank(net4, method = "SUCRA", nsim = 100)

nr4
print(nr4, sort = "common")
print(nr4, sort = FALSE)

## End(Not run)

netsplit Split direct and indirect evidence in network meta-analysis

Description

Methods to split network estimates into the contribution of direct and indirect evidence and to test
for local inconsistency in network meta-analysis.
150 netsplit

Usage

netsplit(
x,
method,
upper = TRUE,
reference.group = x$reference.group,
baseline.reference = x$baseline.reference,
order = NULL,
sep.trts = x$sep.trts,
quote.trts = "",
tol.direct = 5e-04,
common = x$common,
random = x$random,
backtransf = x$backtransf,
warn = FALSE,
warn.deprecated = gs("warn.deprecated"),
verbose = FALSE,
...
)

## S3 method for class 'netsplit'

print(
x,
common = x$x$common,
random = x$x$random,
show = "all",
overall = TRUE,
ci = FALSE,
test = show %in% c("all", "with.direct", "both"),
only.reference = FALSE,
sortvar = NULL,
nchar.trts = x$nchar.trts,
digits = gs("digits"),
digits.stat = gs("digits.stat"),
digits.pval = gs("digits.pval"),
digits.prop = max(gs("digits.pval") - 2, 2),
text.NA = ".",
backtransf = x$backtransf,
scientific.pval = gs("scientific.pval"),
big.mark = gs("big.mark"),
legend = TRUE,
indent = TRUE,
warn.deprecated = gs("warn.deprecated"),
...
)
netsplit 151

Arguments
x An object of class netmeta or netsplit.
method A character string indicating which method to split direct and indirect evidence
is to be used. Either "Back-calculation" or "SIDDE", can be abbreviated. See
Details.
upper A logical indicating whether treatment comparisons should be selected from
the lower or upper triangle of the treatment effect matrices (see list elements
TE.common and TE.random in the netmeta object). Ignored if argument order
is provided.
reference.group
Reference treatment. Ignored if argument order is provided.
baseline.reference
A logical indicating whether results should be expressed as comparisons of other
treatments versus the reference treatment or vice versa. This argument is only
considered if reference.group is not equal to "" and argumentorder is not
provided.
order A optional character or numerical vector specifying the order of treatments in
comparisons.
sep.trts A character string used in comparison names as separator between treatment
labels, e.g., " vs ".
quote.trts A character used to print around treatment labels.
tol.direct A numeric defining the maximum deviation of the direct evidence proportion
from 0 or 1 to classify a comparison as providing only indirect or direct evi-
dence, respectively.
common A logical indicating whether results for the common effects network meta-analysis
should be printed.
random A logical indicating whether results for the random effects network meta-analysis
should be printed.
backtransf A logical indicating whether printed results should be back transformed. For
example, if backtransf = TRUE, results for sm = "OR" are printed as odds ratios
rather than log odds ratios.
warn A logical indicating whether warnings should be printed.
warn.deprecated
A logical indicating whether warnings should be printed if deprecated arguments
are used.
verbose A logical indicating whether progress information should be printed.
... Additional arguments.
show A character string indicating which comparisons should be printed (see Details).
overall A logical indicating whether estimates from network meta-analyis should be
printed in addition to direct and indirect estimates.
ci A logical indicating whether confidence intervals should be printed in addition
to treatment estimates.
152 netsplit

test A logical indicating whether results of a test comparing direct and indirect esti-
mates should be printed.
only.reference A logical indicating whether only comparisons with the reference group should
be printed.
sortvar An optional vector used to sort comparisons (must be of same length as the total
number of comparisons).
nchar.trts A numeric defining the minimum number of characters used to create unique
treatment names.
digits Minimal number of significant digits, see print.default.
digits.stat Minimal number of significant digits for z-value of test of agreement between
direct and indirect evidence, see print.default.
digits.pval Minimal number of significant digits for p-value of test of agreement between
direct and indirect evidence, see print.default.
digits.prop Minimal number of significant digits for direct evidence proportions, see print.default.
text.NA A character string specifying text printed for missing values.
scientific.pval
A logical specifying whether p-values should be printed in scientific notation,
e.g., 1.2345e-01 instead of 0.12345.
big.mark A character used as thousands separator.
legend A logical indicating whether a legend should be printed.
indent A logical indicating whether items in the legend should be indented.

Details
A comparison of direct and indirect treatment estimates can serve as check for consistency of net-
work meta-analysis (Dias et al., 2010).
This function provides two methods to derive indirect estimates:

• Separate Indirect from Direct Evidence (SIDE) using a back-calculation method. The direct
evidence proportion as described in König et al. (2013) is used in the calculation of the indirect
evidence;
• Separate Indirect from Direct Design Evidence (SIDDE) as described in Efthimiou et al.
(2019).

Note, for the back-calculation method, indirect treatment estimates are already calculated in netmeta
and this function combines and prints these estimates in a user-friendly way. Furthermore, this
method is not available for the Mantel-Haenszel and non-central hypergeometric distribution ap-
proach implemented in netmetabin.
For the random-effects model, the direct treatment estimates are based on the common between-
study variance τ 2 from the network meta-analysis, i.e. the square of list element x$tau.
Argument show determines which comparisons are printed:

“all” All comparisons

“both” Only comparisons contributing both direct and indirect evidence
“with.direct” Comparisons providing direct evidence
“direct.only” Comparisons providing only direct evidence
“indirect.only” Comparisons providing only indirect evidence
netsplit 153

The SIDDE approach can be compute-intensive in large networks. Crude information on the com-
putation progress is printed for SIDDE if argument verbose is TRUE. In addition, computation times
are printed if R package tictoc is installed.

Value
An object of class netsplit with corresponding print and forest functions. The object is a list
containing the following components:
common, random As defined above.
comparison A vector with treatment comparisons.
prop.common, prop.random
A vector with direct evidence proportions (common / random effects model).
common, random Results of network meta-analysis (common / random effects model), i.e., data
frame with columns comparison, TE, seTE, lower, upper, z, and p.
direct.common, direct.random
Network meta-analysis results based on direct evidence (common / random ef-
fects model), i.e., data frame with columns comparison, TE, seTE, lower, upper,
z, and p.
indirect.common, indirect.random
Network meta-analysis results based on indirect evidence (common / random ef-
fects model), i.e., data frame with columns comparison, TE, seTE, lower, upper,
z, and p.
compare.common, compare.random
Comparison of direct and indirect evidence in network meta-analysis (common
/ random effects model), i.e., data frame with columns comparison, TE, seTE,
lower, upper, z, and p.
sm A character string indicating underlying summary measure
level.ma The level used to calculate confidence intervals for pooled estimates.
tictoc Computation times for SIDDE approach (if R package tictoc is installed).
version Version of R package netmeta used to create object.

Author(s)
Guido Schwarzer <[email protected]>, Gerta Rücker <[email protected]
Orestis Efthimiou <[email protected]>

References
Dias S, Welton NJ, Caldwell DM, Ades AE (2010): Checking consistency in mixed treatment
comparison meta-analysis. Statistics in Medicine, 29, 932–44
Efthimiou O, Rücker G, Schwarzer G, Higgins J, Egger M, Salanti G (2019): A Mantel-Haenszel
model for network meta-analysis of rare events. Statistics in Medicine, 38, 2992–3012
König J, Krahn U, Binder H (2013): Visualizing the flow of evidence in network meta-analysis and
characterizing mixed treatment comparisons. Statistics in Medicine, 32, 5414–29
Puhan MA, Schünemann HJ, Murad MH, et al. (2014): A GRADE working group approach for rat-
ing the quality of treatment effect estimates from network meta-analysis. British Medical Journal,
349, g5630
154 netsplit

See Also

forest.netsplit, netmeta, netmetabin, netmeasures

Examples
data(Woods2010)
#
p1 <- pairwise(treatment, event = r, n = N,
studlab = author, data = Woods2010, sm = "OR")
#
net1 <- netmeta(p1)
#
print(netsplit(net1), digits = 2)

## Not run:
print(netsplit(net1), digits = 2,
backtransf = FALSE, common = FALSE)

# Sort by increasing number of studies in direct comparisons

print(netsplit(net1), digits = 2, sortvar = k)
# Sort by decreasing number of studies in direct comparisons
print(netsplit(net1), digits = 2, sortvar = -k)

# Sort by increasing evidence proportion under common effects model

print(netsplit(net1), digits = 2, sortvar = prop.common)
# Sort by decreasing evidence proportion under common effects model
print(netsplit(net1), digits = 2, sortvar = -prop.common)

# Sort by decreasing evidence proportion under common effects model

# and number of studies
print(netsplit(net1), digits = 2, sortvar = cbind(-prop.common, -k))

data(Senn2013)
#
net2 <- netmeta(TE, seTE, treat1.long, treat2.long,
studlab, data = Senn2013)
#
print(netsplit(net2), digits = 2)
# Layout of Puhan et al. (2014), Table 1
print(netsplit(net2), digits = 2, ci = TRUE, test = FALSE)

data(Dong2013)
p3 <- pairwise(treatment, death, randomized, studlab = id,
data = Dong2013, sm = "OR")
net3 <- netmetabin(p3)
netsplit(net3)

## End(Not run)
nettable 155

nettable Table with network meta-analysis results

Description
Construct a table with network, direct and indirect estimates from one or more network meta-
analyses.

Usage
nettable(
...,
name = NULL,
method = NULL,
order = NULL,
common,
random,
upper = TRUE,
reference.group = NULL,
baseline.reference = NULL,
backtransf = NULL,
digits = gs("digits"),
digits.I2 = gs("digits.I2"),
digits.pval = gs("digits.pval"),
scientific.pval = gs("scientific.pval"),
zero.pval = gs("zero.pval"),
JAMA.pval = gs("JAMA.pval"),
big.mark = gs("big.mark"),
text.NA = ".",
bracket = gs("CIbracket"),
separator = gs("CIseparator"),
lower.blank = gs("CIlower.blank"),
upper.blank = gs("CIupper.blank"),
tol.direct = 5e-04,
writexl = !missing(path),
path = "nettable.xlsx",
overwrite = FALSE,
warn = FALSE,
verbose = FALSE
)

## S3 method for class 'nettable'

print(x, common = x$x$common, random = x$x$random, ...)

Arguments
... Any number of network meta-analysis objects or a single list with network meta-
analyses.
156 nettable

name An optional character vector providing descriptive names for network meta-
analysis objects.
method A character string indicating which method to split direct and indirect evidence
is to be used. Either "Back-calculation" or "SIDDE", can be abbreviated. See
Details.
order A optional character or numerical vector specifying the order of treatments in
comparisons.
common A logical indicating whether table for the common effects network meta-analysis
should be printed.
random A logical indicating whether table for the random effects network meta-analysis
should be printed.
upper A logical indicating whether treatment comparisons should be selected from
the lower or upper triangle of the treatment effect matrices (see list elements
TE.common and TE.random in the netmeta object). Ignored if argument order
is provided.
reference.group
Reference treatment. Ignored if argument order is provided.
baseline.reference
A logical indicating whether results should be expressed as comparisons of other
treatments versus the reference treatment or vice versa. This argument is only
considered if reference.group is not equal to "" and argumentorder is not
provided.
backtransf A logical indicating whether printed results should be back transformed. For
example, if backtransf = TRUE, results for sm = "OR" are printed as odds ratios
rather than log odds ratios.
digits Minimal number of significant digits, see print.default.
digits.I2 Minimal number of significant digits for I-squared statistic, see print.default.
digits.pval Minimal number of significant digits for p-value of test of agreement between
direct and indirect evidence, see print.default.
scientific.pval
A logical specifying whether p-values should be printed in scientific notation,
e.g., 1.2345e-01 instead of 0.12345.
zero.pval A logical specifying whether p-values should be printed with a leading zero.
JAMA.pval A logical specifying whether p-values for test of overall effect should be printed
according to JAMA reporting standards.
big.mark A character used as thousands separator.
text.NA A character string specifying text printed for missing values.
bracket A character with bracket symbol to print lower confidence interval: "[", "(", "{",
"".
separator A character string with information on separator between lower and upper con-
fidence interval.
lower.blank A logical indicating whether blanks between left bracket and lower confidence
limit should be printed.
nettable 157

upper.blank A logical indicating whether blanks between separator and upper confidence
limit should be printed.
tol.direct A numeric defining the maximum deviation of the direct evidence proportion
from 0 or 1 to classify a comparison as providing only indirect or direct evi-
dence, respectively.
writexl A logical indicating whether an Excel file should be created (R package writexl
must be available).
path A character string specifying the filename of the Excel file.
overwrite A logical indicating whether an existing Excel file should be overwritten.
warn A logical indicating whether warnings should be printed.
verbose A logical indicating whether progress information should be printed.
x An object of class nettable.

