Package ‘berryFunctions’

March 25, 2018

Type Package
Title Function Collection Related to Plotting and Hydrology
Version 1.17.0
Date 2018-03-24
Imports grDevices, graphics, stats, utils, abind
Suggests RColorBrewer, pbapply, knitr, rmarkdown, gstat, RCurl,
colorspace
Author Berry Boessenkool
Maintainer Berry Boessenkool <[email protected]>
Description Draw horizontal histograms, color scattered points by 3rd dimension,
enhance date- and log-axis plots, zoom in X11 graphics, trace errors and warnings,
use the unit hydrograph in a linear storage cascade, convert lists to data.frames and arrays,
fit multiple functions.
License GPL (>= 2)
URL https://github.com/brry/berryFunctions
RoxygenNote 6.0.1.9000
VignetteBuilder knitr
BugReports https://github.com/brry/berryFunctions
NeedsCompilation no
Repository CRAN
Date/Publication 2018-03-25 15:10:06 UTC

R topics documented:
berryFunctions-package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
addAlpha . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
addFade . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
addRows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
almost.equal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
anhang . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

1
2 R topics documented:

approx2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
around . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
betaPlot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
betaPlotComp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
between . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
checkFile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
ci . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
ciBand . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
circle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
classify . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
climateGraph . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
colPoints . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
colPointsHist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
colPointsLegend . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
combineFiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
compareFiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
convertUmlaut . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
createFun . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
createPres . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
dataStr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
distance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
divPal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
dupes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
exp4p . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
expReg . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
exTime . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
funnelPlot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
funSource . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
funTinn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
getColumn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
getName . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
gof . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
googleLink2pdf . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
groupHist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
headtail . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
horizHist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
insertRows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
instGit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
is.error . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
l2array . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
l2df . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
legendmt . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
library2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
lim0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
linLogHist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
linLogTrans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
linReg . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
locArrow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
R topics documented: 3

locLine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
logAxis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
logHist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
logSpaced . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
logVals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
lsc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
lsMem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
monthAxis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
monthLabs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
movAv . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
movAvLines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
mReg . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
na9 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
nameSample . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
newFilename . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
normalizePathCP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
normPlot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
openFile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
owa . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
packagePath . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
panelDim . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
parallelCode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
pdfpng . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
popleaf . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
pretty2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120
quantileBands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
quantileMean . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
rainbow2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
removeSpace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
rescale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
round0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128
roundedRect . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
runAxis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
seasonality . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
seqPal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134
seqR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136
showPal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
smallPlot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
smoothLines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
sortDF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
spiralDate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142
spiralDateAnim . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
superPos . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
tableColVal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
textField . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
TFtest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151
timeAxis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
timer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155
4 berryFunctions-package

toupper1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156
traceCall . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157
truncMessage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158
tryStack . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159
unitHydrograph . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162
yearSample . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163

Index 165

berryFunctions-package
Berry’s functions

Description
Collection of functions, mainly connected with graphics and hydrology.
- zoom in X11 graphics
- plot rainfall-runoff data and optimize parameters for the unit hydrograph in the linear storage cas-
cade
- write text to plots on top of colored fields in label size (halo-effect)
- draw scatterplots colored by 3rd dimension (as in image, which only deals with grids)
- draw histograms horizontally
- advancedly label date axes and logarithmic axes
- fit multiple functions (power, reciprocal, exponential, logarithmic, polynomial, rational) by re-
gression
- convert lists to data.frames
- and more...

Note
dataDWD and readDWD have moved to the package rdwd: https://github.com/brry/rdwd#
rdwd

Get the most recent code updates at https://github.com/brry

At some places you’ll find ## not run in the examples. These code blocks were excluded from
checking while building, mainly because they are interactive and need mouseclicks, or because they
open another device/file. Normally, you should be able to run them in an interactive session. If you
do find non-executable code, please tell me!
Feel free to suggest packages in which these functions would fit well.
I strongly depend on - and therefore welcome - any feedback!

Author(s)
Berry Boessenkool, <[email protected]>, 2011-2017
addAlpha 5

Examples

# see vignette("berryFunctions")

addAlpha Color transparency

Description
Make existing colors semi-transparent (add alpha)

Usage
addAlpha(col, alpha = 0.3)

Arguments
col Vector of color names (colors), hexadecimal or integer that can be interpreted
by col2rgb
alpha Level of semi-transparency. between 0 (transparent) and 1 (intransparent). Can
also be a vector. DEFAULT: 0.3

Value
character vector with hexadecimal color codes.

Author(s)
Berry Boessenkool, <[email protected]>, June 2014 Based on suggestion by Mathias Seibert, Dec.
2013

See Also
addFade, rgb, colors, col2rgb

Examples

addAlpha("red", c(0.1, 0.3, 0.6, 1))

addAlpha(1:3)
addAlpha(1:3, 1:3/3)
NewColors <- addAlpha(c("red","blue","yellow","green", "purple"), 0:200/200)
plot(runif(1000), col=NewColors, pch=16, cex=2)

# use addFade for line segments, because of overlapping dots

set.seed(1); x <- cumsum(rnorm(30)) ; y <- x-2
plot(x, type="n")
6 addFade

segments(x0=1:29,y0=head(x,-1), x1=2:30,y1=x[-1], col=addAlpha(4, 29:0/30), lwd=10)

segments(x0=1:29,y0=head(y,-1), x1=2:30,y1=y[-1], col=addFade (4, 29:0/30), lwd=10)

addFade Color fade out

Description
Make existing colors fade away to white

Usage
addFade(col, fade = 0.3, target = "white", ...)

Arguments
col Vector of color names (colors), hexadecimal or integer that can be interpreted
by col2rgb
fade Level of fading towards target. between 0 (target) and 1 (col). Can also be a
vector. DEFAULT: 0.3
target Target color that should be faded into. DEFAULT: "white"
... Further arguments passed to colorRamp

Value
character matrix with hexadecimal color codes.

Author(s)
Berry Boessenkool, <[email protected]>, Feb 2016

See Also
addAlpha, colorRamp, colors

Examples

plot(1:11, pch=16, cex=3, col=addFade(2, 10:0/10))

plot(1:11, pch=16, cex=3, col=addFade(2, 10:0/10, target="blue"))
plot(1:11, pch=16, cex=3, col=addFade(2, 10:0/10, target=3:4))
plot(1:21, pch=16, cex=3, col=addFade(2:3, 10:0/10))
plot(1:21, pch=16, cex=3, col=addFade(2:3, 10:0/10, target=4:5))
NewColors <- addFade(c("red","blue","yellow","green", "purple"), 0:200/200)
plot(runif(1000), col=NewColors, pch=16, cex=2)
addRows 7

addRows Add n rows to a data.frame

Description

simple Helper-Function to add n rows to a data.frame.

Usage

addRows(df, n, values = NA)

Arguments

df Dataframe object
n Number of rows to add
values Values to be used in the new rows. DEFAULT: NA

Value

A data.frame

Author(s)

Berry Boessenkool, <[email protected]>, Jan 2014

See Also

insertRows, data.frame, matrix, rbind

Examples

MYDF <- data.frame(A=5:3, B=2:4)

addRows(MYDF, 3)
8 almost.equal

almost.equal Vectorized testing for near-equality

Description
Vectorized testing for near-equality with all.equal. Since elements are recycled, this will not
work for environments. You can use almost.equal directly in if expressions.

Usage
almost.equal(x, y, ...)

Arguments
x, y R objects to be compared with each other, recycled to max length
... Further arguments passed to all.equal

Value
Logical vector

Author(s)
Berry Boessenkool, <[email protected]>, Jan 2017

See Also
all.equal

Examples

# General usage:
x <- c(0.4-0.1, 0.5-0.2)
x
x==0.3 # FALSE TRUE # but mathematically, x is 0.3
all.equal(x, rep(0.3,2)) # TRUE
almost.equal(x,0.3) # TRUE TRUE # nice

y <- c(7777, 0.3)

all.equal(x,y) # "Mean relative difference: 25922.33" Not what I want
almost.equal(x,y) # FALSE TRUE Exactly what I want

# Testing vectorization
almost.equal(1:6, 3)
almost.equal(1:6, NA)
almost.equal(1:6, NULL)
anhang 9

# Testing the function for different data types (in order of coercion):
almost.equal(c(TRUE,FALSE,NA), c(TRUE,FALSE,NA)) # logical
almost.equal(as.factor(letters), as.factor(letters)) # factor
all.equal(1:6, 1:6)
almost.equal(1:6, 1:6) # integer numeric see above
0.4+0.4i - 0.1-0.1i == 0.3+0.3i
almost.equal(0.4+0.4i - 0.1-0.1i, 0.3+0.3i) # complex
all.equal(letters, tolower(LETTERS))
almost.equal(letters, tolower(LETTERS)) # character
almost.equal(Sys.Date()+1:4,Sys.Date()+1:4) # Date
x <- Sys.time()+0:2
all.equal(x,x)
almost.equal(x,x) # POSIXt
A <- list(a=1:5, b=0.5-0.2)
B <- list(a=1:5, b=0.4-0.1)
all.equal(A,B)
almost.equal(A,B) # list

anhang open the Appendix of Rclick

Description
Open the Appendix of my R handbook found online at RclickHandbuch.wordpress.com

Usage
anhang()

Value
None, opens pdf in default viewer using system2

Author(s)
Berry Boessenkool, <[email protected]>, Jul 2016

See Also
funSource

Examples
# anhang() # excluded from cran check because of external browser opening policy
10 approx2

approx2 Smart linear NA interpolation

Description

Smart interpolation: as approx, approx2 fills NAs in a vector with linear interpolation, but unlike
approx, it can handle NAs at the ends of a vector (takes the first/last value available for those).
Also, approx2 returns a vector only.

Usage

approx2(x, fill = NULL, n = length(x), quiet = FALSE, ...)

Arguments

x Vector with (numeric) values

fill Function to fill NAs at the start or end of the vector. See Details. DEFAULT:
NULL
n Number of points to interpolate to
quiet Logical: suppress warning for no non-NA values? DEFAULT: FALSE
... Further arguments passed to approx

Details

The function fill is used to fill missing values at the ends of the vector. It could be mean or median,
for example, but must be a function that accepts na.rm=TRUE as an argument. The default (NULL)
means to use the first (or last) observation available.

Value

Vector with NAs replaced with interpolation (not a list, as in approx!)

Author(s)

Berry Boessenkool, <[email protected]>, July 2015

See Also

approx, zoo::na.locf, ciBand for usage example

around 11

Examples

approx2(c(NA,NA)) # yields a message

approx2(c(NA,NA, 6, 4, 8, 9, 3, 2, 1)) # fills with first non-NA value
approx2(c( 2,NA, 6, 4, 8, 9, 3, 2, 1)) # interpolates linearly
approx2(c( 2, 4, 6, 4, 8, 9,NA, 2,NA)) # linear, then last non-NA at end

approx2(c(NA,NA, 6, 4, 8, 9, 3, 2, 1))
approx2(c(NA,NA, 6, 4, 8, 9, 3, 2, 1), fill=median) # first median, then linear
approx2(c(NA,NA, 6, 4, 8, 9, 3, 2, 1), fill=mean)

approx2(c( 3, 4, 6, 4, 8, 9,NA, 2,NA))

approx2(c( 3, 4, 6, 4, 8, 9,NA, 2,NA), fill=median)
approx2(c( 3, 4, 6, 4, 8, 9,NA, 2,NA), fill=mean)

approx2(c(NA,NA, 6, 4, 8, 9, 3, 2, 1), n=17)

approx2(c( 2,NA, 6, 4, 8, 9, 3, 2, 1), n=17)
approx2(c( 2, 4, 6, 4, 8, 9,NA, 2,NA), n=17)

around View values around an index

Description
View index rows of a data.frame with n surrounding rows

Usage
around(x, i, n1 = 2, n2 = n1, convert = is.logical(i))

Arguments
x Data.frame
i Index (logical or integers)
n1 Number of elements shown before each i. DEFAULT: 2
n2 Number of elements shown after each i. DEFAULT: n1
convert Use which to get the row numbers? DEFAULT: TRUE if i is boolean

Value
Nothing, calls View

Author(s)
Berry Boessenkool, <[email protected]>, Nov 2016
12 betaPlot

See Also
sortDF, View

Examples
## Not run: ## View should not be used in examples
myDF <- data.frame(A=1:30, B=cumsum(rnorm(30)))
myDF[c(5,7,23,29),1] <- NA
around(myDF, i=is.na(myDF$A))
around(myDF, i=c(11,19), n2=0)

## End(Not run)

betaPlot Beta density plot

Description
Quick and nice plot of beta density distribution based on just alpha and beta

Usage
betaPlot(shape1 = 1.5, shape2 = 5, lines = NA, fill = rgb(0, 0.3, 0.8,
0.4), cumulative = TRUE, mar = c(2, 3, 3, 3), keeppar = FALSE,
las = 1, main = paste("Beta density with\nalpha =", signif(shape1, 3),
"and beta =", signif(shape2, 3)), ylim = lim0(y), xlim = 0:1, ylab = "",
xlab = "", type = "l", lty = 1, col = par("fg"), ...)

Arguments
shape1 Alpha value as in dbeta. DEFAULT: 1.5
shape2 Beta value. DEFAULT: 5
lines Quantiles at which vertical lines should be plotted. DEFAULT: NA
fill Color passed to polygon. DEFAULT: rgb(0,0.3,0.8, 0.4)
cumulative Should cumulative density distribution be added? DEFAULT: TRUE
mar Margins for plot passed to par. DEFAULT: c(2,3,3,3)
keeppar Should margin parameters be kept instead of being restored to previous value?
DEFAULT: FALSE
las Label orientation, argument passed to plot. DEFAULT: 1
main main as in plot. DEFAULT: paste("Beta density with\nalpha =", shape1, "and
beta =", shape2)
ylim, xlim limit for the y and x axis. DEFAULT: lim0(y), 0:1
ylab, xlab labels for the axes. DEFAULT: ""
type, lty, col arguments passed to plot and lines.
... further arguments passed to plot like lwd, xaxs, cex.axis, etc.
betaPlotComp 13

Details
This function very quickly plots a beta distribution by just specifying alpha and beta.

Value
None. Used for plotting.

Author(s)
Berry Boessenkool, <[email protected]>, July 2014

See Also
betaPlotComp, normPlot, dbeta, https://cran.r-project.org/package=denstrip, https:
//cran.r-project.org/view=Distributions

Examples

betaPlot()
betaPlot(2,1)
betaPlot(0.5, 2)

# beta distribution is often used for proportions or probabilities

# overview of parameters
# alpha = number of successes + 1. beta = number of failures + 1
betaPlotComp()
# a bigger: HDI (Highest Density Interval) further to the right (1)
# b bigger: HDI more to the left (0)
# both bigger: narrower HDI, stronger peak

betaPlotComp Compare beta distributions

Description
Visually understand the effect of the beta distribution parameters

Usage
betaPlotComp(shape1 = c(0.5, 1:4, 10, 20), shape2 = shape1,
cumulative = FALSE, cex = 0.8, las = 1, main = "", ylim = lim0(4),
mar = rep(0, 4), oma = c(2, 2, 4.5, 2), mgp = c(3, 0.7, 0),
keeppar = FALSE, textargs = NULL, ...)
14 betaPlotComp

Arguments

shape1 Vector of alpha values as in dbeta. DEFAULT: c(0.5, 1:4, 10,20)

shape2 Beta values to be compared. DEFAULT: shape1
cumulative Should the cumulative density distribution line be added? DEFAULT: FALSE
cex Character EXpansion size. DEFAULT: 0.8
las Label Axis Style passed to axis. DEFAULT: 1
main Main as in plot. DEFAULT: ""
ylim LIMit for the Y axis. DEFAULT: lim0(4)
mar MARgins for plot passed to par. DEFAULT: rep(0,4)
oma Outer MArgins for plot passed to par. DEFAULT: c(2,2,4.5,2)
mgp MarGin Placement. DEFAULT: c(3,0.7,0)
keeppar Should margin parameters be kept instead of being restored to previous value?
DEFAULT: FALSE
textargs List of arguments passed to textField. DEFAULT: NULL
... Further arguments passed to betaPlot like lines, fill, etc.

Value

None. Used for plotting.

Note

Tries to find suitable subplot for axis labels. This works only for increasing parameter values.

Author(s)

Berry Boessenkool, <[email protected]>, Dec 2015

See Also

betaPlot

Examples

betaPlotComp()
betaPlotComp(oma=c(2,2,2,2), ylim=lim0(5.5), textargs=list(y=NA))
betaPlotComp(shape1=c(3,10,34), shape2=c(7,9,24))
between 15

between Are values between a and b?

Description
Are values within a certain interval? Basically a wrapper for x >= a & x <= b to save
repeating long x names twice.

Usage
between(x, a, b = a, incl = TRUE, aincl = incl, bincl = incl,
quiet = FALSE)

Arguments
x Numerical vector
a, b Numerical values/vectors specifying the borders of the interval. min and max are
used, so they can be a vector.
incl Logical. Include values on the borders? For x == border, TRUE will be returned.
Specify per left and right border separately with the arguments aincl and bincl.
DEFAULT: TRUE
aincl, bincl Logical. Include values on left and right border, respectively? DEFAULT: incl
quiet Logical. Suppress warning if a>b? DEFAULT: FALSE

Value
Logical (boolean) vector with TRUE/FALSE values

Author(s)
Berry Boessenkool, <[email protected]>, Aug 2017

See Also
findInterval

Examples
between(1:10, 4, 8)
between(1:10, 4:8) # range as vector
between(1:10, 8, 4) # warns about interval

data.frame( incl.T=between(1:10, 4, 8),

incl.F=between(1:10, 4, 8, incl=FALSE),
aincl.F=between(1:10, 4, 8, aincl=FALSE),
bincl.F=between(1:10, 4, 8, bincl=FALSE) )
16 checkFile

checkFile check file existence

Description
check whether files exist and give a useful error/warning/message

Usage
checkFile(file, warnonly = FALSE, trace = TRUE, pwd = TRUE)

Arguments
file Filename(s) as character string to be checked for existence.
warnonly Logical: Only issue a warning instead of an error with stop? DEFAULT:
FALSE
trace Logical: Add function call stack to the message? DEFAULT: TRUE
pwd Logical: Print working directory in message? DEFAULT: TRUE

Value
TRUE/FALSE, invisibly

Author(s)
Berry Boessenkool, <[email protected]>, May 2016

See Also
file.exists

Examples
is.error( checkFile("FileThatDoesntExist.txt") )
checkFile("FileThatDoesntExist.txt", warnonly=TRUE)
checkFile("FileThatDoesntExist.txt", warnonly=TRUE, trace=FALSE)

## Not run: ## Excluded from CRAN checks because of file creation

# Vectorized:
file.create("DummyFile2.txt")
checkFile(paste0("DummyFile",1:3,".txt"), warnonly=TRUE)
checkFile(paste0("DummyFile",1:3,".txt") )
file.remove("DummyFile2.txt")

compareFiles("dummy.nonexist", "dummy2.nonexist")
checkFile("dummy.nonexist")

## End(Not run)
ci 17

dingo <- function(k="brute.nonexist", trace=TRUE)

checkFile(k, warnonly=TRUE, trace=trace)
dingo()
dingo("dummy.nonexist")

upper <- function(h, ...) dingo(c(h, "dumbo.nonexist"), ...)

upper("dumbo2.nonexist")
upper(paste0("dumbo",2:8,".nonexist"))
upper(paste0("dumbo",2:8,".nonexist"), trace=FALSE)

ci calculate confidence interval around mean

Description

calculate the ends of the confidence interval around mean using t.test

Usage

ci(dat, lev = 0.95, digits = 3)

Arguments

dat Vector with the data to use.

lev Numeric value for confidence level. DEFAULT: 0.95
digits Integer: Number of digits rounded to in output. DEFAULT: 3

Details

Remember that CIs are used when insecurities about the inference from a sample to a general
population need quantification, not for hypothesis testing. If two confidence intervals overlap, the
difference between the two means still may be significantly different.

Value

A dataframe with the lower and upper confidence interval, as well as the level used.

Author(s)

Berry Boessenkool, <[email protected]>, 2010

18 ciBand

References

For newbies: Charles Wheelan: naked statistics - stripping the dread from the data, 2013, Norton,
ISBN 978-0-393-07195-5.
For statisticians: any of your favorite statistics books should cover confidence intervals ;-)
http://en.wikipedia.org/wiki/Confidence_interval
Wolfe R, Hanley J (Jan 2002). "If we’re so different, why do we keep overlapping? When 1 plus 1
doesn’t make 2"
http://www.ecmaj.ca/content/166/1/65.full.pdf
Goldstein, H.; Healey, M.J.R. (1995). "The graphical presentation of a collection of means". Journal
of the Royal Statistical Society
http://www.jstor.org/stable/2983411

See Also

t.test

Examples

yourdata <- c(5:8,3,14)

ci(yourdata) # confidence interval with the default confidence level (95%)
ci(yourdata, 0.99) # specified with a different confidence level
ci(yourdata, 0.99, 4) # returns 4 decimal places
ci(yourdata,,2) # rounds to 2 decimal places with default level
ci(yourdata)[1,1] # returns lower boundary of the interval as a numeric
ci(yourdata)[1,2] # returns upper boundary of the interval as a numeric
ci # shows the function itself

ciBand polygon confidence bands

Description

polygon for confidence interval bands, can handle NA’s well

Usage

ciBand(yu, yl, ym = NULL, x = 1:length(yu), na = "interpolate",

nastars = TRUE, singlepoints = TRUE, args = NULL, add = FALSE,
lwd = 1, colm = "green3", colb = addAlpha(colm), border = NA,
las = 1, ylim = range(yu, yl, finite = TRUE), ...)
ciBand 19

Arguments
yu y values of upper confidence region boundary
yl y values of lower confidence region boundary
ym y values of middle/median/mean line. Only added if this argument is given.
DEFAULT: NULL
x x values (one ascending vector). DEFAULT: 1:length(yu)
na Method used at NA points. One of "interpolate" or "remove". DEFAULT: "in-
terpolate"
nastars If na="interpolate", should stars be drawn at places that used to be NA? DE-
FAULT: TRUE
singlepoints If na="remove", add points for places surrounded by NAs? can be a boolean
(T/F) vector of length three for upper, lower, median. Code to identify isolated
points is taken from wq::plotTs. DEFAULT: TRUE
args List of arguments passed to points for the previous two arguments. DEFAULT:
NULL
add Add to existing plot? If FALSE, plot is called before adding confidence interval.
DEFAULT: FALSE
lwd Line width of middle line. DEFAULT: 1
colm Color for median/mean line. DEFAULT: "green3"
colb Color of the confidence region band. DEFAULT: addAlpha(colm)
border polygon border. DEFAULT: NA
las LabelAxisStyle (axis labels turned upright, see par). DEFAULT: 1
ylim limits of plot. DEFAULT: range(yu,yl, finite=TRUE)
... Further arguments passed to plot - or maybe better polygon??