Details
Construct a table with network, direct and indirect estimates from one or more network meta-
analyses. The table looks very similar to the statistical part of a GRADE table for a network meta-
analysis (Puhan et al., 2014).
By default, an R object with the network tables is generated. Alternatively, an Excel file is created
if argument writexl = TRUE.
Two methods to derive indirect estimates are available:

• Separate Indirect from Direct Evidence (SIDE) using a back-calculation method. The direct
evidence proportion as described in König et al. (2013) is used in the calculation of the indirect
evidence;
• Separate Indirect from Direct Design Evidence (SIDDE) as described in Efthimiou et al.
(2019).

Note, for the back-calculation method, indirect treatment estimates are already calculated in netmeta
and this function combines and prints these estimates in a user-friendly way. Furthermore, this
method is not available for the Mantel-Haenszel and non-central hypergeometric distribution ap-
proach implemented in netmetabin.
For the random-effects model, the direct treatment estimates are based on the common between-
study variance τ 2 from the network meta-analysis, i.e. the square of list element x$tau.
The SIDDE approach can be compute-intensive in large networks. Crude information on the com-
putation progress is printed for SIDDE if argument verbose is TRUE.

Value
An object of class nettable with corresponding print function if argument writexl = FALSE. The
object is a list containing the network tables in list elements ’common’ and ’random’. An Excel file
is created if writexl = TRUE. In this case, NULL is returned in R.

Author(s)
Guido Schwarzer <[email protected]>
158 pairwise

References
Efthimiou O, Rücker G, Schwarzer G, Higgins J, Egger M, Salanti G (2019): A Mantel-Haenszel
model for network meta-analysis of rare events. Statistics in Medicine, 38, 2992–3012
König J, Krahn U, Binder H (2013): Visualizing the flow of evidence in network meta-analysis and
characterizing mixed treatment comparisons. Statistics in Medicine, 32, 5414–29
Puhan MA, Schünemann HJ, Murad MH, et al. (2014): A GRADE working group approach for rat-
ing the quality of treatment effect estimates from network meta-analysis. British Medical Journal,
349, g5630

See Also
netsplit, netmeta, netmetabin, netmeasures

Examples
data(Woods2010)
#
p1 <- pairwise(treatment, event = r, n = N,
studlab = author, data = Woods2010, sm = "OR")
#
net1 <- netmeta(p1)
#
nt1 <- nettable(net1, digits = 2)
nt1
print(nt1, common = FALSE)
print(nt1, random = FALSE)

## Not run:
# Create a CSV file with network table from random effects model
#
table1 <- nettable(net1, digits = 2, bracket = "(", separator = " to ")
#
write.table(table1$random, file = "table1-random.csv",
row.names = FALSE, col.names = TRUE, sep = ",")
#
# Create Excel files with network tables
# (if R package writexl is available)
#
nettable(net1, digits = 2, bracket = "(", separator = " to ",
path = tempfile(fileext = ".xlsx"))

## End(Not run)

pairwise Transform meta-analysis data from two arm-based formats into

contrast-based format
pairwise 159

Description
This function transforms data that are given in wide or long arm-based format (e.g. input format for
WinBUGS) to a contrast-based format that is needed as input to R function netmeta. The function
can transform data with binary, continuous, or generic outcomes as well as incidence rates from
arm-based to contrast-based format.

Usage
pairwise(
treat,
event,
n,
mean,
sd,
TE,
seTE,
time,
data = NULL,
studlab,
incr = gs("incr"),
allincr = gs("allincr"),
addincr = gs("addincr"),
allstudies = gs("allstudies"),
reference.group,
keep.all.comparisons,
warn = FALSE,
...
)

Arguments
treat A list or vector with treatment information for individual treatment arms (see
Details).
event A list or vector with information on number of events for individual treatment
arms (see Details).
n A list or vector with information on number of observations for individual treat-
ment arms (see Details).
mean A list or vector with estimated means for individual treatment arms (see Details).
sd A list or vector with information on the standard deviation for individual treat-
ment arms (see Details).
TE A list or vector with estimated treatment effects for individual treatment arms
(see Details).
seTE A list or vector with standard errors of estimated treatment effect for individual
treatment arms (see Details).
time A list or vector with information on person time at risk for individual treatment
arms (see Details).
160 pairwise

data An optional data frame containing the study information.

studlab A vector with study labels (optional).
incr A numerical value which is added to cell frequencies for studies with a zero cell
count, see Details.
allincr A logical indicating if incr is added to cell frequencies of all studies if at least
one study has a zero cell count. If FALSE (default), incr is added only to cell
frequencies of studies with a zero cell count.
addincr A logical indicating if incr is added to cell frequencies of all studies irrespective
of zero cell counts.
allstudies A logical indicating if studies with zero or all events in two treatment arms are
to be included in the meta-analysis (applies only if sm is equal to "RR" or "OR").
reference.group
Reference treatment (first treatment is used if argument is missing).
keep.all.comparisons
A logical indicating whether all pairwise comparisons or only comparisons with
the study-specific reference group should be kept (’basic parameters’).
warn A logical indicating whether warnings should be printed (e.g., if studies are
excluded due to only providing a single treatment arm).
... Additional arguments passed-through to the functions to calculate effects.

Details
R function netmeta expects data in a contrast-based format, where each row corresponds to a
comparison of two treatments and contains a measure of the treatment effect comparing two treat-
ments with standard error, labels for the two treatments and an optional study label. In contrast-
based format, a three-arm study contributes three rows with treatment comparison and correspond-
ing standard error for pairwise comparison A vs B, A vs C, and B vs C whereas a four-arm study
contributes six rows / pairwise comparisons: A vs B, A vs C, . . . , C vs D.
Other programs for network meta-analysis in WinBUGS and Stata require data in an arm-based
format, i.e. treatment estimate for each treatment arm instead of a difference of two treatments.
A common (wide) arm-based format consists of one data row per study, containing treatment
and other necessary information for all study arms. For example, a four-arm study contributes one
row with four treatment estimates and corresponding standard errors for treatments A, B, C, and D.
Another possible arm-based format is a long format where each row corresponds to a single study
arm. Accordingly, in the long arm-based format a study contributes as many rows as treatments
considered in the study.
The pairwise function transforms data given in (wide or long) arm-based format into the contrast-
based format which consists of pairwise comparisons and is needed as input to the netmeta func-
tion.
The pairwise function can transform data with binary outcomes (using the metabin function from
R package meta), continuous outcomes (metacont function), incidence rates (metainc function),
and generic outcomes (metagen function). Depending on the outcome, the following arguments are
mandatory:

• treat, event, n (see metabin);

pairwise 161

• treat, n, mean, sd (see metacont);

• treat, event, time (see metainc);
• treat, TE, seTE (see metagen).

Argument treat is mandatory to identify the individual treatments. The other arguments contain
outcome specific data. These arguments must be either lists (wide arm-based format, i.e., one row
per study) or vectors (long arm-based format, i.e., multiple rows per study) of the same length.
For the wide arm-based format, each list consists of as many vectors of the same length as the
multi-arm study with the largest number of treatments. If a single multi-arm study has five arms,
five vectors have to be provided for each lists. Two-arm studies have entries with NA for the third and
subsequent vectors. Each list entry is a vector with information for each individual study; i.e., the
length of this vector corresponds to the total number of studies incorporated in the network meta-
analysis. Typically, list elements are part of a data frame (argument data, optional); see Examples.
An optional vector with study labels can be provided which can be part of the data frame.
In the long arm-based format, argument studlab is mandatory to identify rows contributing to
individual studies.
Additional arguments for meta-analysis functions can be provided using argument ’. . . ’. The most
important argument is sm defining the summary measure. More information on this and other ar-
guments is given in the help pages of R functions metabin, metacont, metainc, and metagen,
respectively.
For standardised mean differences (argument sm = "SMD"), equations (4) and (5) in Crippa & Orsini
(2016) are used to calculated SMDs and standard errors. These equations guarantee consistent
SMDs and standard errors for multi-arm studies. Note, the summary measure is actually Cohen’s d
as Hedges’ g is not consistent in multi-arm studies.
For binary outcomes, 0.5 is added to all cell frequencies (odds ratio) or only the number of events
(risk ratio) for studies with a zero cell count. For odds ratio and risk ratio, treatment estimates and
standard errors are only calculated for studies with zero or all events in both groups if allstudies
is TRUE. This continuity correction is used both to calculate individual study results with confidence
limits and to conduct meta-analysis based on the inverse variance method. For the risk difference,
0.5 is only added to all cell frequencies to calculate the standard error.
For incidence rates, 0.5 is added to all cell frequencies for the incidence rate ratio as summary
measure. For the incidence risk difference, 0.5 is only added to all cell frequencies to calculate the
standard error.
The value of pairwise is a data frame with as many rows as there are pairwise comparisons. For
each study with p treatments, p*(p-1) / 2 contrasts are generated. Each row contains the treatment
effect (TE), its standard error (seTE), the treatments compared ((treat1), (treat2)) and the study
label ((studlab)). Further columns are added according to type of data.
All variables from the original dataset are also part of the output dataset. If data are provided in the
long arm-based format, the value of a variable can differ between treatment arms; for example, the
mean age or percentage of women in the treatment arm. In this situation, two variables instead of
one variable will be included in the output dataset. The values "1" and "2" are added to the names
for these variables, e.g. "mean.age1" and "mean.age2" for the mean age.
In general, any variable names in the original dataset that are identical to the main variable names
(i.e., "TE", "seTE", ...) will be renamed to variable names with ending ".orig".
162 pairwise

A reduced data set with basic comparisons (Rücker & Schwarzer, 2014) can be generated using
argument keep.all.comparisons = FALSE. Furthermore, the reference group for the basic com-
parisons can be specified with argument reference.group.

Value
A data frame with the following columns:
TE Treatment estimate comparing treatment ’treat1’ and ’treat2’.
seTE Standard error of treatment estimate.
studlab Study labels.
treat1 First treatment in comparison.
treat2 Second treatment in comparison.
event1 Number of events for first treatment arm (for metabin and metainc).
event2 Number of events for second treatment arm (for metabin and metainc).
n1 Number of observations for first treatment arm (for metabin and metacont).
n2 Number of observations for second treatment arm (for metabin and metacont).
mean1 Estimated mean for first treatment arm (for metacont).
mean2 Estimated mean for second treatment arm (for metacont).
sd1 Standard deviation for first treatment arm (for metacont).
sd2 Standard deviation for second treatment arm (for metacont).
TE1 Estimated treatment effect for first treatment arm (for metagen).
TE2 Estimated treatment effect for second treatment arm (for metagen).
seTE1 Standard error of estimated treatment effect for first treatment arm (for meta-
gen).
seTE2 Standard error of estimated treatment effect for second treatment arm (for meta-
gen).
time1 Person time at risk for first treatment arm (for metainc).
time2 Person time at risk for second treatment arm (for metainc).
All variables from the original dataset are also part of the output dataset; see Details.

Note
This function must not be confused with netpairwise which can be used to conduct pairwise
meta-analyses for all comparisons with direct evidence in a network meta-analysis.

Author(s)
Gerta Rücker<[email protected]>, Guido Schwarzer <[email protected]

References
Crippa A, Orsini N (2016): Dose-response meta-analysis of differences in means. BMC Medical
Research Methodology, 16:91.
pairwise 163

See Also
netmeta, metacont, metagen, metabin, metainc, netgraph.netmeta, pairwise

Examples
# Example using continuous outcomes (internal call of function
# metacont)
#
data(Franchini2012)
# Transform data from arm-based format to contrast-based format
p1 <- pairwise(list(Treatment1, Treatment2, Treatment3),
n = list(n1, n2, n3),
mean = list(y1, y2, y3), sd = list(sd1, sd2, sd3),
data = Franchini2012, studlab = Study)
p1

## Not run:
# Conduct network meta-analysis
#
net1 <- netmeta(p1)
net1

# Draw network graphs

#
netgraph(net1, points = TRUE, cex.points = 3, cex = 1.5,
thickness = "se.common")
netgraph(net1, points = TRUE, cex.points = 3, cex = 1.5,
plastic = TRUE, thickness = "se.common",
iterate = TRUE)
netgraph(net1, points = TRUE, cex.points = 3, cex = 1.5,
plastic = TRUE, thickness = "se.common",
iterate = TRUE, start = "eigen")

# Example using generic outcomes (internal call of function

# metagen)
#
# Calculate standard error for means y1, y2, y3
Franchini2012$se1 <- with(Franchini2012, sqrt(sd1^2 / n1))
Franchini2012$se2 <- with(Franchini2012, sqrt(sd2^2 / n2))
Franchini2012$se3 <- with(Franchini2012, sqrt(sd3^2 / n3))
# Transform data from arm-based format to contrast-based format
# using means and standard errors (note, argument 'sm' has to be
# used to specify that argument 'TE' is a mean difference)
p2 <- pairwise(list(Treatment1, Treatment2, Treatment3),
TE = list(y1, y2, y3), seTE = list(se1, se2, se3),
n = list(n1, n2, n3),
data = Franchini2012, studlab = Study,
sm = "MD")
p2

# Compare pairwise objects p1 (based on continuous outcomes) and p2

# (based on generic outcomes)
164 pairwise

#
all.equal(p1[, c("TE", "seTE", "studlab", "treat1", "treat2")],
p2[, c("TE", "seTE", "studlab", "treat1", "treat2")])

# Same result as network meta-analysis based on continuous outcomes

# (object net1)
net2 <- netmeta(p2)
net2

# Example with binary data

#
data(smokingcessation)
# Transform data from arm-based format to contrast-based format
# (interal call of metabin function). Argument 'sm' has to be used
# for odds ratio as risk ratio (sm = "RR") is default of metabin
# function.
#
p3 <- pairwise(list(treat1, treat2, treat3),
list(event1, event2, event3), list(n1, n2, n3),
data = smokingcessation,
sm = "OR")
p3

# Conduct network meta-analysis

#
net3 <- netmeta(p3)
net3

# Example with incidence rates

#
data(dietaryfat)

# Transform data from arm-based format to contrast-based format

#
p4 <- pairwise(list(treat1, treat2, treat3),
list(d1, d2, d3), time = list(years1, years2, years3),
studlab = ID,
data = dietaryfat)
p4

# Conduct network meta-analysis using incidence rate ratios (sm =

# "IRR"). Note, the argument 'sm' is not necessary as this is the
# default in R function metainc called internally.
#
net4 <- netmeta(p4, sm = "IRR")
summary(net4)

# Example with long data format

#
data(Woods2010)

# Transform data from long arm-based format to contrast-based

# format Argument 'sm' has to be used for odds ratio as summary
plot.netposet 165

# measure; by default the risk ratio is used in the metabin

# function called internally.
#
p5 <- pairwise(treatment, event = r, n = N,
studlab = author, data = Woods2010, sm = "OR")
p5

# Conduct network meta-analysis

net5 <- netmeta(p5)
net5

## End(Not run)

plot.netposet Scatter plot or biplot showing partially order of treatment ranks

Description
This function generates a scatter plot or biplot of P-scores with an overlay describing partial order
of treatment ranks.

Usage
## S3 method for class 'netposet'
plot(
x,
plottype = "scatter",
pooled = ifelse(x$random, "random", "common"),
dim = "2d",
sel.x = 1,
sel.y = 2,
sel.z = 3,
cex = 1,
col = "black",
cex.text = cex,
col.text = col,
adj.x = 0,
adj.y = 1,
offset.x = 0.005,
offset.y = -0.005,
pch = NULL,
cex.points = cex,
col.points = col,
col.lines = "black",
lty.lines = 1,
lwd.lines = 1,
arrows = FALSE,
166 plot.netposet

length = 0.05,
grid = TRUE,
col.grid = "gray",
lty.grid = 2,
lwd.grid = 1,
...
)

Arguments
x An object of class netmeta (mandatory).
plottype A character string indicating whether a scatter plot or biplot should be produced,
either "scatter" or "biplot". Can be abbreviated.
pooled A character string indicating whether scatter plot should be drawn for common
("common") or random effects model ("random"). Can be abbreviated.
dim A character string indicating whether a 2- or 3-dimensional plot should be pro-
duced, either "2d" or "3d". Can be abbreviated.
sel.x A numeric specifying number of outcome to use for the x-axis in a scatterplot
(argument is not considered for a biplot).
sel.y A numeric specifying number of outcome to use for the y-axis in a scatterplot
(argument is not considered for a biplot).
sel.z A numeric specifying number of outcome to use for the z-axis in a scatterplot
(argument is not considered for a biplot).
cex The magnification to be used for treatment labels and points.
col Colour(s) of treatment labels and points.
cex.text The magnification to be used for treatment labels.
col.text Colour(s) of treatment labels.
adj.x Value(s) in [0, 1] to specify adjustment of treatment labels on x-axis (only con-
sidered in 2-D plots); see text.
adj.y Value(s) in [0, 1] to specify adjustment of treatment labels on y-axis (only con-
sidered in 2-D plots); see text.
offset.x Offset(s) of treatment labels on x-axis (only considered in 2-D plots).
offset.y Offset(s) of treatment labels on y-axis (only considered in 2-D plots).
pch Plot symbol(s) for points; no points printed if equal to NULL.
cex.points Magnification(s) to be used for points.
col.points Colour(s) of points.
col.lines Line colour.
lty.lines Line type.
lwd.lines Line width.
arrows A logical indicating whether arrows should be printed (only considered in 2-D
plots).
length Length of arrows; see arrows.
plot.netposet 167

grid A logical indicating whether grid lines should be added to plot.

col.grid Colour of grid lines.
lty.grid Line type of grid lines.
lwd.grid Line width of grid lines.
... Additional graphical arguments.

Details
By default (arguments plottype = "scatter" and dim = "2d"), a scatter plot is created showing
P-scores (see netrank) for the first two outcomes considered in the generation of a partially ordered
set of treatment ranks (using netposet). In addition to the P-scores, the partially order of treatment
ranks is shown as lines connecting treatments which is analogous to a Hasse diagram. If argument
dim = "3d"), a 3-D scatter plot is generated showing P-scores for the first three outcomes.
To overcome the restriction of two or three dimension, a biplot (Gabriel, 1971) can be generated
using argument plottype = "biplot". This is essentially a scatter plot using the first two (dim =
"2d") or three (dim = "3d") components in a principal components analysis (using prcomp). Note, if
only two / three outcomes are considered in a netposet object, a 2-D / 3-D scatter plot is generated
instead of a biplot as a principal component analysis is superfluous in such a situation.
Arguments sel.x and sel.y can be used to select different outcomes to show on x- and y-axis in
a 2-D scatter plot; argument sel.z can be used accordingly in a 3-D scatter plot. These arguments
are ignored for a biplot.
Note, in order to generate 3-D plots (argument dim = "3d"), R package rgl is necessary. Note, under
macOS the X.Org X Window System must be available (see https://www.xquartz.org).

Author(s)
Gerta Rücker <[email protected]>, Guido Schwarzer <[email protected]

References
Carlsen L, Bruggemann R (2014): Partial order methodology: a valuable tool in chemometrics.
Journal of Chemometrics, 28, 226–34
Gabriel KR (1971): The biplot graphic display of matrices with application to principal component
analysis. Biometrika, 58, 453–67

See Also
netposet, hasse, netrank, netmeta

Examples
## Not run:
data(Linde2015)

# Define order of treatments

#
trts <- c("TCA", "SSRI", "SNRI", "NRI",
"Low-dose SARI", "NaSSa", "rMAO-A", "Hypericum", "Placebo")
168 plot.netposet

#
# Outcome labels
#
outcomes <- c("Early response", "Early remission")

# (1) Early response

#
p1 <- pairwise(treat = list(treatment1, treatment2, treatment3),
event = list(resp1, resp2, resp3), n = list(n1, n2, n3),
studlab = id, data = Linde2015, sm = "OR")
#
net1 <- netmeta(p1, common = FALSE,
seq = trts, ref = "Placebo", small.values = "undesirable")

# (2) Early remission

#
p2 <- pairwise(treat = list(treatment1, treatment2, treatment3),
event = list(remi1, remi2, remi3), n = list(n1, n2, n3),
studlab = id, data = Linde2015, sm = "OR")
#
net2 <- netmeta(p2, common = FALSE,
seq = trts, ref = "Placebo", small.values = "undesirable")

# Partial order of treatment rankings

#
po2 <- netposet(netrank(net1), netrank(net2), outcomes = outcomes)

# Scatter plot
#
plot(po2)

# Same scatter plot as only two outcomes considered in netposet()

#
plot(po2, "biplot")

# Consider three outcomes

#
# Outcome labels
#
outcomes <- c("Early response", "Early remission", "Lost to follow-up")

# (3) Loss to follow-up

#
p3 <- pairwise(treat = list(treatment1, treatment2, treatment3),
event = list(loss1, loss2, loss3), n = list(n1, n2, n3),
studlab = id, data = Linde2015, sm = "OR")
#
net3 <- netmeta(p3, common = FALSE,
seq = trts, ref = "Placebo", small.values = "desirable")

# Partial order of treatment rankings (with three outcomes)

#
plot.netrank 169

po3 <- netposet(netrank(net1), netrank(net2), netrank(net3),

outcomes = outcomes)

# Hasse diagram
#
hasse(po3)

# Scatter plot
#
plot(po3)

# Biplot (reverse limits of y-axis as biplot is upside down)

#
plot(po3, "bi", xlim = c(-1, 1.7), ylim = c(2.5, -2.5))

## End(Not run)

plot.netrank Plot treatment ranking(s) of network meta-analyses

Description
Produce an image plot of treatment ranking(s) generated with R function netrank.