Value
None, currently. Used for drawing.

Author(s)
Berry Boessenkool, <[email protected]>, July 2015

See Also
quantileBands, polygon, approx2

Examples

y1 <- c(1,3,4,2,1,4,6,8,7)
y2 <- c(5,6,5,6,9,8,8,9,10)
y3 <- c(4,4,5,4,4,6,7,8,9)
ciBand(yl=y1, yu=y2, ym=y3)
20 circle

y1[6:7] <- NA
ciBand(yl=y1, yu=y2, ym=y3) # interpolation marked with stars if nastars=TRUE
ciBand(yl=y1, yu=y2, ym=y3, na="remove")
lines(y1, col=3, type="o")
lines(y2, col=3, type="o")

y2[1] <- NA
ciBand(yl=y1, yu=y2, ym=y3) # next observation carried backwards (NAs at begin)
# LOCF (last observation carried forwards if NAs at end)
# See ?approx2 for median/mean imputation in these cases
ciBand(yl=y1, yu=y2, ym=y3, na="remove")
y2[9] <- NA
ciBand(yl=y1, yu=y2, ym=y3)
ciBand(yl=y1, yu=y2, ym=y3, na="remove") # NAs at both ends
y2[1] <- 5
ciBand(yl=y1, yu=y2, ym=y3)
ciBand(yl=y1, yu=y2, ym=y3, na="remove") # NA only at end

# Actual usefull stuff: sample size dependency of max and mean

ssdep_max <- function(n) quantile( replicate(n=200, expr=max(rnorm(n)) ) )
ssdep_mean<- function(n) quantile( replicate(n=200,expr=mean(rnorm(n)) ) )
x <- 1:100
res_max <- sapply(x, ssdep_max)
res_mean <- sapply(x, ssdep_mean)
ciBand(yl=res_max[2,], yu=res_max[4,], ym=res_max[3,], x=x, ylim=c(-0.5, 3))
ciBand(res_mean[2,], res_mean[4,], res_mean[3,], x=x, add=TRUE, colm="purple")

circle Draw circle with a given radius

Description
Draws a filled circle with a certain radius (in existing plot’s units) using polygon and sin

Usage
circle(x, y, r, locnum = 100, ...)

Arguments
x x coordinate of points, numeric value of length 1
y y coordinate
r radius of the circle in units of current plot
locnum number of calculated points on the circle (more means smoother but slower).
DEFAULT: 100
... further arguments passed to polygon, like col, border, lwd
classify 21

Value

none. Used for drawing.

Note

If circles look like ellipsis, use plot(... asp=1)

Author(s)

Berry Boessenkool, <[email protected]>, 2012

See Also

symbols, polygon

Examples

plot(1:20, type="n", asp=1)

circle(5,5, r=3) # 1:1 aspect shows they're really circles and not ellipses.
circle(15,10, r=4, locnum=12, col=2, border=4, lwd=3)

# can not be vectorized:

x <- sample(1:20, 15) ; y <- sample(1:20, 15) ; r <- runif(20)*3
circle(x,y,r, col=rgb(1,0.5,0,alpha=0.4), border=NA)
for(i in 1:15) circle(x[i],y[i],r[i], col=rgb(1,0.5,0,alpha=0.4), border=NA)

classify Classification into groups

Description

classify continuous values into categories with different methods:

- linearly or logarithmically spaced equal intervals,
- intervals based on quantiles (equally filled bins),
- intervals based on distance from the mean in normal distributions,
- user specified class borders (e.g. for legal or critical limits).

Usage

classify(x, method = "linear", breaks = NULL, Range = range(x, finite =

TRUE), sdlab = 1, logbase = 1, quiet = FALSE)
22 classify

Arguments
x Vector with numeric values
method Character string (partial matching is performed). Classification method (type
of binning) to compute the class breakpoints. See section Details. DEFAULT:
"linear"
breaks Specification for method, see Details. DEFAULT: NULL (different defaults for
each method)
Range Ends of intervals. DEFAULT: range(x, finite=TRUE)
sdlab Type of label and breakpoints if method=standarddeviation. 1 means -0.5 sd, 0.5 sd,
2 means -1 sd, mean, 1 sd, 3 means actual numbers for type 1, 4 means num-
bers for type 2. DEFAULT: 1
logbase base for logSpaced. Used only if not 1 and method="log". DEFAULT: 1
quiet Suppress warnings, eg for values outside Range? DEFAULT: FALSE

Details
Binning methods are explained very nicely in the link in the section References.
nbins indicates the number of classes (and thus, colors).

method | explanation | meaning of breaks | default

———- | ———– | ———– | ——-
linear | nbins equally spaced classes | nbins | 100
log | nbins logarithmically spaced | nbins | 100
quantile | classes have equal number of values | the quantiles (or number of them) | 0:4/4
sd | normal distributions | number of sd in one direction from the mean |3
custom | user-given breakpoints | breakpoint values (including ends of Range) | none

The default is set to equalinterval which makes sense for my original intent of plotting lake depth
(bathymetry measured at irregularly distributed points) on a linear color scale.
This is the workhorse for colPoints.

Value
list with class numbers (index) and other elements for colPoints

Author(s)
Berry Boessenkool, <[email protected]>, 2014

References
See this page on the effect of classification (binning) methods:
http://uxblog.idvsolutions.com/2011/10/telling-truth.html
climateGraph 23

See Also

colPoints

Examples

classify( c(1:10, 20), "lin", breaks=12)

classify( c(1:10, 20), "q", breaks=0:10/10)
classify( c(1:10, 20), "s", sdlab=2 )
classify( c(1:10, 20), "s", sdlab=1, breaks=2 )
classify( c(1:10, 20), "c", breaks=c(5,27) )
classify( c(1:10, 20), "log")

set.seed(42); rz <- rnorm(30, mean=350, sd=120)

plot(1)
classleg <- function(method="linear", breaks=100, sdlab=1, logbase=1, ...)
do.call(colPointsLegend, owa(
classify(rz, method=method, breaks=breaks, sdlab=sdlab, logbase=logbase),
list(z=rz, title="", ...)) )
classleg(br=3, met="s", col=divPal(5),mar=c(0,3,1,0),hor=FALSE,x1=0.1,x2=0.25)
classleg(br=3, met="s", col=divPal(6),mar=c(0,3,1,0),hor=FALSE,x1=0.25,x2=0.4, sdlab=2)
classleg(y1=0.85, y2=1)
classleg(br=20, met="log", y1=0.70, y2=0.85)
classleg(br=20, met="log", y1=0.55, y2=0.70, logbase=1.15)
classleg(br=20, met="log", y1=0.45, y2=0.60, logbase=0.90)
classleg(br= 5, met="q", y1=0.30, y2=0.45)# quantiles: each color is equally often used
classleg(met="q", y1=0.15, y2=0.30, breaks=0:15/15, at=pretty2(rz), labels=pretty2(rz) )

climateGraph climate graph after Walter and Lieth

Description

Draw a climate diagramm by the standards of Walter and Lieth.

Usage

climateGraph(temp, rain, main = "StatName\n52\U{00B0}24' N / 12\U{00B0}58' E\n42 m aSL",

units = c("\U{00B0}C", "mm"), labs = substr(month.abb, 1, 1), textprop = 0.25,
ylim = range(temp, rain/2), compress = FALSE, ticklab = -8:30 * 10,
ticklin = -15:60 * 5, box = TRUE, mar = c(1.5, 2.3, 4.5, 0.2),
keeppar = TRUE, colrain = "blue", coltemp = "red", lwd = 2,
arghumi = NULL, argarid = NULL, argcomp = NULL, arggrid = NULL,
argtext = NULL, ...)
24 climateGraph

Arguments
temp monthly temperature mean in degrees C
rain monthly rain sum in mm (12 values)
main location info as character string. can have \n. DEFAULT: "StatName\n52d 24’
N / 12d 58’ E\n42 m aSL"
units units used for labelling. DEFAULT: c("d C", "mm")
labs labels for x axis. DEFAULT: J,F,M,A,M,J,J,A,S,O,N,D
textprop proportion of graphic that is used for writing the values in a table to the right.
DEFAULT: 0.25
ylim limit for y axis in temp units. DEFAULT: range(temp, rain/2)
compress should rain>100 mm be compressed with adjusted labelling? (not recommended
for casual visualization!). DEFAULT: FALSE
ticklab positions for vertical labelling. DEFAULT: -8:30*10
ticklin positions for horizontal line drawing. DEFAULT: -15:60*5
box draw box along outer margins of graph? DEFAULT: TRUE
mar plot margins. DEFAULT: c(1.5,2.3,4.5,0.2)
keeppar Keep the changed graphical parameters? DEFAULT: TRUE
colrain Color for rain line and axis labels. DEFAULT: "blue"
coltemp color for temperature line and axis labels. DEFAULT: "red"
lwd line width of actual temp and rain lines. DEFAULT: 2
arghumi List of arguments for humid polygon, like density, angle. DEFAULT: NULL
(internal x,y, col, border)
argarid List of arguments for arid area. DEFAULT: NULL
argcomp List of arguments for compressed rainfall polygon. DEFAULT: NULL
arggrid List of arguments for background grid lines. DEFAULT: NULL
argtext List of arguments for text at right hand if textprop>0. DEFAULT: NULL
... further arguments passed to plot, like col.main

Value
None. Plots data and table.

Author(s)
Berry Boessenkool, <[email protected]>, June 2013

References
Heinrich Walter, Helmut Lieth: Klimadiagramm-Weltatlas. Gustav Fischer Verlag, Jena 1967
Examples:
https://www.hoelzel.at/__verlag/geojournal/archiv/klima/2006_01/lieth.gif
https://www.hoelzel.at/__verlag/geojournal/archiv/klima/istanbul/istanbul400.gif
http://www.ipb.uni-tuebingen.de/kurs/comp/1_excel2007/1_pic/2007diagramm_verbund02.
jpg
http://www.zivatar.hu/felhotar/albums/userpics/wldp.png
climateGraph 25

See Also
diagwl in package climatol

Examples

temp <- c(-9.3,-8.2,-2.8,6.3,13.4,16.8,18.4,17,11.7,5.6,-1,-5.9)#

rain <- c(46,46,36,30,31,21,26,57,76,85,59,46)

climateGraph(temp, rain)
climateGraph(temp, rain, textprop=0.6)
climateGraph(temp, rain, mar=c(2,3,4,3), textprop=0) # no table written to the right
# vertical lines instead of filled polygon:
climateGraph(temp, rain, arghumi=list(density=15, angle=90))
# fill color for arid without transparency:
climateGraph(temp, rain, argarid=list(col="gold"))
# for the Americans - axes should be different, though!:
climateGraph(temp, rain, units=c("\U{00B0}F","in"))

rain2 <- c(23, 11, 4, 2, 10, 53, 40, 15, 21, 25, 29, 22)
# fix ylim if you want to compare diagrams of different stations:
climateGraph(temp, rain2, ylim=c(-15, 50)) # works with two arid phases as well

op <- par(mfrow=c(2,1)) # mulipanel plot

climateGraph(temp, rain, argtext=list(cex=0.7))
climateGraph(temp, rain2, argtext=list(cex=0.7))
par(op)

rain <- c(54, 23, 5, 2, 5, 70, 181, 345, 265, 145, 105, 80) # with extrema
climateGraph(temp, rain) # August can be visually compared to June
climateGraph(temp, rain, compress=TRUE)
# compressing extrema enables a better view of the temperature,
# but heigths of rain cannot be visually compared anymore
climateGraph(temp, rain, compress=TRUE, ylim=c(-10, 90))
# needs ylim in linearly continued temp units
climateGraph(temp, rain, compress=TRUE, argcomp=list(density=30, col=6))

## Not run:
pdf("ClimateGraph.pdf")
climateGraph(temp, rain, main="Another Station\nlocated somewhere else")
dev.off()
openFile(ClimateGraph.pdf")
unlink("ClimateGraph.pdf")

# further German reading:

browseURL("http://www.klimadiagramme.de/all.html")

# Climate Graphs for the USA:

NOOAlink <- "http://www1.ncdc.noaa.gov/pub/data/normals/1981-2010/"
browseURL(NOOAlink)
# Find your Station here:
26 climateGraph

browseURL(paste0(NOOAlink,"/station-inventories/allstations.txt"))

# Data from Roseburg, Oregon:

download.file(destfile="Roseburg.txt", url=paste0("http://www1.ncdc.noaa.gov/",
"pub/data/normals/1981-2010/products/station/USC00357331.normals.txt"))
RT <- read.table(file="Roseburg.txt", skip=11, nrows=1, as.is=TRUE)[1,-1]
RT <- ( as.numeric(substr(RT,1,3))/10 - 32) * 5/9 # converted to degrees C
RP <- read.table(file="Roseburg.txt", skip=580, nrows=1, as.is=TRUE)[1,-1]
RP <- as.numeric(substr(RP,1,nchar(RP)-1))/100*25.4
meta <- read.table(file="Roseburg.txt", nrows=5, as.is=TRUE, sep=":")
meta <- paste(meta[1,2], paste(meta[3:4 ,2], collapse=" /"), meta[5,2], sep="\n")
unlink("Roseburg.txt")

climateGraph(RT, RP, main=meta)

climateGraph(RT, RP, main=meta, compress=TRUE)

# Climate Graphs for Germany:

browseURL("https://github.com/brry/rdwd#rdwd")
instGit("brry/rdwd")
link <- rdwd::selectDWD("Potsdam", res="monthly", var="kl", per="h")
clim <- rdwd::dataDWD(link, dir=tempdir())
dates <- strptime(clim$MESS_DATUM_BEGINN, "%Y%m%d")
temp <- tapply(clim$LUFTTEMPERATUR, INDEX=format(dates, "%m"), FUN=mean, na.rm=FALSE)
precsums <- tapply(clim$NIEDERSCHLAGSHOEHE, INDEX=format(dates, "%Y-%m"), FUN=sum)
eachmonth <- format(strptime(paste(names(precsums),"01"), "%Y-%m %d"),"%m")
prec <- tapply(precsums, eachmonth, FUN=mean)
meta <- paste("Potsdam\n", paste(range(dates, na.rm=TRUE), collapse=" to "), "\n", sep="")

climateGraph(temp, prec, main=meta, ylim=c(-2, 45))

# Add Quartiles (as in boxplots): numerically sorted, 50% of the data lie inbetween
TQ <- tapply(clim$LUFTTEMPERATUR, INDEX=format(dates, "%m"), FUN=quantile)
TQ <- sapply(TQ, I)
arrows(x0=1:12, y0=TQ["25%",], y1=TQ["75%",], angle=90, code=3, col=2, len=0.1)
#
PQ <- tapply(precsums, eachmonth, FUN=quantile)
PQ <- sapply(PQ, I)
arrows(x0=1:12, y0=PQ["25%",]/2, y1=PQ["75%",]/2, angle=90, code=3, col=4, len=0, lwd=3, lend=1)
mtext("IQR shown als lines", col=8, at=6.5, line=0.7, cex=1.2, font=2)

# Comparison to diagram in climatol

install.packages("climatol")
help(package="climatol")
library(climatol)
data(datcli)
diagwl(datcli,est="Example station",alt=100,per="1961-90",mlab="en")

## End(Not run)
colPoints 27

colPoints Points colored relative to third dimension

Description
Draw colored points for 3D-data in a 2D-plane. Color is relative to third dimension, by different
classification methods. Can take 3 vectors or, as in image, 2 vectors and a matrix for z.
Adding points after smallPlot is called for the legend may be incorrect if the original function
messes with the graph margins, see the note in colPointsLegend.

Usage
colPoints(x, y, z, data, add = TRUE, col = seqPal(100), col2 = c(NA,
"grey", "black"), Range = range(z, finite = TRUE), method = "linear",
breaks = length(col), sdlab = 1, legend = TRUE, legargs = NULL,
lines = FALSE, nint = 30, xlab = gsub("\"", "",
deparse(substitute(x))), ylab = gsub("\"", "", deparse(substitute(y))),
zlab = gsub("\"", "", deparse(substitute(z))), axes = TRUE, log = "",
las = 1, bglines = NULL, pch = 16, x1 = 0.6, y1 = ifelse(horizontal,
0.88, 0.3), x2 = 0.99, y2 = 0.99, density = NULL, horizontal = TRUE,
quiet = FALSE, ...)

Arguments
x, y Vectors with coordinates of the points to be drawn
z z values belonging to coordinates. Vector or matrix with the color-defining
height values
data Optional: data.frame with the column names as given by x,y and z.
add Logical. Should the points be added to current (existing!) plot? If FALSE, a
new plot is started. DEFAULT: TRUE (It’s called colPoints, after all)
col Vector of colors to be used. DEFAULT: 100 colors from sequential palette
seqPal (color-blind safe, black/white-print safe)
col2 Color for points where z is NA, or lower / higher than Range. DEFAULT: c(NA,
1, 8)
Range Ends of color bar. If NULL, it is again the DEFAULT: range(z, finite=TRUE)
method Classification method (partial matching is performed), see classify. DEFAULT:
"linear"
breaks Specification for method, see classify. DEFAULT: different defaults for each
method
sdlab Type of label and breakpoints if method="sd", see classify. DEFAULT: 1
legend Logical. Should a colPointsLegend be drawn? DEFAULT: TRUE
legargs List. Arguments passed to colPointsLegend. DEFAULT: NULL, with some
defaults specified internally
28 colPoints

lines Logical. Should lines be drawn instead of / underneath the points? (color of each
segments is taken from starting point, last point is endpoint.) If lines=TRUE
and pch is not given, pch is set to NA. DEFAULT: FALSE
nint Numeric of length 1. Number of interpolation points between each coordinate
if lines=TRUE. nint=1 means no interpolation. Values below 10 will smooth
coordinates and might miss the original points. DEFAULT: 30
xlab, ylab, zlab
X axis label, y axis label, colPointsLegend title. DEFAULT: gsub("\"", "", deparse(substitute
axes, las Draw axes? Label Axis Style. Only used when add=FALSE. See par. DE-
FAULT: axes=TRUE, las=1 (all labels horizontal)
log Logarithmic axes with log="y", "xy" or "x". DEFAULT: ""
bglines If not NULL, passed to abline to draw background lines before adding colored
points. DEFAULT: NULL
pch Point CHaracter. See par. DEFAULT: 16
x1, x2, y1, y2 Relative coordinates [0:1] of inset plot, see smallPlot. Passed to colPointsLegend.
DEFAULT: x: 0.6-0.99, y: 0.88-0.98
density Arguments for density line in colPointsLegend, or FALSE to suppress drawing
it. DEFAULT: NULL
horizontal Logical passed to colPointsLegend. DEFAULT: TRUE
quiet Turn off warnings? DEFAULT: FALSE
... Further graphical arguments passed to plot, points and segments, eg cex, xlim
(when add=F), mgp, main, sub, asp (when add=F), etc. Note: col does not work,
as it is already another argument

Value
Invisible list of values that can be passed to colPointsLegend or colPointsHist.

Note
Rstudio scales graphics really badly, so don’t expect the right legend width out of the box if you
use Rstudio! Exporting via png("myplot.png", 600,400); colPoints(x,y,z); dev.off()
usually works much better

Author(s)
Berry Boessenkool, <[email protected]>, 2011-2014. I’d be interested in hearing what you used the
function for.