Usage
## S3 method for class 'netrank'
plot(
...,
name,
common,
random,
seq,
low = "red",
mid = "yellow",
high = "green",
col = "black",
main,
main.size = 14,
main.col = col,
main.face = "bold",
legend = TRUE,
axis.size = 12,
axis.col = col,
axis.face = "plain",
na.value = "grey50",
angle = 45,
170 plot.netrank

hjust.x = 1,
vjust.x = 1,
hjust.y = 1,
vjust.y = 0,
nchar.trts,
digits = 3,
fixed,
comb.fixed,
comb.random,
warn.deprecated = gs("warn.deprecated")
)

Arguments
... A single netrank object or a list of netrank objects.
name An optional character vector providing descriptive names for the network meta-
analysis objects.
common A logical indicating whether results for the common effects model should be
plotted.
random A logical indicating whether results for the random effects model should be
plotted.
seq A character or numerical vector specifying the sequence of treatments on the
x-axis.
low A character string defining the colour for a P-score of 0, see scale_fill_gradient2.
mid A character string defining the colour for a P-score of 0.5, see scale_fill_gradient2.
high A character string defining the colour for a P-score of 1, see scale_fill_gradient2.
col Colour of text.
main Title.
main.size Font size of title, see element_text.
main.col Colour of title, see element_text.
main.face Font face of title, see element_text.
legend A logical indicating whether a legend should be printed.
axis.size Font size of axis text, see element_text.
axis.col Colour of axis text, see element_text.
axis.face Font face of axis text, see element_text.
na.value Colour for missing values, see scale_fill_gradient2.
angle Angle for text on x-axis, see element_text.
hjust.x A numeric between 0 and 1 with horizontal justification of text on x-axis, see
element_text.
vjust.x A numeric between 0 and 1 with vertical justification of text on x-axis, see
element_text.
hjust.y A numeric between 0 and 1 with horizontal justification of text on y-axis, see
element_text.
plot.netrank 171

vjust.y A numeric between 0 and 1 with vertical justification of text on y-axis, see
element_text.
nchar.trts A numeric defining the minimum number of characters used to create unique
treatment names.
digits Minimal number of significant digits, see print.default.
fixed Deprecated argument (replaced by ’common’).
comb.fixed Deprecated argument (replaced by ’common’).
comb.random Deprecated argument (replaced by ’random’).
warn.deprecated
A logical indicating whether warnings should be printed if deprecated arguments
are used.

Details
This function produces an image plot of network rankings (Palpacuer et al., 2018, Figure 4). Note,
a scatter plot of two network rankings can be generated with plot.netposet.
By default, treatments are ordered by decreasing P-scores of the first network meta-analysis object.
Argument seq can be used to specify a differenct treatment order.

Value
A ggplot2 object or NULL if no ranking was conducted.

Author(s)
Guido Schwarzer <[email protected]>, Clément Palpacuer <[email protected]>

References
Palpacuer C, Duprez R, Huneau A, Locher C, Boussageon R, Laviolle B, et al. (2018): Pharma-
cologically controlled drinking in the treatment of alcohol dependence or alcohol use disorders: a
systematic review with direct and network meta-analyses on nalmefene, naltrexone, acamprosate,
baclofen and topiramate. Addiction, 113, 220–37

See Also
netrank, netmeta, netposet, hasse

Examples
## Not run:
# Use depression dataset
#
data(Linde2015)

# Define order of treatments

#
trts <- c("TCA", "SSRI", "SNRI", "NRI",
172 plot.netrank

"Low-dose SARI", "NaSSa", "rMAO-A", "Hypericum", "Placebo")

# Outcome labels
#
outcomes <- c("Early response", "Early remission")

# (1) Early response

#
p1 <- pairwise(treat = list(treatment1, treatment2, treatment3),
event = list(resp1, resp2, resp3), n = list(n1, n2, n3),
studlab = id, data = Linde2015, sm = "OR")
#
net1 <- netmeta(p1, common = FALSE,
seq = trts, ref = "Placebo")

# (2) Early remission

#
p2 <- pairwise(treat = list(treatment1, treatment2, treatment3),
event = list(remi1, remi2, remi3), n = list(n1, n2, n3),
studlab = id, data = Linde2015, sm = "OR")
#
net2 <- netmeta(p2, common = FALSE,
seq = trts, ref = "Placebo")

# Image plot of treatment rankings (two outcomes)

#
plot(netrank(net1, small.values = "undesirable"),
netrank(net2, small.values = "undesirable"),
name = outcomes, digits = 2)

# Outcome labels
#
outcomes <- c("Early response", "Early remission",
"Lost to follow-up", "Lost to follow-up due to AEs",
"Adverse events (AEs)")

# (3) Loss to follow-up

#
p3 <- pairwise(treat = list(treatment1, treatment2, treatment3),
event = list(loss1, loss2, loss3), n = list(n1, n2, n3),
studlab = id, data = Linde2015, sm = "OR")
#
net3 <- netmeta(p3, common = FALSE, seq = trts, ref = "Placebo")

# (4) Loss to follow-up due to adverse events

#
p4 <- pairwise(treat = list(treatment1, treatment2, treatment3),
event = list(loss.ae1, loss.ae2, loss.ae3), n = list(n1, n2, n3),
studlab = id, data = subset(Linde2015, id != 55), sm = "OR")
#
net4 <- netmeta(p4, common = FALSE, seq = trts, ref = "Placebo")
plot.rankogram 173

# (5) Adverse events

#
p5 <- pairwise(treat = list(treatment1, treatment2, treatment3),
event = list(ae1, ae2, ae3), n = list(n1, n2, n3),
studlab = id, data = Linde2015, sm = "OR")
#
net5 <- netmeta(p5, common = FALSE, seq = trts, ref = "Placebo")

# Image plot of treatment rankings (two outcomes)

#
plot(netrank(net1, small.values = "undesirable"),
netrank(net2, small.values = "undesirable"),
netrank(net3, small.values = "desirable"),
netrank(net4, small.values = "desirable"),
netrank(net5, small.values = "desirable"),
name = outcomes, digits = 2)

## End(Not run)

plot.rankogram Plot rankograms

Description
This function produces a rankogram, i.e., an image plot of ranking probabilities for all treatments.

Usage
## S3 method for class 'rankogram'
plot(
x,
type = if (cumulative.rankprob) "step" else "bar",
pooled = ifelse(x$random, "random", "common"),
sort = TRUE,
trts,
cumulative.rankprob = x$cumulative.rankprob,
ylim,
ylab,
nchar.trts = x$nchar.trts,
...
)

Arguments
x An object of class rankogram.
type A character string specifying whether a "bar" chart, a "line" graph, or "step"
functions should be drawn. Can be abbreviated.
174 plot.rankogram

pooled A character string indicating whether results for the common ("common") or
random effects model ("random") should be plotted. Can be abbreviated.
sort A logical indicating whether treatments should be sorted by decreasing SU-
CRAs.
trts Treatment(s) to show in rankogram.
cumulative.rankprob
A logical indicating whether cumulative ranking probabilites should be shown.
ylim The y limits (min, max) of the plot.
ylab A label for the y-axis.
nchar.trts A numeric defining the minimum number of characters used to create unique
treatment names.
... Additional graphical arguments (ignored at the moment).

Details
This function produces an image plot of (cumulative) ranking probabilities for all treatments as a
bar graph, a line graph or as step functions (argument type).
By default (argument pooled), results for the random effects model are shown if a network meta-
analysis was conducted for both the common and random effects model.
Treatments are sorted according to their mean effects if argument sort = TRUE (default). A subset
of treatments can be specified using argument trts.
Cumulative ranking probabilites are shown if cumulative.rankprob = TRUE. By default, step func-
tions are shown for cumulative ranking probabilites.

Author(s)
Theodoros Papakonstantinou <[email protected]>, Guido Schwarzer <[email protected]>

References
Salanti G, Ades AE, Ioannidis JP (2011): Graphical methods and numerical summaries for present-
ing results from multiple-treatment meta-analysis: an overview and tutorial. Journal of Clinical
Epidemiology, 64, 163–71

See Also
rankogram

Examples
data(Woods2010)
p1 <- pairwise(treatment, event = r, n = N, studlab = author,
data = Woods2010, sm = "OR")
net1 <- netmeta(p1, small.values = "good")

ran1 <- rankogram(net1, nsim = 100)

ran1
print.decomp.design 175

plot(ran1)
plot(ran1, type = "l")
plot(ran1, cumulative.rankprob = TRUE)

print.decomp.design Print method for objects of class decomp.design

Description
Print method for objects of class decomp.design.

Usage
## S3 method for class 'decomp.design'
print(
x,
digits.Q = gs("digits.Q"),
showall = FALSE,
digits.pval.Q = gs("digits.pval.Q"),
digits.tau2 = gs("digits.tau2"),
scientific.pval = gs("scientific.pval"),
big.mark = gs("big.mark"),
nchar.trts = x$nchar.trts,
sort = TRUE,
legend = TRUE,
...
)

Arguments
x An object of class decomp.design.
digits.Q Minimal number of significant digits for Q statistics, see print.default.
showall A logical indicating whether results should be shown for all designs or only
designs contributing to chi-squared statistics (default).
digits.pval.Q Minimal number of significant digits for p-value of heterogeneity tests, see
print.default.
digits.tau2 Minimal number of significant digits for between-study variance, see print.default.
scientific.pval
A logical specifying whether p-values should be printed in scientific notation,
e.g., 1.2345e-01 instead of 0.12345.
big.mark A character used as thousands separator.
nchar.trts A numeric defining the minimum number of characters used to create unique
treatment names.
176 print.netbind

sort A logical indicating whether to sort results by p-values.

legend A logical indicating whether a legend should be printed.
... Additional arguments (ignored at the moment).

Author(s)
Guido Schwarzer <[email protected]>, Ulrike Krahn <[email protected]>

See Also
decomp.design

Examples
data(Senn2013)

# Only consider first five studies (to reduce runtime of example)

#
studies <- unique(Senn2013$studlab)
Senn2013.5 <- subset(Senn2013, studlab %in% studies[1:5])

# Conduct network meta-analysis with placebo as reference treatment

#
net1 <- netmeta(TE, seTE, treat1, treat2, studlab,
data = Senn2013.5, sm = "MD", reference = "plac")

# Decomposition of Cochran's Q
#
decomp.design(net1)

print.netbind Print method for objects of class netbind

Description
Print method for objects of class netbind.

Usage
## S3 method for class 'netbind'
print(
x,
common = x$x$common,
random = x$x$random,
warn.deprecated = gs("warn.deprecated"),
...
)
print.netbind 177

Arguments
x An object of class netbind or summary.netbind.
common A logical indicating whether results for the common effects model should be
printed.
random A logical indicating whether results for the random effects model should be
printed.
warn.deprecated
A logical indicating whether warnings should be printed if deprecated arguments
are used.
... Additional arguments (to catch deprecated arguments).

Author(s)
Guido Schwarzer <[email protected]>

See Also
netbind

Examples
data(Linde2016)

# Only consider studies including Face-to-face PST (to reduce

# runtime of example)
#
face <- subset(Linde2016, id %in% c(16, 24, 49, 118))

# Standard random effects NMA model (with placebo as reference

# treatment)
#
net1 <- netmeta(lnOR, selnOR, treat1, treat2, id,
data = face, reference.group = "placebo",
sm = "OR", common = FALSE)

# Additive CNMA model with placebo as inactive component and

# reference
#
nc1 <- netcomb(net1, inactive = "placebo")

# Combine results of standard NMA and CNMA

#
nb1 <- netbind(nc1, net1,
name = c("Additive CNMA", "Standard NMA"),
col.study = c("red", "black"), col.square = c("red", "black"))

nb1
print(nb1, common = TRUE)
178 print.netcomb

print.netcomb Print method for objects of class netcomb

Description
Print method for objects of class netcomb.