References
http://uxblog.idvsolutions.com/2011/10/telling-truth.html, http://www.theusrus.de/
blog/the-good-the-bad-22012/

See Also
classify, colPointsLegend, colPointsHist
colPoints 29

Examples

i <- c( 22, 40, 48, 60, 80, 70, 70, 63, 55, 48, 45, 40, 30, 32)
j <- c( 5, 10, 15, 20, 12, 30, 45, 40, 30, 36, 56, 33, 45, 23)
k <- c(175, 168, 163, 132, 120, 117, 110, 130, 131, 160, 105, 174, 190, 183)

# basic usage:
colPoints(i,j,k, cex=1.5, pch="+", add=FALSE)

# with custom Range:

colPoints(i,j,k, cex=1.5, pch="+", add=FALSE, Range=c(150,190), density=FALSE)
# can be used to allow comparison between several plots
# points outside the range are plotted with col2

# with custom colors:

mycols <- colorRampPalette(c("blue","yellow","red"))(50)
colPoints(i,j,k, cex=1.5, pch="+", add=FALSE, col=mycols)

# With legend title:

colPoints(i,j,k, cex=2, add=FALSE, zlab="Elevation [m above NN.]",
legargs=list(density=FALSE))
?colPointsLegend # to see which arguments can be set via legargs

# with lines (nint to change number of linear interpolation points):

colPoints(i,j,k, cex=1.5, add=FALSE, lines=TRUE, nint=10, lwd=2)
# With NAs separating lines:
tfile <- system.file("extdata/rivers.txt", package="berryFunctions")
rivers <- read.table(tfile, header=TRUE, dec=",")
colPoints(x,y,n, data=rivers, add=FALSE, lines=TRUE)
colPoints(x,y,n, data=rivers, add=FALSE, lines=TRUE, pch=3, lwd=3)
colPoints(x,y,n, data=rivers, add=FALSE, lines=TRUE, pch=3, lwd=3, nint=2)
colPoints("x","y","n", data=rivers, add=FALSE)

# different classification methods:

# see ?classify

colPoints(i,j,k, add=FALSE) # use classify separately:

text(i,j+1,k, col=divPal(100,rev=TRUE)[classify(k)$index], cex=1)

# Add histogram:
cp <- colPoints(i,j,k, add=FALSE)
do.call(colPointsHist, cp[c("z","at","labels","bb","nbins")])
do.call(colPointsHist, owa(cp[c("z","at","labels","bb","nbins")],
list(bg=5, breaks=5)))
do.call(colPointsHist, owa(cp[c("z","at","labels","bb","nbins")],
list(mar=c(0,0,0,0), x1=0.5, x2=1, y1=0.8,
y2=0.99, yaxt="n")))
# histogram in lower panel:
layout(matrix(1:2), heights=c(8,4) )
colPoints(i,j,k, add=FALSE, y1=0.8, y2=1)
colPointsHist(z=k, x1=0.05, x2=1, y1=0, y2=0.4, mar=3, outer=TRUE)
30 colPointsHist

layout(1)

# Customizing the legend :

cp <- colPoints(i,j,k, legend=FALSE, add=FALSE)
colPointsLegend(x1=0.2, x2=0.95, y1=0.50, y2=0.40, z=k, labelpos=5, atminmax=TRUE, bg=7)
colPointsLegend(x1=0.5, x2=0.90, y1=0.28, y2=0.18, z=k, Range=c(80, 200), nbins=12, font=3)
colPointsLegend(x1=0.1, x2=0.40, y1=0.15, y2=0.05, z=k, labelpos=5, lines=FALSE, title="")
colPointsLegend(z=k, horizontal=FALSE)
colPointsLegend(x1=0.01, y2=0.80, z=k, horizontal=FALSE, labelpos=4, cex=1.2)
colPointsLegend(x1=0.23, y2=0.95, z=k, horizontal=FALSE, labelpos=5, cex=0.8,
dens=FALSE, title="", at=c(130,150,170), labels=c("y","rr","Be"), lines=FALSE)
# For method other than colPoints' default, it is easiest to include these
# options as a list in legargs, but you can also use the invisible output
# from colPoints for later calls to colPointsLegend
do.call(colPointsLegend, cp)
do.call(colPointsLegend, owa(cp, list(colors=rainbow2(100), cex=1.2)))

# colPoints with matrix:

colPoints(z=volcano, add=FALSE)
# image and contour by default transpose the matrix!
# colPoints shows what is really in the data.
colPointsHist(z=volcano)

# highlight local character of points on a regular grid normally drawn with image:
z <- t(volcano) ; x <- 1:ncol(z) ; y <- 1:nrow(z)
colPoints(x,y,z, add=FALSE) # takes matrix for z
contour(x,y,t(z), add=TRUE)
# image only takes a regular matrix, but not scatterpoints...
image(x,y,t(z), col=rainbow2(100))
# add single newly measured points to image (fictional data):
mx <- c( 22, 40, 80, 45, 60, 63, 30, 70)
my <- c( 5, 33, 12, 56, 20, 40, 45, 45)
mz <- c(135, 155, 120, 105, 140, 130, 190, 110)
colPoints(mx,my,mz, cex=5, pch="*", Range=c(94, 195), col=rainbow2(100), col2=NA, legend=FALSE)
points(mx,my, cex=4)
text(mx,my,mz, adj=-0.5, font=2)

# santiago.begueria.es/2010/10/generating-spatially-correlated-random-fields-with-r
if(require(gstat)){
xyz <- gstat(formula=z~1, locations=~x+y, dummy=TRUE, beta=1,
model=vgm(psill=0.025,model="Exp",range=5), nmax=20)
xyz <- predict(xyz, newdata=data.frame(x=runif(200, 20,40),y=runif(200, 50,70)), nsim=1)
head(xyz)
colPoints(x,y,sim1, data=xyz, col=rainbow2(100), add=FALSE)
}

colPointsHist Histogram for colPoints

colPointsHist 31

Description
Adds Histogram to plots created or enhanced with colPoints

Usage
colPointsHist(z, nbins = 40, colors = seqPal(nbins), bb = seqR(z,
length.out = nbins + 1), at = pretty2(z), labels = at, bg = "white",
x1 = 0, x2 = 0.4, y1 = 0, y2 = 0.3, outer = FALSE, mar = c(2, 2,
1, 0.5), mgp = c(1.8, 0.6, 0), sborder = NA, resetfocus = TRUE,
breaks = 20, freq = TRUE, col = par("fg"), border = NA, main = "",
ylab = "", xlab = "", las = 1, axes = TRUE, ...)

Arguments
z Values of third dimension used in colPoints
nbins Number of classes (thus, colors). DEFAULT: 40
colors Colors that are used for the background. DEFAULT: seqPal(nbins)
bb Borders of bins for the background. DEFAULT: seqR(z, length.out=nbins+1)
at Positions of x-axis labels. DEFAULT: pretty2(z)
labels X-axis labels themselves. DEFAULT: at
bg Background behind background and axis labels. DEFAULT: "white"
x1, x2, y1, y2 Relative coordinates [0:1] of inset plot, see smallPlot. DEFAULT: x: 0-0.3, y:
0-0.4
outer Logical: Should legend be relative to device instead of current figure? use
outer=TRUE when par(mfrow, oma) is set. DEFAULT: FALSE
mar Margins for smallPlot. DEFAULT: c(2, 2, 1, 0.5)
mgp MarGinPlacement: distance of xlab/ylab, numbers and line from plot margin, as
in par, but with different defaults. DEFAULT: c(1.8, 0.6, 0)
sborder Border around inset subplot. DEFAULT: par("fg")
resetfocus Reset focus to original plot? Specifies where further low level plot commands
are directed to. DEFAULT: TRUE
breaks Breaks as in hist, but with a different default. DEFAULT: 20
freq Plot count data in hist? (if FALSE, plot density instead). DEFAULT: TRUE
col Color of histogram bars. DEFAULT: par("fg")
border Border around each bar. DEFAULT: NA
main, ylab, xlab
Labels. DEFAULT: ""
las LabelAxisStyle. DEFAULT: 1
axes Draw axes?. DEFAULT: TRUE
... Further arguments passed to hist. NOT POSSIBLE: x, add
32 colPointsLegend

Value
invisible list of par of smallPlot, adds histogram to current plot

Author(s)
Berry Boessenkool, <[email protected]>, Aug 2014

See Also
colPointsLegend and colPoints for real life examples

Examples

z <- rnorm(50)
plot(1:10)
colPointsHist(z=z)

colPointsLegend Legend for colPoints

Description
Adds legends to plots created or enhanced with colPoints sf plots set par(mar=c(0,0,1.2,0)) but
then reset it to the values before. smallPlot will hence also reset to that, so points added after
calling colpointsLegend will be wrong, unless the margins are set BEFORE sf plot. sf:::plot.sf
alternatively uses c(2.1, 2.1, 1.2, 0) or c(1, 1, 1.2, 1).

Usage
colPointsLegend(z, Range = range(z, finite = TRUE), nbins = 100,
colors = seqPal(nbins), bb = seqR(Range, length.out = nbins + 1),
nlab = 5, at = pretty2(Range, nlab), labels = at, adj = 0.5,
x1 = 0.6, y1 = 0.88, x2 = 0.99, y2 = 0.99, outer = FALSE,
xpd = NA, mar, mgp = c(1.8, 0.6, 0), bg = par("bg"), sborder = NA,
resetfocus = TRUE, plottriangle = FALSE, triangle = 0.14,
tricol = c(8, 1), density = NULL, lines = TRUE, atminmax = FALSE,
horizontal = TRUE, labelpos = 1, titlepos = 3, title = "Legend",
las = 1, x, y, index, above, below, ...)

Arguments
z Values of third dimension used in colPoints, can be a matrix or a vector etc,
but must be numeric
Range Ends of color bar for method=equalinterval. DEFAULT: range(z, finite=TRUE)
colPointsLegend 33

nbins Number of classes (thus, colors). If colors is given, nbins is overwritten with
length(colors). DEFAULT: 100
colors Color vector. DEFAULT: seqPal from yellow (lowest) to blue (highest value in
Range)
bb Borders of bins for the legend (key). DEFAULT: seqR(Range, length.out=nbins+1)
nlab, at, labels
Number of legend labels, their positions and labels. DEFAULT: nlab=5, la-
bels=at=pretty2(Range,nlab)
adj label adjustment parallel to legend bar (only one number!). DEFAULT: 0.5
x1, x2, y1, y2 Relative coordinates [0:1] of inset plot, see smallPlot. DEFAULT: x: 0.6-0.99,
y: 0.88-0.99
outer Logical: Should legend be relative to device instead of current figure? use
outer=TRUE when par(mfrow, oma) is set. DEFAULT: FALSE
xpd Logical: should text be expanded outside of plotting region? Must be NA if
outer=TRUE. DEFAULT: NA
mar Margins for smallPlot. DEFAULT: internal calculations based on title, label-
pos and titlepos.
mgp MarGinPlacement: distance of xlab/ylab, numbers and line from plot margin, as
in par, but with different defaults. DEFAULT: c(1.8, 0.6, 0)
bg Background behind key, labels and title. DEFAULT: par("bg")
sborder Border around inset subplot. DEFAULT: NA
resetfocus Reset focus to original plot? Specifies where further low level plot commands
are directed to. DEFAULT: TRUE
plottriangle Should triangles be plotted at the end of the legend for values outside Range?
Vector of length two (for lower and upper, internally recycled). If this argument
is missing but triangle is given, this is set to TRUE. DEFAULT: FALSE
triangle Percentage of bar length at lower and upper end for triangles (can be a vector
with two different values). DEFAULT: 0.14
tricol Triangle colors for lower and upper end. DEFAULT: c(8,1)
density List of arguments passed to kernel density estimation. Can also be FALSE
to suppress KDE line drawing. DEFAULT: NULL
lines Plot black lines in the color bar at at? DEFAULT: TRUE
atminmax Should the extrema of the legend be added to at? DEFAULT: FALSE
horizontal Horizontal bar? if FALSE, a vertical bar is drawn. DEFAULT: TRUE
labelpos Position of labels relative to the bar. Possible: 1 (below), 2 (left), 3 (above), 4
(right), 5(on top of bar). DEFAULT: 1
titlepos Position of title -"-. DEFAULT: 3
title Legend title. DEFAULT: "Legend"
las LabelAxisStyle. DEFAULT: 1
x, y, index, above, below
Ignored arguments, so that you can pass the result from colPoints via do.call(colPointsLegend, cp_r
... Further arguments passed to text and strwidth, e.g. cex, srt, font, col. But
NOT adj!
34 combineFiles

Value

invisible list of par of smallPlot, adds legend bar to current plot

Note

x1,x2,y1,y2,labelpos,titlepos,title have different defaults when horizontal=FALSE

Author(s)

Berry Boessenkool, <[email protected]>, 2012-2014

See Also

colPointsHist, colPoints for real life example

Examples

z <- rnorm(50)
plot(1:10)
colPointsLegend(z=z)
colPointsLegend(z=z, titlepos=2)
colPointsLegend(z=z, horiz=FALSE) # note the different defaults
# positioning relative to plot:
colPointsLegend(z=z, x1=0.05, x2=0.3, y1=0.7,y2=0.9, title="Booh!", density=FALSE)
# Denote values outside of Range wit a triangle:
colPointsLegend(z=z, Range=c(-1,3), x1=0.2, y1=0.4, y2=0.6, triangle=0.2)
colPointsLegend(z=z, horiz=FALSE, x1=0.7, y1=0.6, plottriangle=TRUE, density=FALSE)
?colPoints # example section for actual usage

combineFiles Combine Textfiles into one

Description

Combine several textfiles into one, regardless of their content.

Usage

combineFiles(inFiles = dir(), outFile = "combined_Textfiles.txt",

overwrite = FALSE, sep = NULL, names = TRUE, selection = NULL,
progbar = !quiet, quiet = FALSE, ...)
combineFiles 35

Arguments

inFiles vector with names of input files, as can be read with scan. DEFAULT: dir()
outFile Character string: name of the file to be created. Passed to newFilename. DE-
FAULT: "combined_Textfiles.txt"
overwrite Logical: overwrite outFile? DEFAULT: FALSE
sep Character string: Separation between content of each file and the following.
DEFAULT: NULL, with which it uses an empty line, two lines with dashes, and
another line break.
names Should File names be included after sep? DEFAULT: TRUE
selection Index of rows that should be written. Can refer to each file separately, e.g.
substr(inFile_i,1,1)=="#". DEFAULT: all lines
progbar Should a progress bar be drawn? Useful if you combine many large files. DE-
FAULT: !quiet, i.e. TRUE
quiet Suppress message about number of files combined? DEFAULT: FALSE
... Arguments passed to scan, but not one of: file, what, blank.lines.skip, sep, quiet.

Value

Final output file, invisibly.

Author(s)

Berry Boessenkool, <[email protected]>, Nov 2012, Dec 2014, Jul 2015

See Also

compareFiles, and the functions used internally here, namely: paste, scan, write.

Examples

## These are skipped by rcmd check (writing to external places is not allowed)
## Not run:
cat("This is Sparta.\nKicking your face.", file="BujakashaBerry1.txt")
cat("Chuck Norris will roundhousekick you.", file="BujakashaBerry2.txt")
combineFiles(inFiles=paste0("BujakashaBerry", 1:2, ".txt"),
outFile="BujakashaBerry3.txt")
file.show("BujakashaBerry3.txt")
unlink(paste0("BujakashaBerry", 1:3, ".txt"))

## End(Not run)
36 compareFiles

compareFiles Compare textfiles for equality

Description

Returns the line numbers where two (text)files differ

Usage

compareFiles(file1, file2, nr = 20, startline = 1, endline = length(f1),

quiet = FALSE, ...)

Arguments

file1, file2 Filenames to be read by readLines.

nr number of results printed. DEFAULT: 20
startline, endline
start and end lines, e.g. to exclude section that is already compared.
quiet show warnings about file lengths? DEFAULT: FALSE
... further arguments passed to readLines

Value

Vector of line numbers that differ, result from head(..., nr)

Author(s)

Berry Boessenkool, <[email protected]>, Aug 2014

See Also

http://text-compare.com/ which I sadly only discovered after writing this function, dupes for
finding duplicate lines, combineFiles

Examples

filenames <- system.file(paste0("extdata/versuch",1:2,".txt"), package="berryFunctions")

compareFiles(filenames[1], filenames[2], warn=FALSE)
convertUmlaut 37

convertUmlaut Convert German Umlaute to ASCII

Description

Convert German Umlaute (ae, oe, ue, ss) to ASCII. Conversion happens case sensitive for the first
three.

Usage

convertUmlaut(x)

Arguments

x Character string(s) containing German Umlaute

Value

Character strings

Author(s)

Berry Boessenkool, <[email protected]>, Oct-Nov 2016

See Also

tools::showNonASCII, gsub, iconv(x, to="ASCII//TRANSLIT")

Examples

## Not run:
link <- paste0("ftp://ftp-cdc.dwd.de/pub/CDC/observations_germany/climate/",
"monthly/kl/recent/KL_Monatswerte_Beschreibung_Stationen.txt")
weatherstations <- read.fwf(link, widths=c(6,9,10,16,11,8,41,99), skip=3)
examples <- removeSpace(weatherstations[c(153, 509, 587, 2, 651, 851),7])
examples
convertUmlaut(examples) # note how lower and upper case is kept

## End(Not run)
38 createFun

createFun create function framework

Description

create a file with a complete (Roxygen) framework for a new function in a package

Usage

createFun(fun, path = ".", open = TRUE)

Arguments

fun Character string or unquoted name. Function that will be created with identical
filename.
path Path to package in development (including package name itself). Is passed to
packagePath. DEFAULT: "."
open Logical: open the file? If several instances of Rstudio are open, the last one (not
necessarily the active one) will be used. DEFAULT: TRUE

Details

Tries to open the file in the standard editor for .R files using system2

Value

file name as character string

Author(s)

Berry Boessenkool, <[email protected]>, March 2016

See Also

system2, funSource, Roxygen2: https://cran.r-project.org/package=roxygen2/vignettes/

rd.html

Examples
#createFun("myNewFunction")
createPres 39

createPres Create .Rnw presentation template

Description

Create folder with .Rnw presentation template and fig_extern folder.

Usage

createPres(presname = "pres", dir = "presentation", path = ".",

open = TRUE)

Arguments

presname Name of .Rnw file to be created. DEFAULT: "pres"

dir Name of directory that will contain .Rnw file and fig_extern folder. "_1" will be
appended if already existing, see newFilename. DEFAULT: "presentation"
path Location of dir. Passed to setwd. DEFAULT: "."
open Logical: run openFile? DEFAULT: TRUE

Author(s)

Berry Boessenkool, <[email protected]>, Mar 2017

See Also

createFun

Examples

## Not run:
createPres("Berry_Conference")

## End(Not run)
40 distance

dataStr str of datasets

Description
Print the str of each dataset returned by data

Usage
dataStr(package = NULL, ...)

Arguments
package Package name. DEFAULT: NULL
... other arguments passed to data

Value
NULL. prints via message in a for loop.

Author(s)
Berry Boessenkool, <[email protected]>, November 2015, in search of good datasets for teaching

See Also
str

Examples

dataStr() # all loaded packages on search path (package=NULL)

dataStr("datasets") # only datasets in base R
dataStr("colorspace") # works with an installed but unloaded package

distance Distance between points

Description
Calculate distance between points on planar surface

Usage
distance(x, y, xref, yref, along = FALSE)
divPal 41

Arguments
x vector with x-coordinate(s) of point(s)
y ditto for y
xref single x coordinate of reference point
yref ditto for y
along Logical: Should distances be computed along vector (x,y)? If TRUE, (xref,yref)
are ignored. If both (xref,yref) are not given, along is set to TRUE.

Details
The function is quite simple: sqrt((xref - x)^2 + (yref - y)^2)

Value
vector with the distances

Author(s)
Berry Boessenkool, <[email protected]>, 2012

See Also
nndist in the package spatstat for distance to nearest neighbour

Examples

A <- c(3, 9,-1)

B <- c(7, -2, 4)
plot(A,B)
text(A,B, paste0("P",1:3), adj=1.1)
points(3,5, col=2, pch=16)
segments(3,5, A,B)
distance(A,B, 3,5)
text(c(3.2,6,1), c(6,1,4), round(distance(A,B, 3,5),2) )

divPal Diverging color palette

Description
Diverging color palette: brown to blue, light colors in the middle, darker at the extremes, good for
displaying values in two directions
42 divPal

Usage
divPal(n = 12, reverse = FALSE, alpha = 1, rwb = FALSE, ryb = FALSE,
gp = FALSE, br = FALSE, colors = NULL, ...)

Arguments
n Number of colors. DEFAULT: 12
reverse Reverse colors? DEFAULT: FALSE
alpha Transparency (0=transparent, 1=fully colored). DEFAULT: 1
rwb Should colors be in red-white-blue instead of brown-blue? DEFAULT: FALSE
ryb Use red-yellow-blue instead of the default, with "khaki" in the center. DE-
FAULT: FALSE
gp Use green-purple instead of the default. DEFAULT: FALSE
br Use blue-red instead of the default. DEFAULT: FALSE
colors If not NULL, a color vector used in colorRampPalette. DEFAULT: NULL
... Further arguments passed to colorRamp

Value
Character string vector with color names

Author(s)
Berry Boessenkool, <[email protected]>, Jan 2016

References
The default palette is originally in 12 shades in the IPCC Assessment Report 5 Chapter 12 Fig
12.22, http://www.ipcc.ch/report/ar5/wg1/.
The green-purple and blue-red palettes are from NYtimes (originally with 8 shades), https://
nyti.ms/2mL0o4J

See Also
showPal, seqPal, addAlpha, colorRampPalette, package RColorBrewer

Examples

plot(rep(1,12), pch=16, cex=5, col=divPal(12), xaxt="n")

showPal()
dupes 43

dupes Duplicate lines in file

Description

Number of duplicates per line of (text) file. Per default saved to file which can be loaded into excel
/ libreoffice. With conditional formatting of the first column, colors show for each line how often
it occurs in the file. A LibreOffice file is included. Note: OpenOffice does not provide color scales
based on cell values.

Usage

dupes(file, ignore.empty = TRUE, ignore.space = TRUE, tofile = missing(n),

n = length(d))

Arguments

file File name (character string)

ignore.empty Should empty lines be ignored? DEFAULT: TRUE
ignore.space Should leading/trailing whitespace be ignored? DEFAULT: TRUE
tofile Logical: should output be directed to a file? Otherwise, a dataframe with line
numbers and number of duplicates of that line will be printed in the console.
DEFAULT: missing(n)
n Show only the first n values if tofile=FALSE. DEFAULT: length(d)

Value

Either: a data.frame with line numbers of duplicate rows and the number of duplicates
Or: a file is written with the number of duplicates and the original file content.

Note

This has not been tested all that much - feedback is heavily welcome!

Author(s)

Berry Boessenkool, <[email protected]>, Dec 2014

See Also

compareFiles
44 exp4p

Examples

file <- system.file("extdata/doublelines.txt", package="berryFunctions")

dupes(file, tofile=FALSE)
dupes(file, tofile=FALSE, ignore.empty=TRUE)

## These are skipped by rcmd check (opening external places is not allowed):
## Not run: dupes(file)

# a template file (dupes.ods) for libreOffice Calc is available here:

system.file("extdata", package="berryFunctions")

## Not run: system2("nautilus", system.file("extdata/dupes.ods", package="berryFunctions"))

# To open folders with system2:

# "nautilus" on linux ubuntu
# "open" or "dolphin" on mac
# "explorer" or "start" on windows

exp4p 4-parametric exponential function

Description
Fits an exponential function of the form a*e^(b*(x+c))+d

Usage
exp4p(x, y, digits = 2, plot = FALSE, las = 1, col = 1:6,
legarg = NULL, ...)

Arguments
x, y x and y Data
digits significant digits for rounding R^2. DEFAULT: 2
plot plot data and fitted functions? DEFAULT: FALSE
las label axis style, see par. DEFAULT: 1
col 6 colors for lines and legend texts. DEFAULT: 1:6
legarg Arguments passed to legend. DEFAULT: NULL
... further graphical parameters passed to plot

Details
This is mainly a building block for mReg
expReg 45

Value

Data.frame with the 4 parameters for each optim method

Note

Optim can be slow! It refers to the functions rmse and rsquare, also in this package. L-BFGS-B
needs finite values. In case it doesn’t get any with the initial parameters (as in the first example
Dataset), it tries again with the parameters optimized via Nelder Mead.

Author(s)

Berry Boessenkool, <[email protected]>, 2012-2013, outsourced from mReg in July 2014

See Also

mReg, lm

Examples
## Not run: ## Skip time consuming checks on CRAN
# exponential decline of temperature of a mug of hot chocolate
tfile <- system.file("extdata/Temp.txt", package="berryFunctions")
temp <- read.table(tfile, header=TRUE, dec=",")
head(temp)
plot(temp)
temp <- temp[-20,] # missing value - rmse would complain about it
x <- temp$Minuten
y <- temp$Temp
rm(tfile, temp)

exp4p(x,y, plot=TRUE)
# y=49*e^(-0.031*(x - 0 )) + 25 correct, judged from the model:
# Temp=T0 - Te *exp(k*t) + Te with T0=73.76, Tend=26.21, k=-0.031
# optmethod="Nelder-Mead" # y=52*e^(-0.031*(x + 3.4)) + 26 wrong

## End(Not run)

expReg Exponential regression with plotting

Description

uses lm; plots data if add=FALSE, draws the regression line with abline and confidence interval
with polygon and writes the formula with legend
46 expReg

Usage
expReg(x, y = NULL, data = NULL, logy = TRUE, predictnew = NULL,
interval = "confidence", plot = TRUE, digits = 2, inset = 0,
xpd = par("xpd"), pos1 = "top", pos2 = NULL, add = FALSE, pch = 16,
col = rgb(0, 0, 0, 0.5), modcol = 2, lwd = 1,
xlab = deparse(substitute(x)), ylab = deparse(substitute(y)),
main = "exponential regression", xlim = range(x), ylim = range(y), ...)

Arguments
x Numeric or formula (see examples). Vector with values of explanatory variable
y Numeric. Vector with values of dependent variable. DEFAULT: NULL
data Dataframe. If x is a formula, the according columns from data are used as x and
y. DEFAULT: NULL
logy Plot with a logarithmic y axis? Calls logAxis. DEFAULT: TRUE
predictnew Vector with values to predict outcome for. Passed as newdata to predict.lm.
DEFAULT: NULL
interval Interval for prediction. DEFAULT: "confidence"
plot Plot things at all? If FALSE, predictnew will still be returned. DEFAULT: TRUE
digits Numeric vector of length ≥ 1. Specifies number of digits a,b,r,e are rounded to
in the formula "y=a*log(x)+b, R^2, RMSE=e", respectively. If values are not
specified, they are set equal to the first. DEFAULT: 2
inset Numeric vector of length ≤ 2. inset distance(s) from the margins as a fraction
of the plot region when formula is placed by keyword. DEFAULT: 0
xpd Logical, specifying whether formula can be written only inside the plot region
(when FALSE) or inside the figure region including mar (when TRUE) or in the
entire device region including oma (when NA). DEFAULT: par("xpd")
pos1 xy.coords-acceptable position of the formula. DEFAULT: "top"
pos2 For numerical coordinates, this is the y-position. DEFAULT: NULL, as in
legend
add Logical. If TRUE, line and text are added to the existing graphic. DEFAULT:
FALSE (plots datapoints first and then the line.)
pch Point Character, see par. DEFAULT: 16
col Color of points, see par. DEFAULT: rgb(0,0,0, 0.5)
modcol color of model line. DEFAULT: 2
lwd Numeric. Linewidth, see par. DEFAULT: 1
xlab, ylab, main
Character / Expression. axis label and graph title if add=FALSE. DEFAULT:
internal from names
xlim, ylim graphic range. DEFAULT: range(x)
... Further arguments passed to plot and abline.
exTime 47

Value
predict.lm result.

Author(s)
Berry Boessenkool, <[email protected]>, Dec. 2014

See Also
lm, mReg, linReg.

Examples

x <- runif(100, 1, 10)

y <- 10^(0.3*x+rnorm(100, sd=0.3)+4)
plot(x,y)
expReg(x,y)
expReg(x,y, logy=FALSE)
expReg(x,y, predictnew=6, plot=FALSE)
expReg(x,y, predictnew=3:6, interval="none", plot=FALSE)

exTime Time to run examples

Description
Time the execution of examples. Useful in package development to identify functions taking much
time.

Usage
exTime(topic = NA, package = NA, echo = FALSE, elapsed = FALSE,
imagefile = TRUE, quiet = FALSE, ...)

Arguments
topic Character string: the online help topic of which the examples should be run.
package Charstring: installed and loaded package from which all examples should be
run.
echo Show the R input when sourcing? DEFAULT: FALSE
elapsed Return *only* the third element (total elapsed time)? DEFAULT: FALSE
imagefile Reroute graphics to pdf device? Will message the tempfile location if quiet=FALSE.
DEFAULT: TRUE
48 funnelPlot

quiet Suppress warnings with both suppressWarnings and suppressMessages, also

capture.output for str and cat results as well as setting pboptions(type="none")
if pbapply is available.
... Further arguments to example, especially run.dontrun, run.donttest and
package, but NOT character.only and ask

Value

Time used as per system.time

Author(s)

Berry Boessenkool, <[email protected]>, May 2016

See Also

example, system.time

Examples
exTime("plot")
exTime("yearSample", quiet=TRUE)
exTime(yearSample) # does NOT work, gives NULL and warning
exTime("yearSample", elapsed=TRUE, quiet=TRUE)
exTime("addFade", elapsed=TRUE, quiet=TRUE, run.dontrun=TRUE, run.donttest=TRUE)

## this takes quite some time if done for all functions in a package:
## Not run:
times <- exTime(package="rdwd")
as.matrix(sort(times))
system2("open", tempdir()) # to view the pdf graphics created by exTime

# times <- exTime(package="rdwd", run.dontrun=FALSE)

## End(Not run)

funnelPlot Funnel plots for proportional data

Description

Funnel plots for proportional data with confidence interval based on sample size. Introduced by
Stephen Few, 2013
funnelPlot 49

Usage
funnelPlot(x, n, labels = NULL, method = "classic", add = FALSE,
xlim = range(n, finite = TRUE), ylim = range(x/n * 100, finite = TRUE),
las = 1, xlab = "Sample size n", ylab = "Success rate [%]",
main = "Funnel plot for Proportions", a3 = NULL, a2 = NULL, am = NULL,
ap = NULL, at = NULL, al = NULL, ...)

Arguments
x Numeric vector with number of successes (cases).
n Numeric vector with number of trials (population).
labels Labels for points. DEFAULT: NULL
method Method to calculate Confidence interval, see "note" below. Can also be "wil-
son". DEFAULT: "classic"
add Add to existing plot instead of drawing new plot? DEFAULT: FALSE
xlim Graphical parameters, see par and plot. DEFAULT: range(n, finite=TRUE)
ylim y limit in [0:1] DEFAULT: range(x/n*100, finite=TRUE)
las DEFAULT: 1
xlab DEFAULT: "Sample size n"
ylab DEFAULT: "Success rate [%]"
main DEFAULT: "Funnel plot for Proportions"
a3 List with arguments for CI lines at 3*sd (eg: col, lty, lwd, lend, etc.). Over-
writes defaults that are defined within the function (if contentually possible).
DEFAULT: NULL
a2 Arguments for line of 2 sd. DEFAULT: NULL
am Arguments for mean line. DEFAULT: NULL
ap Arguments for the data points (cex, etc.). DEFAULT: NULL
at Arguments for text (labels of each point). DEFAULT: NULL
al Arguments for legend (text.col, bty, border, y.intersp, etc.). DEFAULT: NULL
... further arguments passed to plot only!

Value
Nothing - the function just plots

The basic idea

Salesman A (new to the job) has had 3 customers and sold 1 car. So his success rate is 0.33.
Salesman B sold 1372 customers 632 cars, thus having a success rate of 0.46 Promoting B solely
because of the higher rate fails to take experience and opportunity (n) into account! This dilemma
is what the funnel plot with the confidence interval (ci) solves. See Stephen Few and Katherine
Rowel’s PDF for details on the interpretation.
50 funnelPlot

Note
the default for lty is not taken from par("lty"). This would yield "solid". Overwriting lty for one
of the three line categories then produces eg c("2", "solid", "solid"), which cannot be processed by
legend.
Wilson’s Method: algebraic approximation to the binomial distribution, very accurate, even for
very small numbers.
http://webarchive.nationalarchives.gov.uk/20170106081156/http://www.apho.org.uk/
resource/item.aspx?RID=39445 see "contains".
classic = Stephen Few’s Method = the way I knew it: sqrt( mu*(1-mu) / n )
http://www.jerrydallal.com/LHSP/psd.htm
http://commons.wikimedia.org/wiki/File:ComparisonConfidenceIntervals.png
The apho Wilson method first yielded wrong upper limits in my translation (it needs 0:1 instead of
%). Thus I added the wikipedia formula:
http://de.wikipedia.org/wiki/Konfidenzintervall_einer_unbekannten_Wahrscheinlichkeit#
Wilson-Intervall
http://en.wikipedia.org/wiki/Binomial_proportion_confidence_interval
Which other methods should I include? (That’s not the hard part anymore)

Author(s)
Berry Boessenkool, <[email protected]>, Oct 2013

References
https://www.perceptualedge.com/articles/visual_business_intelligence/variation_and_
its_discontents.pdf
http://sfew.websitetoolbox.com/post/variation-and-its-discontents-6555336?
Excellent explanation of bayesian take on proportions: http://varianceexplained.org/r/empirical_
bayes_baseball/

Examples

# Taken directly from Stephen Few's PDF:

funnel <- read.table(header=TRUE, text="
Name SampleSize Incidents
Tony 2 2
Mike 400 224
Jan 100 54
Bob 1000 505
Sheila 2 1
Jeff 10 5
Sandy 500 236
Mitch 200 92
Mary 10 3
John 2 0")

str(funnel)
X <- funnel$Incidents
N <- funnel$SampleSize
funSource 51

barplot(X/N, names=funnel$Name, main="success rate")

# not showing n!

funnelPlot(X,N)
# arguments for subfunctions as text may be given this way:
funnelPlot(x=X, n=N, labels=funnel$Name, at=list(cex=0.7, col="red"))
# Labeling many points is not very clear...
funnelPlot(X,N)
sel <- c(1,4,10) # selection
text(N[sel], (X/N*100)[sel], funnel$Name[sel], cex=0.7)
# You could also pass a vector with partly empty strings to funnelPlot
funnelPlot(x=X, n=N, labels=replace(funnel$Name, c(2,3,5:9), ""), at=list(adj=0.5))

# Even though Jan is more successfull than Mary in succes rate terms, both are
# easily within random variation. Mary may just have had a bad start.
# That Mike is doing better than average is not random, but (with 95% confidence)
# actually due to him being a very good seller.

# one more interesting option:

funnelPlot(X,N, a3=list(lty=2))

funnelPlot(X,N, a3=list(col=2, lwd=5))

# changing round line ends in legend _and_ plot is easiest with
par(lend=1)
funnelPlot(X,N, a3=list(col=2, lwd=5))

# The Wilson method yields slighty different (supposedly better) limits for small n:
funnelPlot(X,N, method="classic", al=list(title="Standard Method"))
funnelPlot(X,N, add=TRUE, method="wilson", a3=list(lty=2, col="red"),
a2=list(lty=2, col="blue"), al=list(x="bottomright", title="Wilson Method"))

# Both Wilson method implementations yield the same result:

funnelPlot(X,N, method="wilson")
funnelPlot(X,N, add=TRUE, method="wilsonapho",
a3=list(lty=2, col="red"), a2=list(lty=2, col="blue"))

# Note on nl used in the function, the n values for the ci lines:

plot( seq( 10 , 300 , len=50), rep( 1, 50) )
points(10^seq(log10(10), log10(300), len=50), rep(0.8, 50) )
abline(v=10)
# CI values change rapidly at small n, then later slowly.
# more x-resolution is needed in the first region, so it gets more of the points

funSource Source code of a function

52 funSource

Description
open source code of a function in a loaded or specified package on github.com/cran or github.com/wch/r-
source

Usage
funSource(x, character.only = is.character(x), trydirect = TRUE)

Arguments
x function name, with or without quotation marks
character.only If TRUE, look for SomeFun instead of MyFun if MyFun <- "SomeFun". DE-
FAULT: is.character(x)
trydirect If TRUE, try direct urls to files x.R and x.r. DEFAULT: TRUE

Value
links that are also opened with browseURL

Author(s)
Berry Boessenkool, <[email protected]>, Jan+Dec 2016

See Also
https://github.com/brry/rskey to add this as a keyboard shortcut

Examples
## Not run: ## browser windows should not be openend in CRAN checks
library("berryFunctions")
funSource(colPoints)
funSource("head")
funSource("require", trydirect=FALSE)

funSource(earthDist)
funSource(OSMscale::earthDist)
funSource("OSMscale::earthDist")

## End(Not run)

## Not run: # developmental testing

require(plotrix); require(scales)
funSource(rescale

tail <- function(...) stop("This is a dummy function. Type: rm(tail)")

funSource("tail")
rm(tail)

## End(Not run)
funTinn 53

funTinn Open function in TinnR

Description
Opens function or object in external editor with an R command

Usage
funTinn(name)

Arguments
name Name of function or object to be opened with the program associated with .r-
files. In my case, the editor Tinn-R

Author(s)
Berry Boessenkool, <[email protected]>, Aug 2014

See Also
edit, http://stackoverflow.com/questions/13873528

Examples

## Not run:
## Rcmd check --as-cran doesn't allow opening external devices,
## so this example is excluded from running in the checks.
## funTinn(boxplot.default)

## End(Not run)

getColumn get column from data.frame

Description
(Try to) extract a column from a data frame with USEFUL warnings/errors.
Watch out not to define objects with the same name as x if you are using getColumn in a function!

Usage
getColumn(x, df, trace = TRUE, convnum = TRUE)
54 getColumn

Arguments
x Column name to be subsetted. The safest is to use character strings or substitute(input).
If there is an object "x" in a function environment, its value will be used as name!
(see upper2 example)
df dataframe object
trace Logical: Add function call stack to the message? DEFAULT: TRUE
convnum Logical: Convert numerical input (even if character) to Column name for that
number?

Value
Vector with values in the specified column

Author(s)
Berry Boessenkool, <[email protected]>, Sep 2016

See Also
subset, getElement, https://mran.revolutionanalytics.com/web/packages/car/vignettes/
embedding.pdf

Examples
head(stackloss)
getColumn(Air.Flow, stackloss)
getColumn("Air.Flow", stackloss)
getColumn(2, stackloss)
getColumn("2", stackloss) # works too...

# useful warnings:
getColumn(1, stackloss[0,])
getColumn(1, data.frame(AA=rep(NA,10)) )

# Code returning a character works as well:

getColumn(c("Air.Flow","Acid.Conc")[1], stackloss)

# Can be used in functions to get useful messages:

upper <- function(x, select) getColumn(x, stackloss[select,])
upper(Water.Temp)
upper(2)
upper(2, select=0)

checkerr <- function(x) invisible(is.error(x, force=TRUE, tell=TRUE))

# Pitfall lexical scoping: R only goes up until it finds things:

upper2 <- function(xx) {xx <- "Timmy!"; getColumn(xx, stackloss)} # breaks!
checkerr( upper2(Water.Temp) ) # Column "Timmy" does not exist
# If possible, use "colname" with quotation marks.
# This also avoids the CRAN check NOTE "no visible binding for global variable"
getName 55

upper3 <- function(char=TRUE)

{
Sepal.Length <- stackloss
if(char) head(getColumn("Sepal.Length", iris), 10)
else head(getColumn( Sepal.Length, iris), 10)
}
checkerr( upper3(char=FALSE) )
upper3(char=TRUE) # use string "Sepal.Length" and it works fine.

# The next examples all return informative errors:

checkerr( upper(Water) ) # partial matching not supported by design
checkerr( getColumn("dummy", stackloss)) # no NULL for nonexisting columns
checkerr( getColumn(2, stackloss[,0]) ) # error for empty dfs
checkerr( getColumn(Acid, stackloss) ) # no error-prone partial matching
checkerr( getColumn(2:3, stackloss) ) # cannot be a vector
checkerr( getColumn(c("Air.Flow","Acid.Conc"), stackloss) )

#getColumn("a", tibble::tibble(a=1:7, b=7:1)) # works but warns with tibbles

# Pitfall numerical column names:

df <- data.frame(1:5, 3:7)
colnames(df) <- c("a","1") # this is a bad idea anyways
getColumn("1", df) # will actually return the first column, not column "1"
getColumn("1", df, convnum=FALSE) # now gives second column
# as said, don't name column 2 as "1" - that will confuse people

# More on scoping and code yielding a column selection:

upp1 <- function(coln, datf) {getColumn(substitute(coln), datf)[1:5]}
upp2 <- function(coln, datf) {getColumn( coln, datf)[1:5]}
upp1(Sepal.Length, iris)
upp2(Sepal.Length, iris)
upp1("Sepal.Length", iris)
upp2("Sepal.Length", iris)
vekt <- c("Sepal.Length","Dummy")
upp1(vekt[1], iris)
upp2(vekt[1], iris)

getName get the name of an input in nested function calls

Description
get the name of an input in nested function calls

Usage
getName(x)
56 getName

Arguments

x input object name or character string

Value

Character string with the name

Author(s)

http://stackoverflow.com/users/2725969/brodieg Implementation Berry Boessenkool, <[email protected]>,

Sep 2016

See Also

http://stackoverflow.com/a/26558733, substitute

Examples
# This does not work well:

lower <- function(x) deparse(substitute(x))

upper <- function(y) lower(y)
lower(pi) # returns "pi", as expected
upper(pi) # returns "y".

# That's why there is getName:

getName(pi) # returns "pi", as expected

upper <- function(y) getName(y)
upper(pi) # yay!

upper("dummy")
upper(dummy) # works also for nonexistent objects
dummy <- 7
upper("dummy") # still stable
upper(dummy) # still stable

upper(stackloss[1:5,])

upper2 <- function(data) upper(data)

upper2("K")
upper2(K)

# getName only works correctly if x is not an evaluated object:

lower2 <- function(inp, assign=FALSE) {if(assign) inp <- inp; getName(inp)}
lower2(pi) # "pi"
lower2(pi, TRUE) # "3.14159265358979"
gof 57

gof GOF measures

Description
Goodness of Fit measures (GOF) for two vectors.
gofNA: not exported, checks input for each of the functions:
rsquare: Coefficient of determination (R2)
rmse: Root Mean Square Error (for minimizing in optim)
nse: Nash-Sutcliffe efficiency, based on RHydro::eval.NSeff
kge: Kling-Gupta efficiency (better than NSE), based on hydroGOF::KGE, where there are many
more options

Usage
gofNA(a, b, quiet = FALSE, fun = "")

rsquare(a, b, quiet = FALSE)

rmse(a, b, quiet = FALSE)

nse(a, b, quiet = FALSE)

kge(a, b, quiet = FALSE)

Arguments
a Numerical vector with observational data
b Simulated data (to be compared to a)
quiet Should NA-removal warnings be suppressed? This may be helpful within func-
tions. DEFAULT: FALSE
fun Character string with function name for error and warning messages

Value
Single numerical value

Note
NAs are omitted with warning.

Author(s)
Berry Boessenkool, <[email protected]>, Sept 2016
58 gof

See Also
cor, lm. http://en.wikipedia.org/wiki/R-squared, http://en.wikipedia.org/wiki/Mean_
squared_error

Examples
# R squared and RMSE --------------------------------------------------------
set.seed(123)
x <- rnorm(20)
y <- 2*x + rnorm(20)
plot(x,y)
legGOF <- function(a,b)
{
text(a,b, paste(c(" R2","RMSE"," NSE"," KGE"), collapse="\n"), adj=1.2)
text(a,b, paste(round(c(rsquare(x,y), rmse(x,y), nse(x,y), kge(x,y)),5),
collapse="\n"), adj=0)
}
legGOF(-1.5, 2) # R2 good, but does not check for bias (distance from 1:1 line)

abline(a=0,b=1) ; textField(-1.5,-1.5, "1:1")

abline(lm(y~x), col="red")
p <- predict(lm(y~x))
points(x, p, pch=3, col="red")
segments(x, y, x, p, col="red")
stopifnot(all.equal( nse(y,p) , rsquare(y,x) ))

# Input checks
is.error( rmse(1:6, 1:8) , tell=TRUE)
nse(replace(x,3,NA), y)
kge(rep(NA,20), y)
rmse(0,0, quiet=TRUE)
rsquare(1:6, tapply(chickwts$weight, chickwts$feed, mean) )

## Not run: # time consuming Simulation

# sample size bias

x <- 1:1000
y <- x+rnorm(1000)
rmse(x,y) # 0.983
ssize <- rep(5:1000, 3)
sgofs <- sapply(ssize, function(n){i <- sample(1:1000,n); c(rsquare(x[i],y[i]),rmse(x[i],y[i]))})
plot(ssize, sgofs[2,]) # RMSE: no bias, symmetric convergence
plot(ssize, sgofs[1,]) # R2: small underestimation in small samples

if(require(pbapply)) sapply <- pbsapply

r2 <- sapply(1:10000, function(i){
x <- rnorm(20); y <- 2*x + rnorm(20); c(rsquare(x,y), rmse(x,y)) })
hist(r2[1,], breaks=70, col=5,
main= "10'000 times x <- rnorm(20); y <- 2*x + rnorm(20); rsquare(x,y)")
# For small samples, R^2 can by chance be far off the 'real' value!
hist(r2[2,], breaks=70, col=5, main= "... rsquare(x,y)")
googleLink2pdf 59

# RMSE is more symmetric and gaussian

## End(Not run)

# NSE and KGE ---------------------------------------------------------------

y <- dbeta(1:40/40, 3, 10) # simulated

x <- y + rnorm(40,0,sd=0.2) # observed
plot(x)
lines(y, col="blue")
legGOF(25, 2)
rmse(x,y) ; rmse(y,x)
nse(x,y) ; nse(y,x) # x=obs, y=sim (second command is wrong)
kge(x,y) ; kge(y,x)

googleLink2pdf extract pdf link from google search result

Description
restrict pdf link from a google search to actual link with text processing

Usage
googleLink2pdf(googlelink)

Arguments
googlelink Character string: A search result address

Value
Characterstring with only the basic link

Note
The function is not vectorized! If you have many links, use a loop around this function...