Usage
## S3 method for class 'netcomb'
print(
x,
common = x$common,
random = x$random,
backtransf = x$backtransf,
nchar.comps = x$nchar.comps,
digits = gs("digits"),
digits.stat = gs("digits.stat"),
digits.pval = gs("digits.pval"),
digits.pval.Q = max(gs("digits.pval.Q"), 2),
digits.Q = gs("digits.Q"),
digits.tau2 = gs("digits.tau2"),
digits.tau = gs("digits.tau"),
digits.I2 = gs("digits.I2"),
scientific.pval = gs("scientific.pval"),
zero.pval = gs("zero.pval"),
JAMA.pval = gs("JAMA.pval"),
big.mark = gs("big.mark"),
text.tau2 = gs("text.tau2"),
text.tau = gs("text.tau"),
text.I2 = gs("text.I2"),
legend = TRUE,
warn.deprecated = gs("warn.deprecated"),
...
)

Arguments
x An object of class netcomb or summary.netcomb.
common A logical indicating whether results for the common effects model should be
printed.
random A logical indicating whether results for the random effects model should be
printed.
backtransf A logical indicating whether results should be back transformed in printouts and
forest plots. If backtransf = TRUE, results for sm = "OR" are presented as odds
ratios rather than log odds ratios, for example.
print.netcomb 179

nchar.comps A numeric defining the minimum number of characters used to create unique
names for components.
digits Minimal number of significant digits, see print.default.
digits.stat Minimal number of significant digits for z- or t-value, see print.default.
digits.pval Minimal number of significant digits for p-value of overall treatment effect, see
print.default.
digits.pval.Q Minimal number of significant digits for p-value of heterogeneity tests, see
print.default.
digits.Q Minimal number of significant digits for heterogeneity statistics, see print.default.
digits.tau2 Minimal number of significant digits for between-study variance, see print.default.
digits.tau Minimal number of significant digits for square root of between-study variance,
see print.default.
digits.I2 Minimal number of significant digits for I-squared statistic, see print.default.
scientific.pval
A logical specifying whether p-values should be printed in scientific notation,
e.g., 1.2345e-01 instead of 0.12345.
zero.pval A logical specifying whether p-values should be printed with a leading zero.
JAMA.pval A logical specifying whether p-values for test of component or combination
effect should be printed according to JAMA reporting standards.
big.mark A character used as thousands separator.
text.tau2 Text printed to identify between-study variance τ 2 .
text.tau Text printed to identify τ , the square root of the between-study variance τ 2 .
text.I2 Text printed to identify heterogeneity statistic I2 .
legend A logical indicating whether a legend should be printed.
warn.deprecated
A logical indicating whether warnings should be printed if deprecated arguments
are used.
... Additional arguments (to catch deprecated arguments).

Author(s)
Guido Schwarzer <[email protected]>

See Also
netcomb, discomb

Examples
data(Linde2016)

# Only consider studies including Face-to-face PST (to reduce

# runtime of example)
#
180 print.netimpact

face <- subset(Linde2016, id %in% c(16, 24, 49, 118))

# Conduct random effects network meta-analysis

#
net1 <- netmeta(lnOR, selnOR, treat1, treat2, id,
data = face, reference.group = "placebo",
sm = "OR", common = FALSE)

# Additive model for treatment components

#
nc1 <- netcomb(net1)
nc1
print(nc1, digits = 2, digits.stat = 3)

## Not run:
# Conduct random effects network meta-analysis
#
net2 <- netmeta(lnOR, selnOR, treat1, treat2, id,
data = Linde2016, reference.group = "placebo",
sm = "OR", common = FALSE)

# Additive model for treatment components

#
nc2 <- netcomb(net2)
nc2
print(nc2, digits = 2, digits.stat = 3)

## End(Not run)

print.netimpact Print method for objects of class netimpact

Description
Print method for objects of class netimpact.

Usage
## S3 method for class 'netimpact'
print(
x,
common = x$x$common,
random = x$x$random,
digits = gs("digits.prop"),
legend = TRUE,
warn.deprecated = gs("warn.deprecated"),
...
)
print.summary.netcomb 181

Arguments
x An object of class netimpact.
common A logical indicating whether results for the common effects model should be
printed.
random A logical indicating whether results for the random effects model should be
printed.
digits Minimal number of significant digits.
legend A logical indicating whether a legend should be printed.
warn.deprecated
A logical indicating whether warnings should be printed if deprecated arguments
are used.
... Additional arguments (to catch deprecated arguments).

Author(s)
Guido Schwarzer <[email protected]>

See Also
netimpact

Examples
data(Franchini2012)

# Only consider first two studies (to reduce runtime of example)

#
studies <- unique(Franchini2012$Study)
p1 <- pairwise(list(Treatment1, Treatment2, Treatment3),
n = list(n1, n2, n3),
mean = list(y1, y2, y3), sd = list(sd1, sd2, sd3),
data = subset(Franchini2012, Study %in% studies[1:2]),
studlab = Study)

net1 <- netmeta(p1)

ni <- netimpact(net1, verbose = TRUE)
ni

print.summary.netcomb Print detailed information for component network meta-analysis

Description
Print detailed information for component network meta-analysis.
182 print.summary.netcomb

Usage
## S3 method for class 'summary.netcomb'
print(
x,
common = x$x$common,
random = x$x$random,
backtransf = x$backtransf,
nchar.comps = x$nchar.comps,
digits = gs("digits"),
digits.stat = gs("digits.stat"),
digits.pval = gs("digits.pval"),
digits.pval.Q = max(gs("digits.pval.Q"), 2),
digits.Q = gs("digits.Q"),
scientific.pval = gs("scientific.pval"),
zero.pval = gs("zero.pval"),
JAMA.pval = gs("JAMA.pval"),
big.mark = gs("big.mark"),
legend = TRUE,
warn.deprecated = gs("warn.deprecated"),
...
)

Arguments
x An object of class summary.netcomb
common A logical indicating whether results for the common effects model should be
printed.
random A logical indicating whether results for the random effects model should be
printed.
backtransf A logical indicating whether results should be back transformed in printouts and
forest plots. If backtransf=TRUE, results for sm="OR" are presented as odds
ratios rather than log odds ratios, for example.
nchar.comps A numeric defining the minimum number of characters used to create unique
component names.
digits Minimal number of significant digits, see print.default.
digits.stat Minimal number of significant digits for z- or t-value, see print.default.
digits.pval Minimal number of significant digits for p-value of overall treatment effect, see
print.default.
digits.pval.Q Minimal number of significant digits for p-value of heterogeneity tests, see
print.default.
digits.Q Minimal number of significant digits for heterogeneity statistics, see print.default.
scientific.pval
A logical specifying whether p-values should be printed in scientific notation,
e.g., 1.2345e-01 instead of 0.12345.
zero.pval A logical specifying whether p-values should be printed with a leading zero.
print.summary.netmeta 183

JAMA.pval A logical specifying whether p-values for test of effects should be printed ac-
cording to JAMA reporting standards.
big.mark A character used as thousands separator.
legend A logical indicating whether a legend should be printed.
warn.deprecated
A logical indicating whether warnings should be printed if deprecated arguments
are used.
... Additional arguments.

Author(s)

Guido Schwarzer <[email protected]>

See Also

netcomb, discomb, summary.netcomb

Examples
data(Linde2016)

# Only consider studies including Face-to-face PST (to reduce

# runtime of example)
#
face <- subset(Linde2016, id %in% c(16, 24, 49, 118))

# Conduct random effects network meta-analysis

#
net1 <- netmeta(lnOR, selnOR, treat1, treat2, id,
data = face, reference.group = "placebo",
sm = "OR", common = FALSE)

# Additive model for treatment components

#
nc1 <- netcomb(net1)
print(summary(nc1), digits = 2)

print.summary.netmeta Print detailed results of network meta-analysis

Description

Print method for objects of class summary.netmeta.

184 print.summary.netmeta

Usage
## S3 method for class 'summary.netmeta'
print(
x,
sortvar,
common = x$x$common,
random = x$x$random,
prediction = x$prediction,
reference.group = x$reference.group,
baseline.reference = x$baseline.reference,
all.treatments = x$all.treatments,
details = TRUE,
nma = TRUE,
backtransf = x$backtransf,
nchar.trts = x$nchar.trts,
nchar.studlab = x$nchar.studlab,
digits = gs("digits"),
digits.se = gs("digits.se"),
digits.pval.Q = max(gs("digits.pval.Q"), 2),
digits.Q = gs("digits.Q"),
digits.tau2 = gs("digits.tau2"),
digits.I2 = gs("digits.I2"),
scientific.pval = gs("scientific.pval"),
big.mark = gs("big.mark"),
truncate,
text.truncate = "*** Output truncated ***",
legend = TRUE,
warn.deprecated = gs("warn.deprecated"),
...
)

Arguments
x An object of class summary.netmeta.
sortvar An optional vector used to sort individual studies (must be of same length as
x$TE).
common A logical indicating whether results for the common effects model should be
printed.
random A logical indicating whether results for the random effects model should be
printed.
prediction A logical indicating whether prediction intervals should be printed.
reference.group
Reference treatment.
baseline.reference
A logical indicating whether results should be expressed as comparisons of other
treatments versus the reference treatment (default) or vice versa. This argument
is only considered if reference.group has been specified.
print.summary.netmeta 185

all.treatments A logical or "NULL". If TRUE, matrices with all treatment effects, and confidence
limits will be printed.
details A logical indicating whether further details for individual studies should be
printed.
nma A logical indicating whether summary results of network meta-analysis should
be printed.
backtransf A logical indicating whether results should be back transformed in printouts and
forest plots. If backtransf = TRUE, results for sm = "OR" are presented as odds
ratios rather than log odds ratios, for example.
nchar.trts A numeric defining the minimum number of characters used to create unique
treatment names.
nchar.studlab A numeric defining the minimum number of characters used to create unique
study labels.
digits Minimal number of significant digits, see print.default.
digits.se Minimal number of significant digits for standard deviations and standard errors,
see print.default.
digits.pval.Q Minimal number of significant digits for p-value of heterogeneity tests, see
print.default.
digits.Q Minimal number of significant digits for heterogeneity statistics, see print.default.
digits.tau2 Minimal number of significant digits for between-study variance, see print.default.
digits.I2 Minimal number of significant digits for I-squared statistic, see print.default.
scientific.pval
A logical specifying whether p-values should be printed in scientific notation,
e.g., 1.2345e-01 instead of 0.12345.
big.mark A character used as thousands separator.
truncate An optional vector used to truncate the printout of results for individual studies
(must be a logical vector of length corresponding to the number of pairwise
comparisons x$TE or contain numerical values).
text.truncate A character string printed if study results were truncated from the printout.
legend A logical indicating whether a legend should be printed.
warn.deprecated
A logical indicating whether warnings should be printed if deprecated arguments
are used.
... Additional arguments.