Author(s)
Berry Boessenkool, <[email protected]>, 2012

See Also
strsplit, gsub
60 groupHist

Examples

Link <- paste0("http://www.google.de/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1",

"&cad=rja&sqi=2&ved=0CDIQFjAA&url=https%3A%2F%2Fsiteproxy.ruqli.workers.dev%3A443%2Fhttp%2Fcran.r-project.org",
"%2Fdoc%2Fmanuals%2FR-intro.pdf&ei=Nyl4UfHeOIXCswa6pIC4CA",
"&usg=AFQjCNGejDwPlor4togQZmQEQv72cK9z8A&bvm=bv.45580626,d.Yms")
googleLink2pdf(Link)

Link <- paste0("https://www.google.de/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1",

"&cad=rja&uact=8&ved=0ahUKEwjLlfmClavRAhWaN1AKHcGSBjEQFgghMAA",
"&url=https%3A%2F%2Fsiteproxy.ruqli.workers.dev%3A443%2Fhttp%2Fstackoverflow.com%2Fquestions%2Ftagged%2Fr",
"&usg=AFQjCNHYj6HjSs6Lvczn9wMWxE3slCdq1Q&bvm=bv.142059868,d.ZWM")
googleLink2pdf(Link)
Link <- paste0("https://www.google.de/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2",
"&cad=rja&uact=8&ved=0ahUKEwjLlfmClavRAhWaN1AKHcGSBjEQFggpMAE&",
"url=https%3A%2F%2Fsiteproxy.ruqli.workers.dev%3A443%2Fhttp%2Fstackoverflow.com%2Fquestions%2Ftagged%2F%3Ftagnames",
"%3Dr%26sort%3Dactive&usg=AFQjCNGkPGHq05qwKLLW4vRXdmk2Olhmig&bvm=bv.142059868,d.ZWM")
googleLink2pdf(Link)

groupHist Histogram for classes

Description
Improvement of tapply(x, g, hist) with x and g taken from a data.frame

Usage
groupHist(df, x, g, xlab = "", ylab = "", las = 1, main = NULL,
unit = NA, ...)

Arguments
df data.frame object name
x column name of variable of interest
g column name of groups (INDEX in tapply, f in split)
xlab, ylab axis labels. DEFAULT: ""
las LabelAxisStyle, see par. DEFAULT: 1, means numbers on y-axis upright
main Main title, internal default based on d, x, unit and g. DEFAULT: NULL
unit Unit to be written into the default title. DEFAULT: NA
... further arguments passed to hist

Details
Uses split to categorize into groups.
headtail 61

Value
NULL, used for plotting

Author(s)
Berry Boessenkool, <[email protected]>, Jan 2015

See Also
hist, tapply

Examples

groupHist(chickwts, weight, "feed", col=2)

groupHist(chickwts, "weight", "feed", col=2, unit="grams at age 6 weeks")
groupHist(chickwts, weight, feed, col=2, breaks=20, main="Hi there")
groupHist(iris, Petal.Width, Species)

headtail head and tail

Description
show head and tail of an object with one command

Usage
headtail(x, n = 1, nh = n, nt = n, na = FALSE, ...)

Arguments
x Object
n Number of elements/rows/lines at begin and end of object to be returned. DE-
FAULT: 1
nh, nt Number for head and tail, respectively. DEFAULT: n
na Add NA values in between to emphasize visibly that there is something inbe-
tween the values? DEFAULT: FALSE
... Further arguments passed to head and tail

Details
Tries to find good methods of combining the two results according to codeclass(x).

Value
head result
62 horizHist

Author(s)

Berry Boessenkool, <[email protected]>, Mrz 2016

See Also

head

Examples

head(letters, n=3)
headtail(letters)
headtail(letters, n=3)
headtail(letters, n=3, na=TRUE)

head(letters, n=-10)
headtail(letters, n=-10, na=TRUE) # doesn't make sense for headtail

head(freeny.x, n=3) # matrix

headtail(freeny.x, n=3, na=TRUE) # no names for head-part
headtail(women, n=3, na=TRUE) # data.frame works fine

head(freeny.y, n=3)
headtail(freeny.y, n=3, na=TRUE)

head(library, n=3)
headtail(library, n=3, na=TRUE)
headtail(library, na=TRUE)

ftable(Titanic)
head(stats::ftable(Titanic), n=4)
headtail(stats::ftable(Titanic), n=4, na=TRUE)

head(table(sample(1:9, 30, TRUE)), n=3)

headtail(table(sample(1:9, 30, TRUE)), n=3, na=TRUE)

head(table(state.division, state.region), n=3)

headtail(table(state.division, state.region), n=3, na=TRUE)

horizHist Horizontal histogram

Description

Draw a histogram with bars horizontally

horizHist 63

Usage
horizHist(Data, breaks = "Sturges", freq = TRUE, plot = TRUE,
col = par("bg"), border = par("fg"), las = 1, xlab = if (freq)
"Frequency" else "Density", main = paste("Histogram of",
deparse(substitute(Data))), ylim = range(HBreaks), labelat = pretty(ylim),
labels = labelat, ...)

Arguments
Data any data that hist would take.
breaks character or numerical as explained in hist. DEFAULT: "Sturges"
freq logical. if TRUE, the histogram graphic is a representation of frequencies, the
counts component of the result; if FALSE, probability densities, component den-
sity, are plotted (so that the histogram has a total area of one). DEFAULT: TRUE
plot logical. Should histogram be plotted? FALSE to get just the hpos function.
DEFAULT: TRUE
col color. DEFAULT: par("bg")
border color of borders of bars. DEFAULT: par("fg")
las integer. Label axis style. DEFAULT: 1
xlab character. Label for x-axis. DEFAULT: "absolute frequency"
main character. Title for graphic. DEFAULT: "Histogram of substitute(Data)"
ylim numerical vector of two elements. Y-axis limits. DEFAULT: range of data
labelat numerical vector. Position of Y-Axis labels. DEFAULT: pretty(ylim)
labels numerical or character. The labels themselves. DEFAULT: labelat
... further arguments passed to barplot and axis

Details
Uses barplot to draw the histogram horizontally.

Value
function to address y-coordinates

Note
Doesn’t work with breakpoints provided as a vector with different widths of the bars.
Please do not forget to use the function for vertical positioning from the current horizontal his-
togram. If It is not working correctly, you might have the function defined from some prior horizHist
result.

Author(s)
Berry Boessenkool, <[email protected]>, 2011-2012
64 insertRows

See Also
hist, barplot, axis

Examples

# Data and basic concept

set.seed(8); ExampleData <- rnorm(50,8,5)+5
hist(ExampleData)
hpos <- horizHist(ExampleData)
# Caution: the labels at the y-axis are not the real coordinates!
# abline(h=2) will draw above the second bar, not at the label value 2.
# Use hpos (horizontal position), the function returned by horizHist:
abline(h=hpos(11), col=2, lwd=2)

# Further arguments
horizHist(ExampleData, xlim=c(-8,20))
horizHist(ExampleData, ylab="the ... argument worked!", col.axis=3)
hist(ExampleData, xlim=c(-10,40)) # with xlim
horizHist(ExampleData, ylim=c(-10,40), border="red") # with ylim
hpos <- horizHist(ExampleData, breaks=20, col="orange")
axis(2, hpos(0:10), labels=FALSE, col=2) # another use of hpos()

insertRows insert rows to data.frame

Description
Insert (multiple) rows to a data.frame, possibly coming from another data.frame, with value and
row recycling

Usage
insertRows(df, r, new = NA)

Arguments
df data.frame
r Row number (not name!), at which the new row is to be inserted. Can be a vector
new Vector with data to be inserted, is recycled. Alternatively, a data.frame, whose
rows are put into the r locations. If it has more rows than length(r), the excess
rows are ignored. DEFAULT: NA

Value
data.frame
instGit 65

Note
Has not yet been tested with RWI (really weird input), so might not be absolutely foolproof

Author(s)
Berry Boessenkool, <[email protected]>, Oct 2015, based on code by Ari B. Friedmann (I added
the for loop, recycling, input controls and data.framification)

References
http://stackoverflow.com/questions/11561856/add-new-row-to-dataframe

See Also
addRows

Examples

existingDF <- as.data.frame(matrix(1:20, nrow=5, ncol=4))

existingDF
insertRows(existingDF, 2) # default new=NA is recycled
insertRows(existingDF, 2, 444:446)
insertRows(existingDF, 3, new=matrix(10:1,ncol=2)) # input warning
insertRows(existingDF, 1)
insertRows(existingDF, 5)
insertRows(existingDF, 6) # weird stuff...
insertRows(existingDF, 9) # not supposed to do that

# Works for multiple rows as well:

insertRows(existingDF, r=c(2,4,5), new=NA)
insertRows(existingDF, r=c(2,4,4), new=NA)

# Also works with a data.frame for insertion:

insertDF <- as.data.frame(matrix(101:112, nrow=3, ncol=4))
insertRows(existingDF, 3, new=insertDF) # excess rows in new are ignored
insertRows(existingDF, c(2,4,5), new=insertDF)
insertRows(existingDF, c(2,4:6), new=insertDF) # rows are recycled

instGit install github package

Description
Quickly install a package from github without having to install devtools with all its dependencies.

Usage
instGit(pk, cleanup = TRUE, ...)
66 is.error

Arguments
pk Character string in the from of "user/package"
cleanup Remove downloaded zipfile and folder with source code. DEFAULT: TRUE
... Further arguments passed to install.packages, untested so far

Details
Works only for pure R package structure repositories from the master branch. Installs package de-
pendencies listed in ’Imports’ and ’Depends’, but ignores version requirements! Tested only on
windows 7 with R3.2.2. Note: devtools::install_github is much more extensive!
Note: drat is also much better than this quick hack. http://dirk.eddelbuettel.com/code/
drat.html, https://github.com/eddelbuettel/drat, http://eddelbuettel.github.io/drat/
DratForPackageAuthors.html Give your github users this code:
source("https://raw.githubusercontent.com/brry/berryFunctions/master/R/instGit.R")
instGit("brry/extremeStat")
library(extremeStat)

Author(s)
Berry Boessenkool, <[email protected]>, Dec 2015 + Mar/Apr 2016

See Also
funSource, install_github in each of the packages devtools, ghit, remotes

Examples

if(FALSE){
instGit("talgalili/installr")
instGit("talgalili/installr", FALSE)
instGit("hadley/readxl")
instGit("mages/googleVis") # many dependencies!
instGit("twitter/AnomalyDetection")
instGit("yihui/knitr")
instGit("ramnathv/slidify")
instGit("jrnold/ggthemes")
}

is.error Check if an expression returns an error

Description
Does a given expression return an error? Useful for tests where you want to make sure your function
throws an error.
l2array 67

Usage
is.error(expr, tell = FALSE, force = FALSE)

Arguments
expr Expression to be tested for returning an error
tell Logical: Should the error message be printed via message? DEFAULT: FALSE
force Logical: Should an error be returned if the expression is not an error? DE-
FAULT: FALSE

Value
TRUE/FALSE

Author(s)
Berry Boessenkool, <[email protected]>, May 2016

See Also
stop, try, inherits

Examples
is.error( log(3) )
is.error( log("a") )
is.error( log(3), tell=TRUE )
is.error( log("a"), tell=TRUE )
stopifnot( is.error( log("a") ) ) # or shorter:
is.error( log("a"), force=TRUE)
# is.error( log(3), force=TRUE)
stopifnot(is.error( is.error(log(3), force=TRUE) ))

l2array Convert list of arrays to array

Description
Convert a list of arrays to a single array, conserving names. If dimnames do not need to be checked,
you can also directly use
do.call(abind::abind, list(LIST, rev.along=0, use.dnns=TRUE))

Usage
l2array(x, ...)
68 l2array

Arguments
x List with arrays. The dimension of the first is target dimension.
... Further arguments passed to abind::abind

Value
array

Author(s)
Berry Boessenkool, <[email protected]>, Dec 2016

See Also
l2df, help, http://stackoverflow.com/a/4310747

Examples

LIST <- lapply(LETTERS[1:5], function(x) array(paste0(x,1:24), dim=c(3,4,2)))

str(LIST)
LIST[[2]]
LISTa1 <- l2array(LIST)
LISTa1
str(LISTa1)

LISTm <- lapply(list(1:6,7:12,13:18,19:24), matrix, ncol=3,

dimnames=list(x=c("a","b"), y=c("i","j","k")) )
l2array(LISTm)

# The old l2array (<1.13.14, 2017-01-06) was very slow on large lists.
# I then found abind, which is much much much faster and easier on memory!
# It now replaces the internal old actual conversion code
# l2array still checks the dimnames
LISTa2 <- do.call(abind::abind, list(LIST, rev.along=0, use.dnns=TRUE))
LISTa2
stopifnot(all(LISTa1==LISTa2))
rm(LIST, LISTa1, LISTa2)

# General intro to arrays -----

A1 <- array(1:24, dim=c(4,2,3), dimnames=list(

my_x=paste0("row",1:4), my_y=c("A","B"), paste0("n",1:3)))
A1
which(A1==20, arr.ind=TRUE)

# Selection:
A1[,,"n2"]
A1[,,1:2]
A1["row2",,] # result rotated against expectation -> transpose with t(...)
l2df 69

A1[,"A",]
# aggregation:
apply(A1, MARGIN=1:2, FUN=sum) # keep first two dimensions
apply(A1, MARGIN=c(1,3), FUN=sum) # aggregate over my_y -> row1: 6, 22, 38
A1["row1",,] # 1+5=6, 9+13=22, 17+21=38

as.vector(A1)

A <- array(1:24, dim=c(3,4,2), dimnames=list(x=paste0("x",1:3),

y=paste0("y",1:4),
z=paste0("z",1:2)))
str(A)
rm(A)

# l2array -----

A2 <- A1+2
A3 <- A1+4
LIST <- list(A1=A1, A2=A2, A3=A3) # list of arrays

LA <- l2array(LIST)
LA
str(LA)
LA[,,,"A2"]
LA["row2", ,"n2",]
avg <- apply(LA, MARGIN=1:3, mean)
stopifnot(all(avg==A2))

# names check -----

LISTN <- LIST

names(dimnames(LISTN[[2]]))[3] <- "intentional"
dimnames(LISTN[[3]])[3] <- list(paste0("k",1:3))
LAN <- l2array(LISTN)
LAN["row2", ,"k2",] # n2 is now changed to k2
LANa <- do.call(abind::abind, list(LISTN, rev.along=0, use.dnns=TRUE))
all(LAN==LANa)
str(LANa)

LISTN <- LIST

rownames(LISTN[[3]])[2] <- "intentional_diff"
LAN <- l2array(LISTN)

# data type check

is.error( A <- l2array(c(LA, 999)), tell=TRUE, force=TRUE)
70 l2df

l2df List to data.frame

Description
Convert list with vectors of unequal length to dataframe, pad with NAs

Usage
l2df(list, byrow = TRUE)

Arguments
list List with vectors of irregular length.
byrow Transposed output? DEFAULT: TRUE

Value
data.frame

Author(s)
Berry Boessenkool, <[email protected]>, Jan 2014

References
http://stackoverflow.com/questions/5531471/combining-unequal-columns-in-r
http://stackoverflow.com/questions/15753091/convert-mixed-length-named-list-to-data-frame
http://stackoverflow.com/questions/5942760/most-efficient-list-to-data-frame-method
http://stackoverflow.com/questions/8799990/converting-given-list-into-dataframe
http://stackoverflow.com/questions/4227223/r-list-to-data-frame

See Also
l2array, sapply. If you have a LARGE list each with the same number of values, use the (much!)
faster: plyr::quickdf.

Examples

eglist <- list(AA=c(6,9,2,6), BB=1:8, CC=c(-3,2) )

eglist
l2df(eglist) # names are even kept
l2df(eglist, byrow=FALSE)
class( l2df(eglist, byrow=FALSE) ) # data.frame (since 2016-05-24)

eglist <- list(AA=c(6,9,2,6), BB="no", CC=c(-3,2) )

eglist
str(l2df(eglist)) # now everything is a character
l2df 71

eg2 <- list(AA=c(6,9,2,6), BB=matrix(1:8, ncol=2), CC=c(-3,2) )

eg2
l2df(eg2, FALSE)
# so a matrix is internally converted to a vector and then used regularly

# Naming ----

eg3 <- list(EE=c(AA=3.4), FF=c(AA=3.5), GG=c(AA=3.6))

eg4 <- list(EE=c(AA=3.4,BB=2.4), FF=c(AA=3.5,BB=2.5), GG=c(AA=3.6,BB=2.6))
l2df(eg3)
l2df(eg4)
l2df(eg3, byrow=FALSE)
l2df(eg4, byrow=FALSE)

eg3 <- list(c(AA=3.4), c(AA=3.5), c(AA=3.6))

eg4 <- list(c(AA=3.4,BB=2.4), c(AA=3.5,BB=2.5), c(AA=3.6,BB=2.6))
l2df(eg3)
l2df(eg4)
l2df(eg3, byrow=FALSE)
l2df(eg4, byrow=FALSE)

eg3 <- list(EE=c(3.4), FF=c(3.5), GG=c(3.6))

eg4 <- list(EE=c(3.4,2.4), FF=c(3.5,2.5), GG=c(3.6,2.6))
l2df(eg3)
l2df(eg4)
l2df(eg3, byrow=FALSE)
l2df(eg4, byrow=FALSE)

eg3 <- list(EE=c(3.4), c(3.5), c(3.6))

eg4 <- list(EE=c(3.4,2.4), c(3.5,2.5), c(3.6,2.6))
l2df(eg3)
l2df(eg4)
l2df(eg3, byrow=FALSE)
l2df(eg4, byrow=FALSE)

# Lists with dfs ----

eg5 <- list(AA=c(6,9,2,6), BB=data.frame(CC=1:8, DD=4:-3), EE=c(-3,2) )

eg5
is.error( l2df(eg5), tell=TRUE )# it is not possible to do this with a data.frame

# If you have a list with only data.frames, you could use the following:
eg6 <- list(AA=data.frame(BB=1:8, CC=4:-3), DD=data.frame(EE=23:24, FF=c(-3,2)))
eg6
do.call(cbind, eg6) # but this recycles the values of shorter tables!
names(eg6$DD) <- names(eg6$AA)
do.call(rbind, eg6)
# check some of the links above for more solutions...
72 legendmt

legendmt legend with multiline title

Description
Draw a legend with title spanning several lines (i.e. with line breaks). Note that this is in develop-
ment and not all inputs are correctly vectorized yet.

Usage
legendmt(x, y = NULL, legend, title, x.intersp = 1, fill = NA,
col = par("col"), border = NA, lty = NA, lwd = NA, pch = NA, ...)

Arguments
x, y, legend Arguments as in legend
title Character with linebreaks or vector of charstrings.
x.intersp, fill, col, border, lty, lwd, pch
Arguments as in legend
... Further arguments passed to legend. If vectorized, please remember to prepend
NAs or whatever.

Value
legend output

Author(s)
Berry Boessenkool, <[email protected]>, Apr 2017

See Also
legend

Examples
plot(1:10)
legend("topleft", letters[1:4], col=1:4, pch=1, title="very long title to be split up")
legendmt("topleft", letters[1:4], col=1:4, pch=1, title="very long title\nnow splat up")

# Alternative:
plot(1:10)
legend("topleft", "very long title to be split up")
legend("topleft", letters[1:4], col=1:4, pch=1, inset=c(0,0.09) )
library2 73

library2 install.package and require

Description
install and load a package. If a package is not available, it is installed before being loaded

Usage
library2(name, libargs = NULL, ...)

Arguments
name Name of the package(s). Can be quoted, must not.
libargs List of arguments passed to library like lib.loc, quietly etc. DEFAULT:
NULL
... Arguments passed to install.packages like lib, repos etc.

Value
messages help instruction.

Note
Passing a vector with packages will work, but give some warnings.

Author(s)
Berry Boessenkool, <[email protected]>, 2014

See Also
install.packages, library

Examples

## Not run:
## Excluded fom CRAN checks. Package installation on server is unnecessary.
require2(ada)
library2("statmod")

## End(Not run)
74 lim0

lim0 axis limits with one end at zero

Description
Calculates the range needed for ylim or xlim in plot, so that axis starts at zero and is extended by
4% at the other end

Usage
lim0(x, f = 1/27, curtail = TRUE)

Arguments
x Numeric. Vector with values
f Numeric. Extension factor. DEFAULT: 0.04 as in extendrange used eg. by
curve
curtail Logical. Should the range returned be trimmed by 4%? That way, plotting
doesn’t need the default par xaxs or yaxs changed. DEFAULT: TRUE

Value
Vector with two values: 0 and by 4

Author(s)
Berry Boessenkool, <[email protected]>, 6.6.2013

References
methods(plot), plot.default. Actually, I found extendrange via plot.function in curve

See Also
The extendrange() utility in package grDevices

Examples

# basic idea:
val <- c(3.2, 1.8, 4.5, 2.8, 0.1, 2.9) # just some numbers
plot(val, ylim=lim0(val) ) # you don't even have to set yaxs="i" ;-)

# "normal" plot:
plot(val)
par("usr") # -0.076 4.676

# if y-axis is not allowed to go below 0, and we're too lazy to set yaxs="i":
linLogHist 75

plot(val, ylim=lim0(val) )
round( par("usr") , digits=5) # 0.00000 4.66296

# with 0.04 extension as claimed by help page (1/27 in source code = 0.037):
plot(val, ylim=lim0(val, f=0.04) )
round( par("usr") , digits=5) # zero is not included on axis anymore

b <- -val
plot(b)
plot(b, ylim=lim0(b) ) # works with only negative values as well

# can handle only-NA input:

lim0(c(7,NA,NA,NA)[-1])
lim0(c(NA,NA,NA))

linLogHist lin-log transition histogram

Description
Draw histograms that gradually transform from a linear to a logarithmic axis (animation)

Usage
linLogHist(x, steps = 100, breaks = 20, col = "blue", las = 1,
xlab = deparse(substitute(x)), xlim = range(x, finite = TRUE),
box = TRUE, parexpr, endexpr, sleep = 0, axisargs = NULL,
axisargs2 = NULL, firstplot = TRUE, lastplot = TRUE, write_t = TRUE,
values_t = NULL, ...)

Arguments
x x values to be plotted in animation
steps Number of steps in transition. DEFAULT: 100
breaks hist breaks. DEFAULT: 20
col hist color. DEFAULT: "blue"
las par LabelAxisStyle (numbers upright). DEFAULT: 1
xlab Label for the x axis. DEFAULT: deparse(substitute(x))
xlim xlim range in non-log units. DEFAULT: range(x, finite=TRUE)
box Draw box at the end to overplot ablines crossing the box? DEFAULT: TRUE
parexpr Characterized Expression to set par, eg. parexpr='par(mar=c(2,0.5,1.5,0.5), mpg=c(1.8,1,0))'
endexpr Characterized Expression executed at the end of the plot, eg. endexpr='mtext("Probability Density"
sleep Pause time between frames, in seconds, passed to Sys.sleep. DEFAULT: 0
axisargs List of arguments passed to logVals, like base. DEFAULT: NULL
76 linLogHist

axisargs2 List of arguments passed to logAxis in the final plot. DEFAULT: NULL
firstplot plot on linear scale first? DEFAULT: TRUE
lastplot plot on logarithmic scale at the end? DEFAULT: TRUE
write_t write transformation value in lower right corner? DEFAULT: TRUE
values_t Supply vector with values for transformation (1/t). Overrides steps. If you have
a better algorithm than I do, please let me know! DEFAULT: NULL
... further arguments passed to hist, like freq, main, xlim, ylab. Excluded: x, xaxt,
possibly add

Value
Returned invisibly: transformation values used. Plotted: steps number of images.