Author(s)
Guido Schwarzer <[email protected]>

See Also
netmeta, summary.netmeta
186 print.summary.netmeta

Examples
data(smokingcessation)

# Transform data from arm-based format to contrast-based format

#
p1 <- pairwise(list(treat1, treat2, treat3),
event = list(event1, event2, event3), n = list(n1, n2, n3),
data = smokingcessation, sm = "OR")

# Conduct random effects network meta-analysis and print detailed

# summary
#
net1 <- netmeta(p1, common = FALSE)
summary(net1)

## Not run:
data(Senn2013)

# Conduct common effects network meta-analysis

#
net2 <- netmeta(TE, seTE, treat1, treat2, studlab,
data = Senn2013, sm = "MD", random = FALSE, ref = "plac")
snet2 <- summary(net2)
print(snet2, digits = 3)

# Only show individual study results for multi-arm studies

#
print(snet2, digits = 3, truncate = multiarm)

# Only show first three individual study results

#
print(snet2, digits = 3, truncate = 1:3)

# Only show individual study results for Kim2007 and Willms1999

#
print(snet2, digits = 3, truncate = c("Kim2007", "Willms1999"))

# Only show individual study results for studies starting with the
# letter "W"
#
print(snet2, ref = "plac", digits = 3,
truncate = substring(studlab, 1, 1) == "W")

# Conduct random effects network meta-analysis

#
net3 <- netmeta(TE, seTE, treat1, treat2, studlab,
data = Senn2013, sm = "MD", common = FALSE, ref = "plac")
print(summary(net3), digits = 3)

## End(Not run)
radial.netmeta 187

radial.netmeta ‘Comparison-adjusted’ radial plot

Description
Draw a ‘comparison-adjusted’ radial plot to assess funnel plot asymmetry in network meta-analysis.

Usage
## S3 method for class 'netmeta'
radial(
x,
order,
pooled = ifelse(x$random, "random", "common"),
level = x$level,
pch,
col = "black",
legend = FALSE,
pos.legend = "topright",
pos.tests = "topleft",
lump.comparator = FALSE,
text.comparator = "comparator",
method.bias,
text.linreg = "(Egger)",
text.rank = "(Begg-Mazumdar)",
text.mm = "(Thompson-Sharp)",
sep.trts = x$sep.trts,
nchar.trts = x$nchar.trts,
digits.pval = gs("digits.pval"),
warn.deprecated = gs("warn.deprecated"),
linreg = FALSE,
rank = FALSE,
mm = FALSE,
...
)

Arguments
x An object of class netmeta.
order A mandatory character or numerical vector specifying the order of treatments or
list of comparators (see Details).
pooled A character string indicating whether results for the common ("common") or
random effects model ("random") should be plotted. Can be abbreviated.
level The confidence level utilised in the plot.
pch The plotting symbol(s) used for individual studies within direct comparisons.
188 radial.netmeta

col The colour(s) used for individual studies within direct comparisons.
legend A logical indicating whether a legend with information on direct comparisons
should be added to the plot.
pos.legend The position of the legend describing plotting symbols and colours for direct
comparisons.
pos.tests The position of results for test(s) of funnel plot asymmetry.
lump.comparator
A logical indicating whether comparators should be lumped, e.g., to specify
inactive treatments. information on direct comparisons should be added to the
plot.
text.comparator
A character string used in the plot to label the comparator if lump.comparator
is TRUE.
method.bias A character vector indicating which test(s) for funnel plot asymmetry to use.
Admissible values are "Begg", "Egger", and "Thompson", can be abbreviated.
See function metabias.
text.linreg A character string used in the plot to label the Egger test for funnel plot asym-
metry.
text.rank A character string used in the plot to label the Begg test for funnel plot asym-
metry.
text.mm A character string used in the plot to label the Thompson-Sharp test for funnel
plot asymmetry.
sep.trts A character used in comparison names as separator between treatment labels.
nchar.trts A numeric defining the minimum number of characters used to create unique
treatment names (see netmeta).
digits.pval Minimal number of significant digits for p-value of test(s) for funnel plot asym-
metry.
warn.deprecated
A logical indicating whether warnings should be printed if deprecated arguments
are used.
linreg Deprecated argument (replaced by method.bias).
rank Deprecated argument (replaced by method.bias).
mm Deprecated argument (replaced by method.bias).
... Additional graphical arguments passed as arguments to radial.meta.

Details
A ‘comparison-adjusted’ radial plot is drawn in the active graphics window. The idea of this radial
plot is similar to a ‘comparison-adjusted’ funnel plot (Chaimani & Salanti, 2012).
Argument order is mandatory to determine the order of treatments (Chaimani et al., 2013):
“Before using this plot, investigators should order the treatments in a meaningful way and make
assumptions about how small studies differ from large ones. For example, if they anticipate that
newer treatments are favored in small trials, then they could name the treatments from oldest to
radial.netmeta 189

newest so that all comparisons refer to ‘old versus new intervention’. Other possibilities include
defining the comparisons so that all refer to an active treatment versus placebo or sponsored versus
non-sponsored intervention.”
Alternatively, it is possible to only provide a single or few treatment name(s) in argument order
to define the comparator(s). In this case only comparisons with this / these treatment(s) will be
considered. If argument lump.comparator is TRUE, all comparators will be lumped into a single
group. The text for this group can be specified with argument text.comparator.

Value
A data frame with the following columns:

studlab Study label.

treat1 Label/Number for first treatment.
treat2 Label/Number for second treatment.
comparison Treatment comparison.
TE Estimate of treatment effect, e.g., log odds ratio.
TE.direct Pooled estimate from direct evidence.
TE.adj ‘Comparison-adjusted’ treatment effect (TE - TE.direct).
seTE Standard error of treatment estimate.
pch Plotting symbol(s).
col Colour of plotting symbol(s).

Author(s)
Guido Schwarzer <[email protected]>

References
Chaimani A & Salanti G (2012): Using network meta-analysis to evaluate the existence of small-
study effects in a network of interventions. Research Synthesis Methods, 3, 161–76
Chaimani A, Higgins JP, Mavridis D, Spyridonos P, Salanti G (2013): Graphical tools for network
meta-analysis in STATA. PLOS ONE, 8, e76654

See Also
netmeta, radial.meta, funnel.meta, metabias

Examples
## Not run:
data(Senn2013)

net1 <- netmeta(TE, seTE, treat1, treat2, studlab,

data = Senn2013, sm = "MD")

# 'Comparison-adjusted' radial plot not created as argument 'order'

190 rankogram

# is missing
#
try(radial(net1))

# Only show comparisons with placebo

#
radial(net1, order = "pl")

# Add result for Egger test of funnel plot asymmetry

#
radial(net1, order = "pl", method.bias = "Egger",
digits.pval = 2)

# (Non-sensical) alphabetic order of treatments with placebo as

# last treatment
#
ord <- c("a", "b", "me", "mi", "pi", "r", "si", "su", "v", "pl")
radial(net1, order = ord)

# Add results for tests of funnel plot asymmetry and use different
# plotting symbols and colours
#
radial(net1, order = ord,
pch = rep(c(15:18, 1), 3), col = 1:3,
method.bias = c("Egger", "Begg", "Thompson"), digits.pval = 2)

# Same results for tests of funnel plot asymmetry using reversed

# order of treatments
#
radial(net1, order = rev(ord),
pch = rep(c(15:18, 1), 3), col = 1:3,
method.bias = c("Egger", "Begg", "Thompson"), digits.pval = 2)

# Calculate tests for funnel plot asymmetry

#
f1 <- radial(net1, order = ord)
#
metabias(metagen(TE.adj, seTE, data = f1))
metabias(metagen(TE.adj, seTE, data = f1), method = "Begg")
metabias(metagen(TE.adj, seTE, data = f1), method = "Thompson")

## End(Not run)

rankogram Calculate rankogram

Description
This function calculates the probabilities of each treatment being at each possible rank and the
SUCRAs (Surface Under the Cumulative RAnking curve) in frequentist network meta-analysis.
rankogram 191

Usage
rankogram(
x,
nsim = 1000,
common = x$common,
random = x$random,
small.values = x$small.values,
cumulative.rankprob = FALSE,
nchar.trts = x$nchar.trts,
warn.deprecated = gs("warn.deprecated"),
...
)

## S3 method for class 'rankogram'

print(
x,
common = x$common,
random = x$random,
cumulative.rankprob = x$cumulative.rankprob,
nchar.trts = x$nchar.trts,
digits = gs("digits.prop"),
legend = TRUE,
warn.deprecated = gs("warn.deprecated"),
...
)

Arguments
x An object of class netmeta.
nsim Number of simulations.
common A logical indicating to compute ranking probabilities and SUCRAs for the com-
mon effects model.
random A logical indicating to compute ranking probabilities and SUCRAs for the ran-
dom effects model.
small.values A character string specifying whether small treatment effects indicate a benefi-
cial ("desirable") or harmful ("undesirable") effect, can be abbreviated.
cumulative.rankprob
A logical indicating whether cumulative ranking probabilites should be printed.
nchar.trts A numeric defining the minimum number of characters used to create unique
treatment names.
warn.deprecated
A logical indicating whether warnings should be printed if deprecated arguments
are used.
... Additional arguments for printing.
digits Minimal number of significant digits, see print.default.
legend A logical indicating whether a legend should be printed.
192 rankogram

Details
We derive a matrix showing the probability of each treatment being at each possible rank. To this
aim, we use resampling from a multivariate normal distribution with estimated network effects as
means and corresponding estimated variance covariance matrix. We then summarise them using the
ranking metric SUCRAs (Surface Under the Cumulative RAnking curve).

Value
An object of class rankogram with corresponding print and plot function. The object is a list
containing the following components:
ranking.matrix.common
Numeric matrix giving the probability of each treatment being at each possible
rank for the common effects model.
ranking.common SUCRA values for the common effects model.
ranking.matrix.random
Numeric matrix giving the probability of each treatment being at each possible
rank for the random effects model.
ranking.random SUCRA values for the random effects model.
cumrank.matrix.common
Numeric matrix giving the cumulative ranking probability of each treatment for
the common effects model.
cumrank.matrix.random
Numeric matrix giving the cumulative ranking probability of each treatment for
the random effects model.
nsim, common, random
As defined above

,
small.values, x
As defined above

Author(s)
Theodoros Papakonstantinou <[email protected]>, Guido Schwarzer <[email protected]>

References
Salanti G, Ades AE, Ioannidis JP (2011): Graphical methods and numerical summaries for present-
ing results from multiple-treatment meta-analysis: an overview and tutorial. Journal of Clinical
Epidemiology, 64, 163–71

See Also
netmeta, netrank, plot.rankogram
Senn2013 193

Examples
data(Woods2010)
p1 <- pairwise(treatment, event = r, n = N, studlab = author,
data = Woods2010, sm = "OR")
net1 <- netmeta(p1, small.values = "desirable")

ran1 <- rankogram(net1, nsim = 100)

ran1
print(ran1, cumulative.rankprob = TRUE)

plot(ran1)

Senn2013 Network meta-analysis in diabetes

Description
Network meta-analysis in diabetes comparing effects of a number of drugs on the HbA1c value.
These data are used as an example in Senn et al. (2013) and have been preprocessed for use in R
package netmeta.

Format
A data frame with the following columns:

TE treatment effect
seTE standard error of treatment effect
treat1 treatment 1
treat2 treatment 2
treat1.long treatment 1 (full treatment names)
treat2.long treatment 2 (full treatment names)
studlab Study label

Details
Treatment labels provided by columns treat1 and treat2 have been abbreviated:

• acar = Acarbose
• benf = Benfluorex
• metf = Metformin
• migl = Miglitol
• piog = Pioglitazone
• plac = Placebo
• rosi = Rosiglitazone
194 Senn2013

• sita = Sitagliptin
• sulf = Sulfonylurea
• vild = Vildagliptin

Full treatment names are available in columns treat1.long and treat2.long.