Note
It’s best to save the plots into a pdf or wrap it within
png("Transition%03d"); linLogHist(x); dev.off()

Author(s)
Berry Boessenkool, <[email protected]>, April 2015

See Also
linLogTrans

Examples

x <- rlnorm(700, m=3)

hist(x, col=4)
hist(log10(x), xaxt="n"); logAxis(1); hist(log10(x), col=4, add=TRUE)

op <- par()
linLogHist(x, steps=8, sleep=0.01) # 0.05 might be smoother

linLogHist(x, xlab="ddd", breaks=30, steps=3, write_t=FALSE, yaxt="n", freq=FALSE,

main="", parexpr='par(mar=c(2,0.5,1.5,0.5), mgp=c(1.8,1,0))',
endexpr='mtext("Probability Density", line=-1.2, adj=0.03, outer=T)')
par(op)

## Not run:
## Rcmd check --as-cran doesn't like to open external devices such as pdf,
## so this example is excluded from running in the checks.
pdf("LinLogTransitionAnimation.pdf")
linLogHist(x, main="Example Transition", steps=20, freq=FALSE)
dev.off()

# if you have FFmpeg installed, you can use the animation package like this:
library2(animation)
linLogTrans 77

saveVideo(linLogHist(x, steps=50), video.name="linlog_anim.mp4", interval=0.08,

ffmpeg="C:/ffmpeg-20150424-git-cd69c0e-win64-static/bin/ffmpeg.exe")

## End(Not run)

linLogTrans Animation for transition from linear to logarithmic axis

Description
draw images that gradually transform from a linear to a logarithmic axis

Usage
linLogTrans(x, y, log = "x", steps = 100, base = 1, las = 1,
plot = TRUE, xlim = range(x, finite = TRUE), ylim = range(y, finite =
TRUE), box = TRUE, parexpr, endexpr, sleep = 0, firstplot = TRUE,
lastplot = TRUE, write_t = TRUE, values_t = NULL, pointsarg = NULL,
...)

Arguments
x x values to be plotted in animation
y Vector with corresponding y values
log Which axis is logarithmic, "x" or "y". DEFAULT: "x"
steps Number of steps (images) in transition (About 30% are taken out). DEFAULT:
100
base Base passed to logVals. DEFAULT: 1
las par LabelAxisStyle (numbers upright). DEFAULT: 1
plot Plot animations at all? False to just get the t-vector (used in linLogHist). DE-
FAULT: TRUE
xlim xlim range in non-log units. DEFAULT: range(x, finite=TRUE)
ylim ylim range in non-log units. DEFAULT: range(y, finite=TRUE)
box Draw box at the end to overplot ablines crossing the box? DEFAULT: TRUE
parexpr Characterized Expression to set par, eg. parexpr='par(mar=c(2,0.5,1.5,0.5), mpg=c(1.8,1,0))'
endexpr Characterized Expression executed at the end of the plot, eg. endexpr='mtext("Probability density"
sleep Pause time between frames, in seconds, passed to Sys.sleep. DEFAULT: 0
firstplot Plot data on linear axis as additional first image? DEFAULT: TRUE
lastplot Plot data on logarithmic axis as additional last image? DEFAULT: TRUE
write_t Write transformation value in lower right corner? DEFAULT: TRUE
78 linLogTrans

values_t Supply vector with values for transformation (1/t). Overrides steps. If you have
a better algorithm than I do, please let me know! DEFAULT: NULL for internal
calculation based on size of steps.
pointsarg List of further arguments passed to points, like pch, cex, col. DEFAULT: NULL
... Further arguments passed only to plot, like main, xlim, ylab. Excluded: x, y, las,
xaxt, type

Value
Returned invisibly: transformation values used. Plotted: steps number of images.

Note
if(steps>1000) steps <- 1000. In the unlikely case you need more steps, please let me know and I’ll
change the code.
It’s best to save the plots into a pdf (see the example) or wrap it within
png("Transition%03d"); linLogTrans(x,y); dev.off()

Author(s)
Berry Boessenkool, <[email protected]>, June 2014

References
x^(1/t) is based on the first comment on http://stackoverflow.com/questions/15994442/
besides the nice graphic properties of logtransformations, check this page for the implications on
rates of change:
http://sfew.websitetoolbox.com/post/show_single_post?pid=1282690259&postcount=4
http://sfew.websitetoolbox.com/post/show_single_post?pid=1282691799&postcount=5

See Also
logVals

Examples

set.seed(42); x <- 10^rnorm(100, 3); y <- runif(100)

linLogTrans(x,y, steps=15, sleep=0.01) # 0.05 might be smoother...
linLogTrans(x,y, steps=15, log="y", ylim=c(0.1, 0.8), base=c(1,2,5))

## Not run:
## Rcmd check --as-cran doesn't like to open external devices such as pdf,
## so this example is excluded from running in the checks.
pdf("LinLogTransitionAnimation.pdf")
linLogTrans(x,y, main="Example Transition")
dev.off()

# if you have FFmpeg installed, you can use the animation package like this:
library2(animation)
linLogTrans 79

saveVideo(linLogTrans(x,y, steps=300), video.name="linlog_anim.mp4", interval=0.01,

ffmpeg="C:/ffmpeg-20150424-git-cd69c0e-win64-static/bin/ffmpeg.exe")

# old t values were dependent on the value of steps

findt <- function(steps) {
# t-values for x^(1/t):
allt <- 10^(seq(0,2.5,len=1e4) )
# selection at upper half of these values;
# Otherwise, the animation slows down too much at the end
f <- 1.4 # multiplication factor due to length loss by unique
sel <- round(seq(1, 10, len=f*steps)^4) #0.5*seq(1, 100, len=1.3*steps)^2 + 0.5*
sel2 <- unique(round(log10(seq(1, 10, len=f*steps))*f*steps))
sel2[1] <- 1
sel <- sel[sel2]
# final t-values for transition:
allt <- unique(round(allt[sel], 2))
data.frame(x=seq(1,1000,len=length(allt)), t=allt)
}

plot(findt(1000), type="l", log="y", las=1)

for(i in 5:999) lines(findt(i), col=rainbow2(1000)[i])
d <- findt(300)
lines(d) # good average

plot(d$x[-1], diff(d$t), type="l", ylim=c(3e-3,10), yaxt="n", log="y", main="t value growth rate")
logAxis(2) ; lines(d$x[-1], diff(d$t))
d2 <- findt(1000)
lines(d2$x[-1], diff(d2$t), col=2)
lines(2:1000, diff(linLogTrans(1,1, steps=1000, plot=F)), col=4)

d <- findt(300)
pdf("degreepoly.pdf")
for(i in 5:30)
{
plot(d, log="y", type="l", lwd=3, main=i, xlim=c(0,300), ylim=c(1,2))
modell <- lm(t ~ poly(x,i, raw=T), data=d)
lines(x2, predict(modell, data.frame(x=1:1300)), col=2)
}
dev.off() # 17 is good

cf <- coef(lm(t ~ poly(x,17, raw=T), data=d)) # these are currently used in the function
x <- 1:1000
y <- rowSums(sapply(1:18, function(i) cf[i]*x^(i-1)), na.rm=TRUE)
lines(x, y, lwd=3)
y[1] <- 1
plot(x, round(y, 3), ylim=c(1,3), xlim=c(0,500), type="l", log="")
dput(round(y, 3))

findn <- function(steps) nrow(findt(steps))

plot(1:1000, sapply(1:1000, findn), type="l")
abline(b=1, a=0)
80 linReg

## End(Not run)

linReg linear regression with plotting

Description
uses lm; plots data if add=FALSE, draws the regression line with abline and writes the formula
with legend

Usage
linReg(x, y = NULL, data = NULL, add = FALSE, digits = 2, pch = 16,
col = 2, colband = addAlpha(col), level = 0.95,
plotrange = par("usr")[1:2], lwd = 1, xlab = deparse(substitute(x)),
ylab = deparse(substitute(y)), main = "linear regression", pos1 = "top",
pos2 = NULL, inset = 0, legargs = NULL, ...)

Arguments
x Numeric or formula (see examples). Vector with values of explanatory variable
y Numeric. Vector with values of dependent variable. DEFAULT: NULL
data Dataframe. If x is a formula, the according columns from data are used as x and
y. DEFAULT: NULL
add Logical. If TRUE, line and text are added to the existing graphic. DEFAULT:
FALSE (plots datapoints first and then the line.)
digits Numeric vector of length ≥ 1. Specifies number of digits a,b,r,e are rounded to
in the formula "y=a*x+b \n R^2=r \n RMSE=e", respectively. If values are not
specified, they are set equal to the first. DEFAULT: 2
pch Point Character of datapoints, see par. DEFAULT: 16
col Color of the regression line, see par. DEFAULT: 2
colband Color of the confidence region band. DEFAULT: addAlpha(col)
level Confidence level, see predict.lm. DEFAULT: 0.95
plotrange x range for which regression line and uncertainty band should be plotted. Is
passed to seqR and can hence be a vector. DEFAULT: par("usr")[1:2]
lwd Numeric. Linewidth, see par. DEFAULT: 1
xlab Axis label if add=FALSE. DEFAULT: deparse(substitute(x))
ylab Axis label if add=FALSE. DEFAULT: deparse(substitute(y))
main Title if add=FALSE. Changed (if not specified) for x=formula with data. DE-
FAULT: "linear regression"
linReg 81

pos1 xy.coords-acceptable position of the formula. DEFAULT: "top"

pos2 For numerical coordinates, this is the y-position. DEFAULT: NULL, as in
legend
inset Numeric vector of length ≤ 2. inset distance(s) from the margins as a fraction
of the plot region when formula legend is placed by keyword. DEFAULT: 0
legargs list of arguments passed to legend, like list(cex=0.8, xpd=TRUE, bg="white"),
... xpd specifies whether formula can be written only inside the plot region
(when FALSE) or inside the figure region including mar (when TRUE) or in the
entire device region including oma (when NA). DEFAULT: NULL
... Further arguments passed to plot

Value

None, used for plotting and drawing.

Author(s)

Berry Boessenkool, <[email protected]>, 2011-2012, 2015

See Also

lm, mReg, expReg, legend, par, abline.

Examples

a <- 1:30
b <- a/2.345+rnorm(30,0,3)

linReg(a,b)
linReg(a,b, ylab="Hallo", pch=1, col=3, main="Regression by Berry")
linReg(a, b, pos1=15, pos2=0) # position of topleft corner of legend
linReg(a, b, pos1=NA, col="orange") # to suppress legend
linReg(a, b, plotrange=5:20) # only for plotting, all data points are used!

# Formula specification:
linReg(b~a)
linReg(Volume~Height, data=trees)

# For more flexibility with the datapoints, plot first, then use linReg with add=TRUE:
plot(a,b, xlim=c(-5,45))
linReg(a, b, pos1="bottomright", add=TRUE, inset=.1) # inset: distance from plot border
linReg(a, b, digits=c(7,4,3), add=TRUE, col=3, lty=2, lwd=4, level=0.8)
linReg(a, b, pos1="topleft", inset=c(-0.1, 0.3), legargs=list(xpd=TRUE), add=TRUE)
82 locArrow

locArrow arrow at locator point in graph

Description

Draw arrow at positions in a graph located by clicking and return the code to recreate it

Usage

locArrow(digits = 2, length = 0.1, code = 2, ...)

Arguments

digits Number of digits coordinates are rounded to with signif

length Length of the edges of the arrow head (in inches). DEFAULT: 0.1
code Direction of arrow head. DEFAULT: 2 (from first to last point clicked)
... Further arguments passed to arrows like lwd, col etc

Details

Not tested across platforms yet...

Value

Character string with code

Author(s)

Berry Boessenkool, <[email protected]>, Jun 2016

See Also

locLine, locator, abline

Examples

plot(cumsum(rnorm(60)), type="l")
## locArrow() # only do this manually in interactive() mode
## locArrow(col="blue", lwd=3)
locLine 83

locLine abline at locator point in graph

Description

Draw vertical and/or horizontal lines at positions in a graph located by clicking

Usage

locLine(h = TRUE, v = TRUE, n = 1, ...)

Arguments

h Draw horizontal line at clicked location? DEFAULT: TRUE

v Draw vertical line at clicked location? DEFAULT: TRUE
n Number of points to be clicked. DEFAULT: 1
... Further arguments passed to abline like lty, lwd, col, etc

Details

Not tested across platforms yet...

Value

locator result

Author(s)

Berry Boessenkool, <[email protected]>, Mar 2016

See Also

locator, abline

Examples

plot(cumsum(rnorm(60)), type="l")
## locLine() # only do this manually in interactive() mode
84 logAxis

logAxis Label logarithmic axes

Description
Shortcut to calling logVals, axis and abline

Usage
logAxis(side = 1, log = NULL, lcol = "grey", lty = 1, lwd = 1,
labels = NULL, allticks = FALSE, allargs = NULL, expr, las = 1, from,
to, Range, base = NA, big.mark = "'", decimal.mark = ".",
scientific = FALSE, exponent = 5, expobase1 = FALSE, allbase = 1:9,
box = TRUE, ...)

Arguments
side Which axis are to be labeled? Can be a vector within 1:4. DEFAULT: 1
log Is the axis logarithmic by plot(log="x")? internal DEFAULT: par("xlog") or
"ylog". DEFAULT: NULL
lcol Color of gridlines drawn in the graph with abline, NA to suppress. DEFAULT:
"grey"
lty, lwd Type of gridlines. DEFAULT: 1
labels Labels passed to axis. "FALSE" to suppress labeling. DEFAULT: NULL (in-
ternally, logVals$labs
allticks Place all intermediate ticklines at the axis (without labeling). DEFAULT: FALSE
allargs List of arguments passed to axis for allticks=TRUE. DEFAULT: NULL
expr Expression drawing over the ablines, like (points(x,y). Can be code within
braces.
las LabelAxisStyle for the orientation of the labels. DEFAULT: 1
from Lower exponent OR vector with data, as in logVals. DEFAULT based on
par("usr")
to High end exponent. DEFAULT: internally based on par("usr")
Range Override from and to as range.
base Bases to be used in logVals. DEFAULT: NA -> c(1,2,5) or 1, depending on
from and to.
big.mark Symbol separating thousands, eg. space, comma, dot, etc. see "format" and
"prettyNum". DEFAULT: "’"
decimal.mark Character separating comma values, see "format" and "prettyNum". DEFAULT:
"."
scientific See format. DEFAULT: FALSE
logAxis 85

exponent Starting at which exponent should logVals return an expression with expo-
nents? DEFAULT: 5
expobase1 Should "n * " be appended before 10^exp if n=1? DEFAULT: FALSE
allbase base for $all (for horizontal lines). DEFAULT: 1:9
box Draw box at the end to overplot ablines crossing the box? DEFAULT: TRUE
... Further arguments passed to axis, like lwd, col.ticks, hadj, lty, ...

Value
An invisible list with

vals Values for lines and label positions

labs Formatted values for labels
all Values for lines

Author(s)
Berry Boessenkool, <[email protected]>, Sept 2014

See Also
logVals, log10

Examples

x <- 10^runif(200, -1, 2)

plot(x, yaxt="n", log="y", pch=16)
logAxis(2)
# overplot vertical lines:
logAxis(2, expr=points(x, pch=16), base=1, col.axis=4, font=2)

# plots where log="x" is not possible:

hist(log10(x), breaks=20, col.axis="grey", main="")
logAxis(side=3, expr=hist(log10(x), breaks=20, add=TRUE, col=3))
# or just use the new logHist function (Feb 2016):
logHist(x, breaks=20, col=3)

# automatic calculation of from, to and base:

plot(1:3, axes=FALSE)
logAxis(1:2) # side can be a vector - nice, huh?
plot(-1:4, axes=FALSE)
logAxis(1:2) # treshold for base 1 instead of c(1,2,5) at 4 exponents exceeded.

plot(1:3, axes=FALSE)
logAxis(1:2, allticks=TRUE, lcol=NA)

par(mar=c(3,3,1,4))
plot(8:15) ; logAxis(4) # with exponents if they are above 5
plot(10^(1:4), ylim=10^c(4,1), type="o", log="y") # reverse axis:
86 logHist

plot(10^(1:5), log="y"); logAxis(4, exponent=3) # different treshold

plot(10^(1:5), log="y"); logAxis(4, expon=3, base=c(1,2,5), expobase1=TRUE)
plot(-8:5); logAxis(4, allbase=c(1,2,5)) # In case you want to mislead...

logHist Histogram of logarithmic values

Description
Draw histogram of values on a logarithmic scale with nice axis labels

Usage
logHist(x, logargs = NULL, main = xmain, xlab = xname, col = "tan",
add = FALSE, las = 1, ylim = NULL, freq = TRUE, quiet = FALSE, ...)

Arguments
x Vector of numerical values
logargs A list of arguments passed to logAxis. DEFAULT: NULL
main Title of graph, internally from x. DEFAULT: internal name representation
xlab X axis label. DEFAULT: internal: name of x
col Color of histogram bars
add Logical: add to existing plot?
las Integer: label axis style. DEFAULT: 1 (numbers upright)
ylim 2 Numbers: y-axis range. DEFAULT: NULL
freq Logical: counts instead of density? DEFAULT: TRUE
quiet Logical: suppress warning about non-positive values? DEFAULT: FALSE
... further arguments passed to hist like breaks, xlim=c(-1,3), ..., but not xaxt

Value
none

Author(s)
Berry Boessenkool, <[email protected]>, Feb 2016

See Also
logAxis, hist
logSpaced 87

Examples

dat <- rbeta(1e4, 2, 18)*100

hist(dat, col="tan", breaks=50)
logHist(dat)
logHist(dat, freq=FALSE)
logHist(dat, breaks=50)
logHist(dat,xlim=c(0,2)) # xlim in powers of ten
logHist(c(-1,0,1,2,2,3,3,4,8,10,50)) # warning for negative values

logSpaced Logarithmically spaced points

Description
Calculates values that are in logarithmic distance from each other e.g. to produce logarithmic
interval borders.
For exact logarithmic spacing, use 10^seq(from=log10(1), to=log10(100), len=100)

Usage
logSpaced(base = 1.1708, n = 20, min = 1, max = n, plot = TRUE,
pch = 3, las = 1, ylab = "base", ...)

Arguments
base Base for calculations, can be a vector to compare several bases. DEFAULT:
1.1708
n Number of values to be calculated. DEFAULT: 30
min, max Range where n values are to be distributed, single values each. DEFAULT: 1,n
plot Should the points be plotted on a line? DEFAULT: TRUE
pch, las PointCharacter and Label Axis Style. DEFAULT: 3,1
ylab Y axis label. DEFAULT: "base"
... Further arguments passed to plot

Value
Vector or matrix, depending on base input

Note
base >1 concentrates points at low values, base<1 at high values. base does not relate to base in
log!
88 logVals

Author(s)
Berry Boessenkool, <[email protected]>, Oct 2014

See Also
classify, log

Examples

logSpaced()
logSpaced(base=c(1.1, 1.5, 2), n=6, min=5, max=10)
d <- logSpaced(seq(0.8, 1.2, 0.025), main="logarithmically spaced points")

# the default base for the default n (20) will give an approximately equal
# bin width across the range on a logarithmic scale:
d <- logSpaced()
plot(d, rep(1,20), log="x")

# For exactly spacing logarithmically, use

plot(10^seq(from=log10(1), to=log10(100), len=100), log="y")
browseURL("https://stackoverflow.com/a/29963530")

logVals Create log-axis values and labels

Description
Create nice values and labels to write at logarithmic axes

Usage
logVals(from = -7, to = 7, Range, base = 1, big.mark = "'",
decimal.mark = ".", scientific = FALSE, exponent = Inf,
expobase1 = FALSE, allbase = 1:9, ...)

Arguments
from Lower exponent OR vector with data
to High end
Range Or give from and to as range
base Bases to be used, eg. c(1,2,5). Use base=NA to switch between 1 and c(1,2,5)
depending on range. DEFAULT 1
big.mark Symbol separating thousands, eg. space, comma, dot, etc. see format and
prettyNum
decimal.mark Character separating comma values, see format and prettyNum
logVals 89

scientific See format

exponent Starting at which exponent should labs be an expression with exponents? Com-
pare to options("scipen"). This is mainly for logAxis and only for base 1.
DEFAULT: Inf
expobase1 Should "n * " be appended before 10^exp if n=1? DEFAULT: FALSE
allbase Base for $all (for horizontal lines). DEFAULT: 1:9
... Ignored arguments

Value
A list with
vals Values for lines and label positions
labs Formatted values for labels
all Values for lines

Author(s)
Berry Boessenkool, <[email protected]>, Feb 2014

See Also
log10, logAxis, http://r.789695.n4.nabble.com/expression-exponent-labeling-td4661174.
html

Examples

# Easiest use: vector with data (logVals automatically finds range):

y <- 10^runif(50, -1, 2)
plot(y, log="y") # not much control over placement and format of labels
plot(y, log="y", yaxt="n")
# now do this better, with custom bases:
lv <- logVals(y, base=c(1,2,5) )
axis(2, lv$vals, lv$labs, las=1)

# Default arguments:
lv <- logVals()
str(lv) # values, formatted labels, all 10^x values for lines
plot(1, ylim=c(1e-3, 1e4), log="y", yaxt="n", yaxs="i")
abline(h=lv$all, col=8 )
box("plot")
axis(2, lv$vals, lv$labs, las=1)
lines(seq(0.5, 1.5, len=50), 10^runif(50, -3, 4), col=2)

# Formatting labels:
logVals( )$labs
logVals(scient=TRUE )$labs
logVals(exponent=5 )$labs # expression with exponent, see logAxis
logVals(big.mark=" " )$labs
90 lsc

logVals(big=".", dec=",")$labs # German style (not recommended)

lsc Linear storage cascade, unit hydrograph

Description
Optimize the parameters for unit hydrograph as in the framework of the linear storage cascade. Plot
observed & simulated data

Usage
lsc(P, Q, area = 50, Qbase = Q[1], n = 2, k = 3, x = 1:length(P),
fit = 1:length(Q), plot = TRUE, main = "Precipitation and discharge",
plotsim = TRUE, returnsim = FALSE, type = c("o", "l"),
legx = "center", legy = NULL, ...)