Source

Senn S, Gavini F, Magrez D, Scheen A (2013): Issues in performing a network meta-analysis.

Statistical Methods in Medical Research, 22, 169–89

See Also

netmeta

Examples

data(Senn2013)
head(Senn2013)

## Not run:
# Common effects model
#
net1 <- netmeta(TE, seTE, treat1.long, treat2.long, studlab,
data = Senn2013, sm = "MD", random = FALSE, nchar.trts = 4)
net1
net1$Q.decomp

# Forest plot
#
forest(net1, ref = "plac")

# Comparison with reference group

#
netmeta(TE, seTE, treat1.long, treat2.long,
studlab, data = Senn2013, reference = "plac")

# Random effects model

#
net2 <- netmeta(TE, seTE, treat1.long, treat2.long, studlab,
data = Senn2013, common = FALSE)
net2
forest(net2, ref = "plac")

## End(Not run)
smokingcessation 195

smokingcessation Network meta-analysis of interventions for smoking cessation

Description
Network meta-analysis comparing the effects of a number of interventions for smoking cessation.
These data are used as an example in Dias et al. (2013), page 651.

Format
A data frame with the following columns:

event1 number of individuals with successful smoking cessation in arm 1

n1 number of individuals in arm 1
event2 number of individuals with successful smoking cessation in arm 2
n2 number of individuals in arm 2
event3 number of individuals with successful smoking cessation in arm 3
n3 number of individuals in arm 3
treat1 treatment 1
treat2 treatment 2
treat3 treatment 3

Source
Dias S, Welton NJ, Sutton AJ, Caldwell DM, Lu G and Ades AE (2013): Evidence Synthesis for
Decision Making 4: Inconsistency in networks of evidence based on randomized controlled trials.
Medical Decision Making, 33, 641–56

See Also
pairwise, metabin, netmeta, netgraph.netmeta

Examples
data(smokingcessation)

# Transform data from arm-based format to contrast-based format

# Argument 'sm' has to be used for odds ratio as summary measure;
# by default the risk ratio is used in the metabin function called
# internally.
#
p1 <- pairwise(list(treat1, treat2, treat3),
event = list(event1, event2, event3), n = list(n1, n2, n3),
data = smokingcessation, sm = "OR")
p1

# Conduct network meta-analysis

#
196 Stowe2010

net1 <- netmeta(p1)

net1

# Draw network graph

#
netgraph(net1, points = TRUE, cex.points = 3, cex = 1.25)
tname <- c("No intervention", "Self-help",
"Individual counselling", "Group counselling")
netgraph(net1, points = TRUE, cex.points = 3, cex = 1.25, labels = tname)

Stowe2010 Network meta-analysis of adjuvant treatments to levodopa therapy for

Parkinson’s disease

Description
This data set contains data from a Cochrane review assessing efficacy and safety of three drug
classes as adjuvant treatment to levodopa therapy in patients with Parkinson’s disease and motor
complications (Stowe et al., 2010). The authors conducted three pairwise meta-analyses comparing
dopamine agonists, catechol-O-methyl transferase inhibitors (COMTIs), and monoamine oxidase
type B inhibitors (MAOBIs), respectively, with placebo.
The primary outcome was the mean reduction of the time spent in a relatively immobile ’off’ phase
(mean off-time), calculated in hours per day. Relative treatment effects were expressed as mean
difference. Data on this outcome were available for 5,331 patients from 28 studies comparing
an active treatment with placebo and one three-arm study comparing two active treatments with
placebo.

Format
A data frame with the following columns:

study study label

id study id
t1 treatment 1
y1 treatment effect arm 1
sd1 Standard deviation arm 1
n1 Sample size arm 1
t2 treatment 2
y2 treatment effect arm 2
sd2 Standard deviation arm 2
n2 Sample size arm 2
t3 treatment 3
y3 treatment effect arm 3
sd3 Standard deviation arm 3
n3 Sample size arm 3
subset.pairwise 197

Source
Stowe R, Ives N, Clarke CE, Deane K, Hilten V, Wheatley K, et al. (2010): Evaluation of the
efficacy and safety of adjuvant treatment to levodopa therapy in Parkinson’s disease patients with
motor complications. Cochrane Database of Systematic Reviews

See Also
pairwise, metacont, netmeta, netgraph.netmeta

Examples
data(Stowe2010)

# Transform data from arm-based format to contrast-based format

#
p1 <- pairwise(list(t1, t2, t3),
n = list(n1, n2, n3),
mean = list(y1, y2, y3), sd = list(sd1, sd2, sd3),
data = Stowe2010, studlab = study)
p1

# Conduct network meta-analysis

net1 <- netmeta(p1, ref = "plac")
net1

subset.pairwise Return subset of pairwise object

Description
The subset method returns a subset of a pairwise object.

Usage
## S3 method for class 'pairwise'
subset(x, subset, ...)

Arguments
x An object of class pairwise.
subset A logical expression indicating elements or rows to keep: missing values are
taken as false.
... Additional arguments.

Value
A pairwise object is returned.
198 summary.netcomb

Author(s)
Guido Schwarzer <[email protected]>

See Also
pairwise

Examples
# Transform data from arm-based format to contrast-based format
data(Franchini2012)
p1 <- pairwise(list(Treatment1, Treatment2, Treatment3),
n = list(n1, n2, n3),
mean = list(y1, y2, y3), sd = list(sd1, sd2, sd3),
data = Franchini2012, studlab = Study)
p1[, 1:5]

# Subset without Lieberman studies

subset(p1, !grepl("Lieberman", studlab))[, 1:5]

summary.netcomb Summary method for objects of class netcomb

Description
Summary method for objects of class netcomb.

Usage
## S3 method for class 'netcomb'
summary(
object,
common = object$common,
random = object$random,
backtransf = object$backtransf,
nchar.comps = object$nchar.comps,
warn.deprecated = gs("warn.deprecated"),
...
)

Arguments
object An object of class netcomb.
common A logical indicating whether results for the common effects model should be
printed.
random A logical indicating whether results for the random effects model should be
printed.
summary.netcomb 199

backtransf A logical indicating whether results should be back transformed in printouts and
forest plots.
nchar.comps A numeric defining the minimum number of characters used to create unique
component names.
warn.deprecated
A logical indicating whether warnings should be printed if deprecated arguments
are used.
... Additional arguments (to catch deprecated arguments).

Value
A list is returned with the same elements as a netcomb object.

Author(s)
Guido Schwarzer <[email protected]>

See Also
netcomb, discomb

Examples
data(Linde2016)

# Only consider studies including Face-to-face PST (to reduce

# runtime of example)
#
face <- subset(Linde2016, id %in% c(16, 24, 49, 118))

# Conduct random effects network meta-analysis

#
net1 <- netmeta(lnOR, selnOR, treat1, treat2, id,
data = face, reference.group = "placebo",
sm = "OR", common = FALSE)

# Additive model for treatment components

#
nc1 <- netcomb(net1)
summary(nc1)
print(summary(nc1), digits = 2, digits.stat = 3)

## Not run:
# Conduct random effects network meta-analysis
#
net2 <- netmeta(lnOR, selnOR, treat1, treat2, id,
data = Linde2016, reference.group = "placebo",
sm = "OR", common = FALSE)

# Additive model for treatment components

#
200 summary.netmeta

nc2 <- netcomb(net2)

summary(nc2)
print(summary(nc2), digits = 2, digits.stat = 3)

## End(Not run)

summary.netmeta Summary method for objects of class netmeta

Description
Summary method for objects of class netmeta.

Usage
## S3 method for class 'netmeta'
summary(
object,
common = object$common,
random = object$random,
prediction = object$prediction,
reference.group = object$reference.group,
baseline.reference = object$baseline.reference,
all.treatments = object$all.treatments,
backtransf = object$backtransf,
nchar.trts = object$nchar.trts,
warn.deprecated = gs("warn.deprecated"),
...
)

Arguments
object An object of class netmeta.
common A logical indicating whether results for the common effects model should be
printed.
random A logical indicating whether results for the random effects model should be
printed.
prediction A logical indicating whether prediction intervals should be printed.
reference.group
Reference treatment.
baseline.reference
A logical indicating whether results should be expressed as comparisons of other
treatments versus the reference treatment (default) or vice versa. This argument
is only considered if reference.group has been specified.
summary.netmeta 201

all.treatments A logical or "NULL". If TRUE, matrices with all treatment effects, and confidence
limits will be printed.
backtransf A logical indicating whether results should be back transformed in printouts and
forest plots.
nchar.trts A numeric defining the minimum number of characters used to create unique
treatment names (see Details).
warn.deprecated
A logical indicating whether warnings should be printed if deprecated arguments
are used.
... Additional arguments (to catch deprecated arguments).

Value
A list is returned with the following elements:
comparison Results for pairwise comparisons (data frame with columns studlab, treat1, treat2,
TE, seTE, lower, upper, z, p).
comparison.nma.common
Results for pairwise comparisons based on common effects model (data frame
with columns studlab, treat1, treat2, TE, seTE, lower, upper, z, p, leverage).
comparison.nma.random
Results for pairwise comparisons based on random effects model (data frame
with columns studlab, treat1, treat2, TE, seTE, lower, upper, z, p).
common Results for common effects model (a list with elements TE, seTE, lower, upper,
z, p).
random Results for random effects model (a list with elements TE, seTE, lower, upper,
z, p).
predict Prediction intervals (a list with elements seTE, lower, upper).
studies Study labels coerced into a factor with its levels sorted alphabetically.
narms Number of arms for each study.
k Total number of studies.
m Total number of pairwise comparisons.
n Total number of treatments.
d Total number of designs (corresponding to the unique set of treatments com-
pared within studies).
Q Overall heterogeneity / inconsistency statistic.
df.Q Degrees of freedom for test of heterogeneity / inconsistency.
pval.Q P-value for test of heterogeneity / inconsistency.
I2, lower.I2, upper.I2
I-squared, lower and upper confidence limits.
tau Square-root of between-study variance.
Q.heterogeneity
Overall heterogeneity statistic.
202 summary.netmeta

df.Q.heterogeneity
Degrees of freedom for test of overall heterogeneity.
pval.Q.heterogeneity
P-value for test of overall heterogeneity.
Q.inconsistency
Overall inconsistency statistic.
df.Q.inconsistency
Degrees of freedom for test of overall inconsistency.
pval.Q.inconsistency
P-value for test of overall inconsistency.
sm A character string indicating underlying summary measure.
method A character string indicating which method is to be used for pooling of studies.
level The level used to calculate confidence intervals for individual studies.
level.ma The level used to calculate confidence intervals for pooled estimates.
common, random As defined above.
prediction, level.predict
As defined above.
reference.group, baseline.reference
As defined above.
all.treatments, backtransf
As defined above.
ci.lab Label for confidence interval.
seq A character specifying the sequence of treatments.
tau.preset An optional value for the square-root of the between-study variance τ 2 .
sep.trts A character used in comparison names as separator between treatment labels.
nchar.trts A numeric defining the minimum number of characters used to create unique
treatment names.
title Title of meta-analysis / systematic review.
call Function call.
version Version of R package netmeta used to create object.