Arguments
P Vector with precipitation values in mm in hourly spacing
Q Vector with observed discharge (runoff) in m^3/s with the same length as pre-
cipitation.
area Single numeric. Catchment area in km^2
Qbase baseflow that is added to UH-induced simulated Q, thus cutting off baseflow in
a very simple manner.
n Numeric. Initial number of storages in cascade. not necessarily integer. DE-
FAULT: 2
k Numeric. Initial storage coefficient (resistance to let water run out). High damp-
ing, slowly reacting landscape, high k. DEFAULT: 3
x Vector for the x-axis of the plot. DEFAULT: sequence along P
fit Integer vector. Indices for a subset of Q that Qsim is fitted to. DEFAULT: all of
Q
plot Logical. plot input data? DEFAULT: TRUE
main Character string. DEFAULT: "Precipitation and discharge"
plotsim Logical. add best fit to plot? DEFAULT: TRUE
returnsim Logical. Return simulated Q instead of parameters of UH? DEFAULT: FALSE
type Vector with two characters: type as in plot, repeated if only one is given. 1st
for obs, 2nd for sim. DEFAULT: c("o","l")
legx legend position. DEFAULT: "center"
legy legend position. DEFAULT: NULL
... arguments passed to optim
lsc 91

Value
Either vector with optimized n and k and the Nash-Sutcliffe Index, or simulated discharge, depend-
ing on the value of returnsim

Author(s)
Berry Boessenkool, <[email protected]>, July 2013

References
http://ponce.sdsu.edu/onlineuhcascade.php
Skript ’Abflusskonzentration’ zur Vorlesungsreihe Abwasserentsorgung I von Prof. Krebs an der
TU Dresden
http://tu-dresden.de/die_tu_dresden/fakultaeten/fakultaet_forst_geo_und_hydrowissenschaften/
fachrichtung_wasserwesen/isiw/sww/lehre/dateien/abwasserbehandlung/uebung_ws09_10/
uebung_awe_1_abflusskonzentration.pdf
http://www.uni-potsdam.de/fs-g3/file.php?fileserver=klausuren&file=%2FMaster_of_
Science%2FHydroII_Lernzettel.pdf

See Also
unitHydrograph, superPos, nse, rmse. deconvolution.uh in the package hydromad, http:
//hydromad.catchment.org

Examples

qpfile <- system.file("extdata/Q_P.txt", package="berryFunctions")

qp <- read.table(qpfile, sep="\t", dec=",", header=TRUE)
calib <- qp[1:90,]
valid <- qp[-(1:90),]

# Area can be estimated from runoff coefficient (proportion of N becoming Q):

# k*P * A = Q * t A = Qt / kP
# Q=0.25 m^3/s * t=89 h * 3600 s/h k=psi* P =34mm = 0.034m = m^3/m^2
# / 1e6 m^2/km^2 = km^2
mean(calib$Q) * length(calib$Q) *3600 / ( 0.7 * sum(calib$P)/1000) / 1e6
# 3.368 km^2

# calibrate Unit Hydrograph:

UHcalib <- lsc(calib$P, calib$Q, area=3.4)
UHcalib # n 0.41 k 244.9 NSE 0.74 psi 0.45
# Psi is lower than 0.7, as it is now calculated on direct runoff only

# Corresponding Unit Hydrograph:

UH <- unitHydrograph(n=UHcalib["n"], k=UHcalib["k"], t=1:length(calib$P))
plot(UH, type="l") # That's weird anyways...
sum(UH) # 0.58 - we need to look at a longer time frame

# calibrate Unit Hydrograph on peak only:

92 lsc

lsc(calib$P, calib$Q, area=3.4, fit=17:40) # n 0.63 k 95.7 NSE 0.67

# for fit, use index numbers, not x-axis units (if you have specified x)

# Simulated discharge instead of parameters:

lsc(calib$P, calib$Q, area=3.4, returnsim=TRUE, plot=FALSE)

## Not run: ## Time consuming tests excluded from CRAN checks

# Apply this to the validation event

dummy <- lsc(valid$P, valid$Q, area=3.4, plotsim=FALSE, type="l")
Qsim <- superPos(valid$P, UH)
Qsim <- Qsim + valid$Q[1] # add baseflow
lines(Qsim, lwd=2, xpd=NA)
legend("center", legend=c("Observed","Simulated from calibration"),
lwd=c(1,2), col=c(2,1) )
nse(valid$Q, Qsim[1:nrow(valid)]) # 0.47, which is not really good.
# performs OK for the first event, but misses the peak from the second.
# this particular UH is apparently not suitable for high pre-event soil moisture.
# Along with longer events, UH properties may change!!!
dummy # in-sample NSE 0.75 is a lot better

# Now for the second peak in the validation dataset:

lsc(valid$P, valid$Q, type="l", area=3.4, fit=60:90) # overestimates first peak
# Area cannot be right - is supposedly 17 km^2.

# Different starting points for optim:

lsc(calib$P, calib$Q, area=3.4, n= 2 , k= 3, plot=FALSE) # Default
lsc(calib$P, calib$Q, area=3.4, n= 5 , k= 20, plot=FALSE) # same result
lsc(calib$P, calib$Q, area=3.4, n=10 , k= 20, plot=FALSE) # ditto
lsc(calib$P, calib$Q, area=3.4, n=10 , k= 3, plot=FALSE) # ditto
lsc(calib$P, calib$Q, area=3.4, n= 1.9, k=900, plot=FALSE) # ditto
lsc(calib$P, calib$Q, area=3.4, n=50 , k= 20) # nonsense
# the catchment is small, so n must be low.

#sensitivity against area uncertainty:

Asens <- data.frame(A=seq(1,15,0.5),
t(sapply(seq(1,15,0.5), function(A) lsc(calib$P, calib$Q, area=A, plot=FALSE))))
Asens
plot(Asens$A, Asens$NSE, type="l", ylim=c(-0.3,2), las=1, main="lsc depends on area")
abline(v=3.4, lty=2)
lines(Asens$A, Asens$n, col=2)
points(3.4, 2, col=2)
lines(Asens$A, Asens$psi, col=5)
text(rep(13,4),y=c(1.5, 0.8, 0.4,0), c("k ->","<- NSE","<- n","<- psi"), col=c(4,1,2,5))
par(new=TRUE); plot(Asens$A, Asens$k, type="l", ann=FALSE, axes=FALSE, col=4)
axis(4, col.axis=4)
points(3.4, 3, col=4)

# Autsch - that shouldn't happen!

# Still need to find out what to do with optim
lsMem 93

lsc(calib$P, calib$Q, area=1.6) # not bad indeed

## End(Not run)

lsMem Show memory size of objects in MB

Description
Show memory size of the biggest objects in MB. Helps you find the biggest memory killers.

Usage
lsMem(n = 6, pos = 1, ...)

Arguments
n Number of Objects to be shown separately. The rest is combined into "sum rest".
DEFAULT: 6
pos Environment where ls looks for objects.
... Further arguments passed to ls

Value
Named vector with object sizes in MB (MegaBytes)

Author(s)
Berry Boessenkool, <[email protected]>, Feb 2014

References
http://stackoverflow.com/questions/1358003/tricks-to-manage-the-available-memory-in-an-r-session

See Also
object.size, ls

Examples

## Not run:
## excluded from CRAN check - I forgot why, but there's probably a good reason
lsMem()

## End(Not run)
94 monthAxis

monthAxis Label date axis

Description
Labels date axes at sensible monthly intervals in the time domain of years to decades.

Usage
monthAxis(side = 1, time = NA, origin = "1970-01-01",
mlabels = substr(month.abb, 1, 1), yformat = "%Y", nmonths = 3,
nym_half = 3.5, nym_none = 5, mcex = 0.7, ycex = 1,
mtcl = par("tcl"), ytcl = par("tcl") - 1.7, mline = -1, yline = 0.2,
las = 1, lrange = NA, ym = TRUE, mgp = c(3, 1, 0), mt = NULL,
ml = NULL, yt = NULL, yl = NULL, quiet = FALSE, ...)

Arguments
side Which axis is to be labeled? DEFAULT: 1
time Logical indicating whether the axis is POSIXct, not Date. DEFAULT: NA,
meaning axis value >1e5
origin Origin foras.Date and as.POSIXct. DEFAULT: "1970-01-01"
mlabels Labels for the months. DEFAULT: J,F,M,A,M,J,J,A,S,O,N,D
yformat Format of year labels, see details in strptime. Use yformat=" " (with space)
to suppress year labeling. DEFAULT: "%Y"
nmonths Minimum number of months required before a year at the axis boundary is la-
beled. DEFAULT: 3
nym_half Number of years on axis above which only every second month is labeled. DE-
FAULT: 3.5
nym_none Number of years on axis above which the months are not labeled. DEFAULT: 5
mcex cex.axis (letter size) for month labels. DEFAULT: 0.7
ycex cex.axis (letter size) for year labels. DEFAULT: 1
mtcl Month tick length (negative text line height units). 0 to suppress ticks. DE-
FAULT: par("tcl") = -0.5
ytcl Year tick length (negative text line height units). 0 to suppress ticks. DEFAULT:
par("tcl")-1.7 = -2.2
mline Line of month labels. DEFAULT: -1
yline Line of year labels. DEFAULT: 0.2
las LabelAxisStyle for orientation of labels. DEFAULT: 1 (upright)
lrange Label range (two Date values). DEFAULT: NA = internally computed from
par("usr")
ym Kept for back reference. DEFAULT: TRUE
monthAxis 95

mgp MarGin Placement. Suggested not to change this, since _tcl and _line defaults
are chosen for the DEFAULT: c(3,1,0)
mt, ml, yt, yl Lists with further arguments passed to axis, like lwd, col.ticks, lwd.ticks, hadj, lty,
separately for month ticks, month labels, year ticks, year labels. DEFAULT:
NULL
quiet Suppress warning about short time axis? DEFAULT: FALSE
... Arguments passed to axis for all 4 elements.

Value
List with locations of month and year labels and ticks, each a Date vector.

Author(s)
Berry Boessenkool, <[email protected]>, Feb + Dec 2015, Oct 2017

See Also
monthLabs for the numbercrunching itself, timeAxis for shorter or longer time frames, axis.Date
with defaults that are less nice.

Examples

set.seed(007) # for reproducibility

timePlot <- function(nydays, start="2013-08-25", ...)
plot(as.Date(start)+sort(c(0,sample(1:nydays, 50))),
cumsum(rnorm(51)), type="l", xaxt="n", ann=FALSE, las=1, ...)

timePlot(1100)
monthAxis()
monthAxis(1, nmonths=6, col.axis="red") # 2013 not labeled anymore
monthAxis(side=3, nym_half=2) # if axis > 2 years, label only partially

timePlot(2e3)
monthAxis() # long time series (>nym_none) only have years labeled
monthAxis(side=3, font=2)

timePlot(900)
monthAxis(side=3, mtcl=0) # no tick lines between months
monthAxis(ycex=1.4, ytcl=2, lwd.ticks=2)
monthAxis(yline=1, col.axis=4, col=4)
monthAxis(mcex=1, col.axis="red", yformat=" ") # no years labeled

timePlot(800)
monthAxis()
monthAxis(mgp=c(2,1,0)) # the same. element 2 is relevant here
monthAxis(mgp=c(3,0,0)) # requires change in mline andy yline placement

timePlot(400)
ma <- monthAxis(lwd=3, yl=list(col.axis=3), mlabels=letters[1:12], mcex=1)
96 monthLabs

abline(v=ma$mtics, col=8) # use output from monthAxis for other functions

timePlot(80)
monthAxis(mlabels=month.abb, mcex=1) # short time series give a warning

timePlot(80, "2013-11-14")
monthAxis(mlabels=month.abb, mcex=1, nmonths=0, quiet=TRUE)

# Time axis instead of date axis:

plot(as.POSIXct(Sys.time()+c(0,2)*360*24*3600), 1:2, xaxt="n")
monthAxis(nmonths=2)

timePlot(800, "2015-01-01")
monthAxis()
timePlot(900, "2015-01-01", xaxs="i")
monthAxis()
timePlot(300, "2015-01-01", xaxs="i")
monthAxis() # if less than a full year is covered, the year label is centered

monthLabs Nicely spaced labels along a month

Description
Create dates of certain days of the month for labeling

Usage
monthLabs(startyear = 2002, stopyear = 2018, npm = 2, npy = NA)

Arguments
startyear Integer. starting year. DEFAULT: 2002
stopyear Integer. ending year. DEFAULT: 2018
npm Integer, one of 1,2,3,6 or 31. Number of labels per month. DEFAULT: 2
npm : days of the month
1 : first day of each month within the given years
2 : 1st and 15th day
3 : 1, 10, 20
6 : 1, 5, 10, 15, 20, 25. 31 : each day
npy Integer, one of 1,2,3,4 or 6. Number of labels per year at equally spaced month-
beginnings. If specified, npm is not considered at all. DEFAULT: NA

Value
Vector with Dates as returned by as.Date.
movAv 97

Note
Spacing of days is not equal, but set to certain days of the month! This was originally developed for
time series movie frames

Author(s)
Berry Boessenkool, <[email protected]>, early 2013

See Also
timeAxis for nice labeling, timeAxis for automatic determination of npm/npy, as.Date, paste

Examples

monthLabs(2014,2014, 3) # 3 days per month

monthLabs(2013,2014, npy=3) # 3 months per year, equally spaced
monthLabs(2014,2014, npy=4) # 4 months per year

# see monthAxis for automatic plot labeling

movAv Moving average

Description
Weighted moving average (running mean) with overlapping windows

Usage
movAv(dat, width = 7, weights = rep(1, width), quiet = FALSE)

Arguments
dat Vector with regularly spaced data
width Odd integer specifying window width. DEFAULT: 7
weights Vector with weights. Sum is normalized to 1. DEFAULT: rep(1,width)
quiet Logical: suppress allNA message and even width warning? DEFAULT: FALSE

Details
Width has to be odd, so there is a defined middle point of each window. Even inputs will be changed
with a warning (unless quiet=TRUE).
Weights doesn’t have to be symmetrical, but is always mapped to the middle of each window!
If there are NAs in the window, the corresponding weight is distributed evenly to the other weights.
98 movAv

Value
Vector of the same length as the original input. Padded with NAs at width/2 margin elements

Note
You can specify just one of weights or width.

Author(s)
Berry Boessenkool, <[email protected]>, ca 2012

See Also
filter, decompose, smooth, loess, rollapply (no overlapping!)

Examples
# general usage -------------------------------------------------------------
set.seed(29); a <- runif(40, 5,50)
data.frame(a, movAv(a))

# final and commencing NAs are kept, middle ones are filled:
a[c(1:10, 18:26, 32:40)] <- NA
data.frame(a, movAv(a))

set.seed(29); a <- runif(60, 5,50)

plot(a, type="o", pch=16, las=1)
lines(movAv(a), col=2, lwd=3) # shows trends, signal in the noise
lines(movAv(a,3), col=4, lwd=3)
lines(movAv(a,15), col=3, lwd=3) # degree of smoothing depends on window width

# Weights:
plot(a, type="o", pch=16, las=1)
lines(movAv(a), col=2, lwd=3) # uniform weight within running window
# Triangular weights react stronger to extrema:
lines(movAv(a, weights=c(1,2,4,6,4,2,1)), col=4, lwd=3)

plot(c(Nile), type="l")
lines(movAv(Nile,20), col=4, lwd=4)
lines(movAv(Nile,21), col=3) # even widths are changed to a higher value

# smoothing intenstiy -------------------------------------------------------

plot(1871:1970, Nile, type="l", col=8)
movAvLines(1871:1970, Nile, lwd=3)

for(i in 1:30*2-1)
{
plot(a, type="o", pch=16, las=1, main=paste("moving average, width =", i))
lines(movAv(a, i), col=2, lwd=4)
}
# How to lie with moving averages: compare width 29 with 49 - the "trend"
movAvLines 99

# appears to be in opposite direction! (OK, this is random data anyways).

b <- rep(a, each=10)+runif(600, -10, 20)

plot(b, type="l")
lines(movAv(b), col=2, lwd=4)
lines(movAv(b, 35), col=4, lwd=4)
lines(movAv(b, 101), col=5, lwd=4) # choose width according to scale!

# Deviance from running mean can identify outlier:

nile <- c(Nile)
op <- par(mfrow=c(3,1), mar=c(1,3,2.5,0), cex.main=1, las=1)
plot(nile, type="l", main=c("original Nile data",""), xlab="", xaxt="n")
lines(movAv(nile,5), lwd=2, col=2)
title(main=c("", "5-element running mean (moving average)"), col.main=2)
box("figure")
plot(nile-movAv(nile,5), type="o", pch=16, col=4,
main="difference ( original data - moving average )", xlab="", xaxt="n")
abline(h=0)
box("figure")
par(mar=c(3,3,1,0))
hist(nile-movAv(nile,5), breaks=25, xlim=c(-500,500), col=4, main="Deviances")
abline(v=0, lwd=5) # the deviances are pretty symmetric.
# If this were shifted more strongly to the left, we could say:
# movav(5) overestimates minima more than it underestimates maxima
# This would happen if low values peak away further and more shortly
par(op)

movAvLines Moving average with different window widths

Description
Add moving average lines with different window widths to a plot

Usage
movAvLines(x = 1:length(y), y, widths = c(3, 5, 7, 9, 11, 13), weights,
col = "blue", alpha = 0.3, add = TRUE, las = 1, ...)

Arguments
x x values of data. DEFAULT: 1:length(y)
y y values that are smoothed with several window widths
widths widths of movAv windows. DEFAULT: 2:7*2-1
weights weights within each window
col color passed to addAlpha. DEFAULT: "blue"
100 mReg

alpha transparency passed to addAlpha. DEFAULT: 0.3

add Logical: Add to existing plot?Set to FALSE to first create the scatterplot. DE-
FAULT: TRUE
las LabelAxisStyle (only relevant if add=FALSE). DEFAULT: 1
... further arguments passed to lines

Author(s)

Berry Boessenkool, <[email protected]>, May 2015

See Also

movAv, addAlpha

Examples

set.seed(42)
movAvLines(y=cumsum(rnorm(50)), add=FALSE, lwd=3)

mReg Multiple regression

Description

Multiple regression fitting various function types including e.g. linear, cubic, logarithmic, exponen-
tial, power, reciprocal. Quick way to find out what function type fits the data best. Plots data and
fitted functions and adds a legend with the functions (or their types=structure) sorted by R squared.
Returns the fitted functions with their parameters and R^2 values in a data.frame.

Usage

mReg(x, y = NULL, data = NULL, Poly45 = FALSE, exp_4 = FALSE,

xf = deparse(substitute(x)), yf = deparse(substitute(y)), ncolumns = 9,
plot = TRUE, add = FALSE, nbest = 12, R2min, selection = NULL,
digits = 2, extend = 0.4, xlim = extendrange(x, f = extend),
ylim = extendrange(y, f = extend), xlab = xf, ylab = yf, las = 1,
lwd = rep(1, 12), lty = rep(1, 12), col = NULL, pcol = par("col"),
pch = 16, legend = TRUE, legargs = NULL, legendform = "nameform",
quiet = FALSE, ...)
mReg 101

Arguments
x Vector with x coordinates or formula (like y~x), the latter is passed to model.frame
y Vector with y values. DEFAULT: NULL (to enable x to be a formula)
data data.frame in which formula is applied. DEFAULT: NULL
Poly45 Logical. Should 4th and 5th degree polynomials also be fitted? DEFAULT:
FALSE, as the formulas are very long.
exp_4 Logical. Return 4-parametric exponential distribution fits (via exp4p) in the
output table? (only best fit is plotted). exp_4par_ini has the initial values of
exponential fitting with the data relocated to first quadrant. The others are opti-
mized with the methods of optim. DEFAULT: FALSE
xf Character. x name for Formula. DEFAULT: substitute(x) before replacing zeros
in x and y
yf Ditto for y
ncolumns Number of columns in output. Set lower to avoid overcrowding the console.
DEFAULT: 9
plot Logical. plot data and fitted functions? DEFAULT: TRUE
add Logical. add lines to existing plot? DEFAULT: FALSE
nbest Integer. Number of best fitting functions to be plotted (console output table
always has all). DEFAULT: 12
R2min Numerical. Minimum Rsquared value for function type to be plotted. Sugges-
tion: 0.6 (2/3 of variation of y is explained by function of x). DEFAULT: empty
selection Integers of functions to be plotted, assigned as in list in section "note". DE-
FAULT: NULL, meaning all
digits Integer. number of significant digits used for rounding formula parameters and
R^2 displayed. DEFAULT: 2
extend Numerical. Extention of axis ranges (proportion of range). DEFAULT: 0.4
xlim Numerical vector with two values, defining the x-range of the lines to be plotted.
DEFAULT: extended range(x)
ylim Ditto for Y-axis
xlab Character. default labels for axis labeling and for formulas. DEFAULT: substi-
tute(x) before replacing zeros in x and y
ylab Ditto for y axis.
las Integer in 0:4. label axis style. See par. DEFAULT: 1
lwd Numerical of length 12. line width for lines. DEFAULT: rep(1,12)
lty Numerical of length 12. line type. DEFAULT: rep(1,12)
col Numerical of length 12. line colors. DEFAULT: NULL, means they are speci-
fied internally
pcol Color used for the data-points themselves. DEFAULT: par(’col’)
pch Integer or single character. Point CHaracter for the data points. See par. DE-
FAULT: 16
102 mReg

legend Logical. Add legend to plot? DEFAULT: TRUE

legargs List. List of arguments passed to legend. Will overwrite internal defaults. DE-
FAULT: NULL
legendform One of ’full’, ’form’, ’nameform’ or ’name’. Complexity (and length) of legend
in plot. See Details. DEFAULT: ’nameform’
quiet Suppress warnings about value removal (NAs, smaller 0, etc)? DEFAULT:
FALSE
... Further graphical parameters passed to plot

Details
legendform : example
full : 7.8*x + 6.31
form : a*x+b
nameform : linear a*x+b
name : linear

full can be quite long, especially with Poly45=TRUE!

Value
data.frame with rounded R squared, formulas, and full R^2 and parameters for further use. Row-
names are the names (types) of function. Sorted decreasingly by R^2

warning
A well fitting function does NOT imply correct causation!
A good fit does NOT mean that you describe the behaviour of a system adequately!
Extrapolation can be DANGEROUS!
Always extrapolate to see if a function fits the expected results there as well.
Avoid overfitting: Poly45 will often yield good results (in terms of R^2), but can be way overfitted.
And outside the range of values, they act wildly.