Author(s)

Guido Schwarzer <[email protected]>

See Also

netmeta
treats 203

Examples
data(smokingcessation)

p1 <- pairwise(list(treat1, treat2, treat3),

event = list(event1, event2, event3), n = list(n1, n2, n3),
data = smokingcessation, sm = "OR")
net1 <- netmeta(p1)

summary(net1)

## Not run:
data(Senn2013)

# Conduct common effects network meta-analysis

#
net2 <- netmeta(TE, seTE, treat1, treat2, studlab,
data = Senn2013, sm = "MD", random = FALSE)
print(net2, ref = "plac", digits = 3)
summary(net2)

# Conduct random effects network meta-analysis

#
net3 <- netmeta(TE, seTE, treat1, treat2, studlab,
data = Senn2013, sm = "MD", common = FALSE)
print(net3, ref = "plac", digits = 3)
summary(net3)

## End(Not run)

treats Abbreviate treatment names

Description
Auxiliary functions to create uniquely abbreviated treatment names.

Usage
treats(x, nchar.trts = 8, row = TRUE)

comps(x, trts, sep.trts, nchar.trts = 8, row = TRUE)

Arguments
x A vector with treatment or comparison names or a matrix with treatment or
comparison names as row and / or column names.
nchar.trts A numeric defining the minimum number of characters used to create unique
treatment names.
204 treats

row A logical indicating whether row or column names should be used (only consid-
ered if argument x is a matrix).
trts A character vector with treatment names.
sep.trts A character used in comparison names as separator between treatment labels.

Details
These auxiliary functions can be used to create uniquely abbreviated treatment names (and are used
internally in several R functions for this purpose).
In order to construct uniquely abbreviated treatment names, treats uses substring to extract the
first nchar.trts characters. If these abbreviated treatment names are not unique, abbreviate with
argument minlength = nchar.trts is used.
In order to construct comparisons with uniquely abbreviated treatment names, comps calls treats
internally.

Author(s)
Guido Schwarzer <[email protected]>

See Also
netmeta, print.netmeta, print.summary.netmeta

Examples
data(smokingcessation)

# Transform data from arm-based format to contrast-based format

#
p1 <- pairwise(list(treat1, treat2, treat3),
event = list(event1, event2, event3), n = list(n1, n2, n3),
data = smokingcessation, sm = "OR")

# Conduct random effects network meta-analysis and show data frame

#
net1 <- netmeta(p1, common = FALSE)

# Full treatment names

#
net1$trts

# Treatment names with maximal four characters

#
treats(net1$trts, nchar.trts = 4)

## Not run:
data(Senn2013)
#
net2 <- netmeta(TE, seTE, treat1.long, treat2.long, studlab,
data = Senn2013)
Woods2010 205

# Full treatment names

#
net2$trts

# Treatment names with four characters

#
treats(net2$trts, nchar.trts = 4)

# With two characters

#
treats(net2$trts, nchar.trts = 2)

# With one character (if possible)

#
treats(net2$trts, nchar.trts = 1)

# Full comparison names

#
net2$comparisons

# Abbreviated comparison names

#
with(net2, comps(comparisons, trts, sep.trts, nchar = 4))

## End(Not run)

Woods2010 Count statistics of survival data

Description
Count mortality statistics in randomised controlled trials of treatments for chronic obstructive pul-
monary disease (Woods et al. (2010), Table 1).

Format
A data frame with the following columns:

author first author / study name

treatment treatment
r number of deaths in treatment arm
N number of patients in treatment arm

Source
Woods BS, Hawkins N, Scott DA (2010): Network meta-analysis on the log-hazard scale, com-
bining count and hazard ratio statistics accounting for multi-arm trials: A tutorial. BMC Medical
206 Woods2010

Research Methodology, 10, 54

See Also
pairwise, metabin, netmeta

Examples
data(Woods2010)

# Transform data from long arm-based format to contrast-based

# format Argument 'sm' has to be used for odds ratio as summary
# measure; by default the risk ratio is used in the metabin
# function called internally.
#
p1 <- pairwise(treatment, event = r, n = N,
studlab = author, data = Woods2010, sm = "OR")
p1

# Conduct network meta-analysis

#
net1 <- netmeta(p1)
net1

## Not run:
# Show forest plot
#
forest(net1, ref = "Placebo", drop = TRUE,
leftlabs = "Contrast to Placebo")

## End(Not run)
Index

∗ contribution ∗ plot
netcontrib, 84 hasse, 49
∗ datagen ∗ print
pairwise, 158 netleague, 108
∗ datasets print.decomp.design, 175
Baker2009, 9 print.netbind, 176
dietaryfat, 13 print.netcomb, 178
Dogliotti2014, 22 print.netimpact, 180
Dong2013, 23 print.summary.netcomb, 181
Franchini2012, 42 print.summary.netmeta, 183
Gurusamy2011, 48 summary.netcomb, 198
Linde2015, 58 ∗ summary
Linde2016, 59 summary.netmeta, 200
Senn2013, 193
abbreviate, 17, 67, 75, 79, 86, 123, 133, 204
smokingcessation, 195
arrows, 166
Stowe2010, 196
as.data.frame.netconnection, 7
Woods2010, 205
as.data.frame.netmeta, 8
∗ hplot
forest.netbind, 24 Baker2009, 9
forest.netcomb, 26 baujat.netpairwise (netpairwise), 137
forest.netcomparison, 29
forest.netcomplex, 32 colours, 94
forest.netmeta, 34 comps (treats), 203
forest.netsplit, 38
funnel.netmeta, 43 decomp.design, 4, 10, 123, 133, 176
heatplot, 54 dietaryfat, 13
heatplot.netmeta, 55 discomb, 4, 14, 28, 31, 33, 65, 71, 74, 76, 78,
netgraph, 88 80, 81, 83, 90, 179, 183, 199
netgraph.discomb, 90 Dogliotti2014, 22
Dong2013, 23
netgraph.netcomb, 91
netgraph.netconnection, 92 eigen, 99
netgraph.netimpact, 94 element_text, 170, 171
netgraph.netmeta, 96
netheat, 104 factor, 114
plot.netposet, 165 forest.meta, 25–28, 30–33, 36, 37, 40, 41
plot.netrank, 169 forest.netbind, 5, 24, 65
radial.netmeta, 187 forest.netcomb, 4, 21, 26, 71
∗ package forest.netcomparison, 29
netmeta-package, 4 forest.netcomplex, 32

207
208 INDEX

forest.netcomt (forest.netcomb), 26 netgraph.netconnection, 89, 92

forest.netmeta, 4, 34, 128 netgraph.netimpact, 89, 94, 108
forest.netpairwise (netpairwise), 137 netgraph.netmeta, 14, 43, 89–93, 95, 96,
forest.netsplit, 38, 154 114, 163, 195, 197
Franchini2012, 42 netheat, 4, 11, 12, 53, 104
funnel.meta, 45, 46, 189 netimpact, 5, 95, 107, 181
funnel.netmeta, 5, 43, 62 netleague, 4, 108
funnel.netpairwise (netpairwise), 137 netmatrix, 113
netmeasures, 5, 36, 115, 154, 158
Gurusamy2011, 48 netmeta, 4, 8, 12, 14–17, 21, 43, 45, 46,
50–53, 57, 58, 60, 62, 65–67, 71, 83,
hasse, 4, 49, 49, 144, 167, 171 87, 88, 97, 99, 102, 106, 108, 111,
hatmatrix, 51, 85 114, 116, 118, 132, 136, 139, 140,
heatplot, 54 144, 148, 152, 154, 157–160, 163,
heatplot.crossnma, 54 167, 171, 185, 188, 189, 191, 192,
heatplot.netmeta, 54, 55 194, 195, 197, 202, 204, 206
I, 100, 101 netmeta-package, 4
invmat, 56 netmetabin, 4, 10, 22, 23, 48, 107, 108, 129,
152, 154, 157, 158
Linde2015, 58 netpairwise, 5, 137, 162
Linde2016, 59 netposet, 4, 50, 58, 111, 141, 167, 171
netrank, 4, 35, 36, 50, 110, 111, 120, 128,
metabias, 45, 46, 62, 188, 189 143, 144, 146, 167, 171, 192
metabias.meta, 61 netsplit, 4, 139, 140, 149, 158
metabias.netmeta, 60 nettable, 4, 155
metabias.netpairwise (netpairwise), 137
metabin, 10, 22, 23, 48, 58, 123, 160, 161, order, 28, 36
163, 195, 206
metacont, 43, 123, 160, 161, 163, 197 pairwise, 10, 14, 15, 22, 23, 43, 48, 58, 82,
metacum.netpairwise (netpairwise), 137 120, 121, 123, 127, 128, 132, 136,
metagen, 123, 128, 139, 140, 160, 161, 163 140, 158, 163, 195, 197, 198, 206
metainc, 14, 123, 160, 161, 163 parkinson (Franchini2012), 42
metainf.netpairwise (netpairwise), 137 paste, 123, 133
metareg.netpairwise (netpairwise), 137 plot.netbind (forest.netbind), 24
plot.netcomb (forest.netcomb), 26
netbind, 5, 26, 63, 177 plot.netcomparison
netcomb, 4, 17, 21, 26, 28, 31, 33, 60, 65, 65, (forest.netcomparison), 29
74, 76, 78, 80, 92, 179, 183, 199 plot.netcomplex (forest.netcomplex), 32
netcomparison, 5, 20, 21, 31, 71, 73, 79, 80 plot.netmeta (forest.netmeta), 34
netcomplex, 5, 20, 21, 33, 71, 75, 76, 77 plot.netpairwise (netpairwise), 137
netconnection, 5, 7, 21, 88, 93 plot.netposet, 4, 144, 165, 171
netconnection (netconnection.default), plot.netrank, 50, 144, 169
81 plot.netsplit (forest.netsplit), 38
netconnection.default, 81 plot.rankogram, 148, 173, 192
netcontrib, 5, 53, 84 prcomp, 99, 167
netdistance, 83, 87 print.data.frame, 147
netgraph, 4, 88 print.decomp.design, 175
netgraph.discomb, 89, 90 print.default, 35, 82, 147, 191
netgraph.netcomb, 89, 91 print.hatmatrix (hatmatrix), 51
INDEX 209

print.metabias.netpairwise summary.netmeta, 185, 200

(netpairwise), 137 summary.netpairwise (netpairwise), 137
print.metacum.netpairwise
(netpairwise), 137 text, 166
print.metainf.netpairwise treats, 17, 67, 75, 79, 86, 123, 133, 203
(netpairwise), 137 trimfill.netpairwise (netpairwise), 137
print.metareg.netpairwise
(netpairwise), 137 Woods2010, 205
print.netbind, 176
print.netcomb, 71, 178
print.netcomparison (netcomparison), 73
print.netcomplex (netcomplex), 77
print.netconnection
(netconnection.default), 81
print.netcontrib (netcontrib), 84
print.netimpact, 108, 180
print.netleague (netleague), 108
print.netmeta, 204
print.netmeta (netmeta), 118
print.netpairwise (netpairwise), 137
print.netposet (netposet), 141
print.netrank (netrank), 146
print.netsplit (netsplit), 149
print.nettable (nettable), 155
print.rankogram (rankogram), 190
print.summary.netcomb, 181
print.summary.netmeta, 123, 133, 183, 204
print.summary.netpairwise
(netpairwise), 137
print.trimfill.netpairwise
(netpairwise), 137

radial.meta, 188, 189

radial.netmeta, 187
radial.netpairwise (netpairwise), 137
rainbow, 101
rankogram, 4, 148, 173, 174, 190
rma.mv, 121, 127

scale_fill_gradient2, 170
Senn2013, 193
sequential_hcl, 101
smokingcessation, 195
solve, 57
sqrt, 100, 101
Stowe2010, 196
subset.pairwise, 197
substring, 204
summary.netcomb, 21, 183, 198