Note
If you’re adjusting the appearance (lwd, lty, col) of single lines, set parameters in the following
order:
# 1 linear a*x + b
# 2 quadratic (parabola) a*x^2 + b*x + c
# 3 cubic a*x^3 + b*x^2 + c*x + d
# 4 Polynom 4th degree a*x^4 + b*x^3 + c*x^2 + d*x + e
# 5 Polynom 5 a*x^5 + b*x^4 + c*x^3 + d*x^2 + e*x + f
# 6 logarithmic a*log(x) + b
# 7 exponential a*e^(b*x)
# 8 power/root a*x^b
# 9 reciprocal a/x + b
# 10 rational 1 / (a*x + b)
mReg 103

# 11 exponential 4 Param a*e^(b*(x+c)) + d

Negative values are not used for regressions containing logarithms; with warning.
exp_4par was originally developed for exponential temperature decline in a cup of hot water.

Author(s)
Berry Boessenkool, <[email protected]>, Dec 2012, updated April and Aug 2013, sept 2015

References
Listed here: http://rclickhandbuch.wordpress.com/rpackages

See Also
glm, lm, optim

Examples

set.seed(12)
x <- c(runif(100,0,3), runif(200, 3, 25)) # random from uniform distribution
y <- 12.367*log10(x)+7.603+rnorm(300) # random from normal distribution
plot(x,y, xlim=c(0,40))
mReg(x,y) # warning comes from negative y-values (suppress with quiet=TRUE)

# Formula specification:
mReg(Volume~Height, data=trees)

# NA management
x[3:20] <- NA
mReg(x,y)

# Passing arguments to legend:

mReg(x,y, pch=1, legargs=list(x="bottomright", cex=0.7), legendform="form")

mReg(x,y, col=rainbow2(11))
mReg(x,y, extend=0.2) # less empty space around data points
mReg(x,y, nbest=4) # only 4 distributions plotted
mReg(x,y, legargs=list(x=7, y=8, bty="o", cex=0.6)) # Legend position as coordinates

## Not run: # Excluded from Rcmd check (opening external devices)

View(mReg(x,y, Poly45=TRUE, exp_4=TRUE, plot=FALSE)) # exp_4: fit more distributions

## End(Not run)
# optim methods often yield different results, so be careful using this.
# I might insert a possibility to specify initial values for optim.
# 4 Parameters allow several combinations to yield similarly good results!
plot( 0:10, 3.5*exp(0.8*( 0:10 + 2 )) + 15 , type="l")
lines(0:10, 18*exp(0.8*( 0:10 - 2.5e-05)) - 5, col=2)
104 mReg

# okay, different dataset:

x <- c(1.3, 1.6, 2.1, 2.9, 4.4, 5.7, 6.6, 8.3, 8.6, 9.5)
y <- c(8.6, 7.9, 6.6, 5.6, 4.3, 3.7, 3.2, 2.5, 2.5, 2.2)
mReg(x,y, legargs=list(cex=0.7, x="topright"), main="dangers of extrapolation")
points(x,y, cex=2, lwd=2)
# Polynomial fits are good within the data range, but, in this case obviously,
# be really careful extrapolating! If you know that further data will also be low,
# add another point to test differences:
mReg(c(x,11,13,15), c(y,2,2,2), xf="myX", yf="myY", Poly45=TRUE, legendform="name")
points(x,y, cex=2, lwd=2)
# The Polynomials are still very good: they have 5 to 6 Parameters, after all!
# Poly45 is set to FALSE by default to avoid such overfitting.

mReg(x,y, pcol=8, ncol=0) # no return to console

# only plot a subset: best n fits, minimum fit quality, or user selection
mReg(x,y, pcol=8, ncol=2, nbest=4)
mReg(x,y, pcol=8, ncol=2, R2min=0.7)
mReg(x,y, pcol=8, ncol=2, selection=c(2,5,8))
# selecting the fifth degree polynomial activates Poly45 (in the output table)

# Add to axisting plot:

plot(x,y, xlim=c(0,40))
mReg(x,y, add=TRUE, lwd=12:1/2, ncol=0)
# lwd, lty can be vectors of length 12, specifying each line separately.
# Give those in fix order (see section notes), not in best-fit order of the legend.
# The order is Polynomial(1:5), log, exp, power, reciprocal, rational, exp_4_param
# color has to be a vector of 12
# opposedly, lwd and lty are repeated 12 times, if only one value is given

# One more dataset:

j <- c(5,8,10,9,13,6,2) ; k <- c(567,543,587,601,596,533,512)
# Inset from margin of plot region:
mReg(j,k, legargs=list(x="bottomright", inset=.05, bty="o"), legendform="name")
# Legend forms
mReg(j,k, legargs=list(x="bottomright"), legendform="name")
mReg(j,k, legargs=list(x="bottomright"), legendform="form")
mReg(j,k, legargs=list(x="bottomright"), legendform="nameform")
mReg(j,k, legargs=list(x="bottomright"), legendform="full")

## Not run: # Excluded from Rcmd check (long computing time)

# The question that got me started on this whole function...

# exponential decline of temperature of a mug of hot chocolate
tfile <- system.file("extdata/Temp.txt", package="berryFunctions")
temp <- read.table(tfile, header=TRUE, dec=",")
head(temp)
plot(temp)
temp <- temp[-20,] # missing value - rmse would complain about it

x <- temp$Minuten
y <- temp$Temp
mReg 105

mReg(x,y, exp_4=TRUE, selection=11)

# y=49*e^(-0.031*(x - 0 )) + 25 correct, judged from the model:
# Temp=T0 - Te *exp(k*t) + Te with T0=73.76, Tend=26.21, k=-0.031
# optmethod="Nelder-Mead" # y=52*e^(-0.031*(x + 3.4)) + 26 wrong

x <- seq(1, 1000, 1)

y <- (x+22)/(x+123) # can't find an analytical solution so far. Want to check out nls
mReg(x, y, legargs=list(x="right"))

## End(Not run)

# Solitaire Results. According to en.wikipedia.org/wiki/Klondike_(solitaire):

# Points=700000/Time + Score
# I recorded my results as an excuse to play this game a lot.
sfile <- system.file("extdata/solitaire.txt", package="berryFunctions")
solitaire <- read.table(sfile, header=TRUE)
mReg(solitaire$Time, solitaire$Points) # and yes, reciprocal ranks highest! Play Fast!
mReg(solitaire$Time, solitaire$Bonus, xlim=c(50,200), extend=0, nbest=3)
sol <- unique(na.omit(solitaire[c("Time","Bonus")]))
sol
sol$official <- round(700000/sol$Time/5)*5
mReg(sol$Time, sol$Bonus, extend=0, selection=9, col=rep(4,10), legendform="full")
plot(sol$Time, sol$official-sol$Bonus, type="l")

# multivariate regression should be added, too:

sfile <- system.file("extdata/gelman_equation_search.txt", package="berryFunctions")
mv <- read.table(sfile, header=TRUE)

sfile <- system.file("extdata/mRegProblem.txt", package="berryFunctions")

x <- read.table(sfile, header=TRUE)$x
y <- read.table(sfile, header=TRUE)$y
mReg(x,y, digits=6) # all very equal
x2 <- x-min(x)
mReg(x2,y, digits=6) # Formulas are wrong if digits is too low!!
#mReg(x2,y, legendform="full")

# Zero and NA testing (to be moved to unit testing someday...)

mReg(1:10, rep(0,10))
mReg(1:10, c(rep(0,9),NA))
mReg(1:10, rep(NA,10))
mReg(rep(1,10), 1:10)
mReg(rep(0,10), 1:10)
mReg(c(rep(0,9),NA), 1:10)
mReg(rep(NA,10), 1:10)

mReg(1:10, rep(0,10), quiet=TRUE)

mReg(1:10, c(rep(0,9),NA), quiet=TRUE)
mReg(1:10, rep(NA,10), quiet=TRUE)
mReg(rep(1,10), 1:10, quiet=TRUE)
mReg(rep(0,10), 1:10, quiet=TRUE)
106 na9

mReg(c(rep(0,9),NA), 1:10, quiet=TRUE)

mReg(rep(NA,10), 1:10, quiet=TRUE)

na9 Prepend spaces before na.strings

Description
Returns a number of useful character strings with varying amount of spaces prepended. It can be
used as na.strings=na9() in read.table.

Usage
na9(nspace = 5, base = c(-9999, -999, -9.99, -9.999), sep = c(",", "."),
digits = 0:4, more = NULL, ...)

Arguments
nspace number of spaces prepended. DEFAULT: 5
base Numeric: basic na.string numbers
sep Separator string (comma or decimal point or both). DEFAULT: c(",",".")
digits Number(s) of zeros to be appended. DEFAULT: 0:4
more More structures added to base, like "NA", "–". digits and sep is not added to
this! DEFAULT: NULL
... Arguments passed to nothing currently

Value
Character strings

Author(s)
Berry Boessenkool, <[email protected]>, Jan 2016

See Also
paste

Examples

na9()
na9(nspace=0, sep=".")
na9(nspace=0, sep=".", more=c(NA,"-"))
nameSample 107

nameSample Nonrandom character sequence with sample

Description
Find the seed necessary to produce a character sequence by using sample

Usage
nameSample(name, progress = FALSE, estimatetime = nc > 4,
continue = FALSE)

Arguments
name Character string. long strings (»5) will compute a VERY long time!
progress Logical. Monitor progress by printing a dot every 10000 tries? DEFAULT:
TRUE for long names (nchar(name)>3).
estimatetime Estimate computation time? DEFAULT: nc>4
continue Continue without asking? DEFAULT: FALSE

Value
cats command into the console that can be copypasted to anyone’s R script.

Note
nameSample may take a lot of time, due to nchar^26 possibilities. That’s why it warns about strings
longer than 5 characters

Author(s)
Berry Boessenkool, <[email protected]>, April 2014

See Also
yearSample to wish a happy new year, set.seed, sample, letters

Examples

## Not run in RCMD check as they're very time consuming

## Not run:
nameSample("berry") # After that, you can send the result to colleagues:
# Kind regards from
set.seed(1248272); paste(sample(letters,5,TRUE), collapse='')

# calculation time
# on my slow laptop: # on PC
108 newFilename

system.time(nameSample("berr")) # 25 s # berry: 57 s 10 23
system.time(nameSample("berr", FALSE)) # 23 s 53 s 9 20

# let <- sapply(1:4, function(n) apply(replicate(n, letters[sample(15)]), 1, paste, collapse=""))

# calctime <- sapply(let, function(x) system.time(nameSample(x, progress=F))[3])
# write.table(calctime, "calctime_nameSample.txt")
ctfile <- system.file("extdata/calctime_nameSample.txt", package="berryFunctions")
ctfile2 <- system.file("extdata/calctime_nameSample2.txt", package="berryFunctions")
calctime <- read.table(ctfile)
# regression result in hours:
expReg(nchar(rownames(calctime))-8, calctime[,1], xlim=c(1,7), ylim=c(-3,4),
predict=7)/3600

# For my 3 times faster computer:

calctime <- read.table(ctfile2)
expReg(nchar(rownames(calctime))-8, calctime[,1], xlim=c(1,7), ylim=c(-3,4),
predict=c(4,7))/c(1,3600)
# 4 sec for 4 letters are expected to be 10 hours for 7 letters...

## End(Not run)

newFilename Create new filename if file already exists

Description
Check if files already exist and append _1 or _2, etc to the filename if needed, thereby giving useful
messages.

Usage
newFilename(filename, ignore = FALSE, overwrite = FALSE,
tellignore = TRUE, pre = "", mid = "\n", end = "", quiet = FALSE,
ntrunc = 3)

Arguments
filename Char (vector): file name(s).
ignore Logical (vector, recycled): Ignore file? DEFAULT: FALSE
overwrite Logical (vector, recycled): overwrite file? DEFAULT: FALSE
tellignore Logical: Message about ignored files? DEFAULT: TRUE
pre, mid, end Char: strings to append after traceback / message / filenames. DEFAULT: "",
"\n ", ""
quiet Logical: Suppress messages about creating file(s)? DEFAULT: FALSE
ntrunc Integer: Number of filenames printed in messages before they get truncated with
message "(and xx more)". DEFAULT: 3
normalizePathCP 109

Value
newFilename returns the input with an added "_n" in the filename for each file that already existed.

Author(s)
Berry Boessenkool, <[email protected]>, Oct 2016 + Jan 2017

See Also
file.exists

Examples

fns <- c("dummy1", "dummy2.txt", "berryFunctions.Rproj",

"README.md", "dummy2.dummy", "DESCRIPTION", "dummy4.R", "dummy5")
newFilename(fns)
newFilename(fns, ignore=TRUE)
newFilename(fns, ignore=rep(c(TRUE,FALSE), each=4) )
newFilename(fns, ignore=rep(c(TRUE,FALSE), each=4), tellignore=FALSE)
newFilename(fns, ntrunc=2)
newFilename(fns, overwrite=TRUE, ign=c(TRUE,TRUE,rep(FALSE,6)))
newFilename("README.md")
newFilename("dummy", mid=" ") # no line break

normalizePathCP normalizePath Cross Platform

Description
normalizePath Cross Platform: Returns absolute path even for not (yet) existing files even on
Linux. On Windows, this is the default behaviour.

Usage
normalizePathCP(path, winslash = "/", mustWork = FALSE)

Arguments
path Character vector of file paths
winslash Path separator on Windows. DEFAULT: "/" (unlike normalizePath)
mustWork Logical for normalizePath. DEFAULT: FALSE

Value
path character string(s)
110 normPlot

Author(s)
Berry Boessenkool, <[email protected]>, Nov 2017

See Also
normalizePath, newFilename

Examples

normalizePath ("doesnotexist.file", mustWork=FALSE) # on unix not full path

normalizePathCP("doesnotexist.file") # full path on all platforms

normalizePath ("../doesnotexist.file", mustWork=FALSE)

normalizePathCP("../doesnotexist.file")

checknp <- function(a,b=a,d=getwd())

{
aa <- normalizePathCP(a)
bb <- if(d=="") b else paste0(d,"/",b)
if(aa != bb) stop("'", a, "' -> '", aa, "', should be '",bb, "'.")
aa
}

checknp("notexist.file")
checknp("../notexist.file", "notexist.file", dirname(getwd()))
checknp("notexistfolder/notexist.file")
#checknp("/home/berry/notexist.file", d="") # fails on windows
#checknp("S:/Dropbox/notexist.file",d="") # fails on linux

normPlot Normal density plot

Description
Nice plot of normal density distribution

Usage
normPlot(mean = 0, sd = 1, width = 3, lines = TRUE, quant = TRUE,
fill = addAlpha("blue", c(2:6, 7:2)/10), cumulative = TRUE, las = 1,
main = paste("Normal density with\nmean =", signif(mean, 2), "and sd =",
signif(sd, 2)), ylim = lim0(dnorm(mean, mean, sd)), ylab = "",
xlab = "", type = "n", lty = 1, col = par("fg"), mar = c(2, 3, 3,
3), keeppar = FALSE, ...)
normPlot 111

Arguments
mean average value as in dnorm. DEFAULT: 0
sd standard deviation. DEFAULT: 1
width distance (in sd) from plot ends to mean. DEFAULT: 3
lines Should vertical lines be plotted at mean +- n*sd? DEFAULT: TRUE
quant should quantile regions be drawn with fill colors? DEFAULT: TRUE
fill color(s) passed to polygon. DEFAULT: addAlpha("blue",c(2:6,7:2)/10)
cumulative Should cumulative density distribution be added? DEFAULT: TRUE
las arguments passed to plot. DEFAULT: 1
main main as in plot. DEFAULT: paste("Normal density with\nmean =", mean, "and
sd =", sd)
ylim limit for the y axis. DEFAULT: lim0(y)
ylab, xlab labels for the axes. DEFAULT: ""
type, lty, col arguments passed to lines. type="l" to add pdf line
mar margins for plot passed to par. DEFAULT: c(2,3,3,3)
keeppar should margin parameters be kept instead of being restored to previous value?
DEFAULT: FALSE
... further arguments passed to plot like lwd, xaxs, cex.axis, etc.

Details
This function finds some nice defaults for very quickly plotting a normal distribution by just speci-
fying mean and sd.

Value
None. Used for plotting.

Author(s)
Berry Boessenkool, <[email protected]>, July 2014

See Also
betaPlot, dnorm, https://cran.r-project.org/package=denstrip, https://cran.r-project.
org/view=Distributions

Examples

normPlot()
normPlot(81.7, 11.45)
normPlot(180, 11, quant=FALSE, width=2)
112 openFile

openFile open file in default application

Description
open a file using system2 with command based on operating system. Tries to open the file with the
program associated with its file extension.

Usage
openFile(file, ...)

Arguments
file Filename to be opened, as character string.
... Further arguments passed to system2

Value
Result of try(system2, ...), invisibly

Author(s)
Berry Boessenkool, <[email protected]>, Aug 2017

References
https://askubuntu.com/questions/15354, https://apple.stackexchange.com/questions/
212583

See Also
system2, checkFile

Examples
## Not run: # excluded from CRAN checks, file opening not wanted
openFile("README.md")
openFile("Tests.R")
openFile("dummydummydoesntexist.R")
openFile(tempdir())

## End(Not run)
#' # To open folders with system2:
# "nautilus" on linux ubuntu
# "open" or "dolphin" on mac
# "explorer" or "start" on windows
owa 113

owa Overwrite argument default lists

Description

Second ellipsis (three dots) passed to particular functions, combining default and user-specified ar-
gument lists.
owa can be used in functions that pass argument lists separately to several functions. Internal de-
faults can be set per function (eg. one list for plot and one for legend).
You can specify which defaults can be overwritten and which should be left unchanged. See the
example section on how to implement this.

Usage

owa(d, a, ..., quiet = FALSE)

Arguments

d Default arguments (list or vector)

a Arguments specified by user (list or vector). Can also be a single TRUE, in
which case d will be returned.
... Names of unchangeable arguments (that will not be overwritten) as character
strings. Can also be a vector with characters strings.
quiet Logical: Should message be suppressed if arguments are ignored? If FALSE
(the DEFAULT), this helps users debugging, as they get notified when arguments
they specified were ignored.

Value

Always a list, disregarding list/vector mode of input

Author(s)

Berry Boessenkool, <[email protected]>, Early 2014, Update Oct 2016

References

http://stackoverflow.com/questions/3057341
http://stackoverflow.com/questions/5890576
http://stackoverflow.com/questions/4124900
http://stackoverflow.com/questions/16774946
114 packagePath

Examples
# The motivation behind owa:
testfun <- function(...) {plot(7:11, ...) ; legend("top", "some text", ...)}
testfun()
is.error( testfun(type="o") , tell=TRUE)
# Error: legend doesn't have the argument 'type'!

# How to solve this:

testfun <- function(legargs=NULL, ...) # dots passed to plot
{
plot(7:11, ...)
legend_defaults <- list(x="top", lty=1, col="red", legend="owa rocks!")
# combine defaults and user specified into final argument list,
# overwrite arguments ('owa') in the default list unless protected:
legend_final <- owa(d=legend_defaults, a=legargs, "col", "lwd")
do.call(legend, args=legend_final)
}

testfun()
testfun(type="l", col="blue")
testfun(type="o", legargs=list(col="blue", pch=16, lty=3) )
# color in legargs is ignored, as it is defined as unchangeable

#----------------------------------------------------------------------------

# basic tests of owa itself:

d <- list(bb=1:5, lwd="was d", lty=1, col="gray")
a <- list(bb=3, lwd=5, lty="from a", wachs="A")
owa(d,a) # all changed, wachs added
owa(d, a, "bb", "lwd") # lty is overwritten, bb and lwd are ignored
owa(d, NULL, "bb", "wachs") # NULL is a good default for argument lists
owa(d, c(HH=2, BBB=3) ) # vectors and lists are all converted to lists
owa(d, list(lwd=5, bb=3, lty="1") ) # order of arguments doesn't matter
owa(d, a, c("bb","lwd") ) # unchangeable can also be a named vector
owa(d, a, c("bb","lwd"), c("lty","dummy") ) # or several vectors

packagePath Base path of package

Description
Base path of package (with DESCRIPTION file), per default at current getwd. Derived from dev-
tools::package_file

Usage
packagePath(path = ".", warnonly = FALSE)
panelDim 115

Arguments
path Path to (or below) package directory. DEFAULT: "."
warnonly Logical: if no part of the path is a package, give a warning and return the original
input instead of stopping with an error. DEFAULT: FALSE

Value
Path character string

Author(s)
Berry Boessenkool, <[email protected]>, Sep 2017

See Also
getwd

Examples
# packagePath() # may fail on cran checks

panelDim Arrange panels in a multipanel plot (par mfrow)

Description
Returns the optimum where deviation from ncol=nrow and number of panels left empty have a
minimum sum.

Usage
panelDim(n, weight = c(1, 1), maxempty = round(n/4), landscape = FALSE,
all = FALSE, plot = FALSE, mfcol = FALSE)

Arguments
n Number of panels to be arranged
weight Weights to avoid empty panels and discrepancy between ncol and nrow, respec-
tively. DEFAULT: c(1,1)
maxempty Maximum number of panels that are allowed to be left empty. If maxempty=0,
no panel is left blank, so 11 plots would be beneath each other instead of in a
4x3 grid with one panel left blank. DEFAULT: round(n/4)
landscape Use landscape orientation instead of portrait? DEFAULT: FALSE
all Show all reasonable possibilities in a data.frame? DEFAULT: FALSE
plot Show the panel layout result? (the 4 best options are compared if all=TRUE).
DEFAULT: FALSE
mfcol use mfcol instead of mfrow. DEFAULT: FALSE
116 panelDim

Details
There probably are other ways to find the optimal way to arrange panels, so if you find anything,
please give me a hint.

Value
vector with 2 values, can be passed to par(mfrow), or a data.frame if all=TRUE.

Author(s)
Berry Boessenkool, <[email protected]>, Dec 2014, Jan 2015

See Also
groupHist, which is using this function

Examples

# basic usage
op <- par(mfrow=panelDim(6))
for(i in 1:6) plot(i:10, main=i)
par(op)

# Adcanced options
panelDim(7)
g <- panelDim(7, all=TRUE)
panelDim(7, plot=TRUE)
panelDim(7, plot=TRUE, all=TRUE) # compares 4 best options

panelDim(26, all=TRUE)
panelDim(26, plot=TRUE, all=TRUE) # compares 4 best options
panelDim(26, plot=TRUE, all=TRUE, weight=c(3,0) ) # fewer empty panels

# effect of maxempty:
panelDim(13, plot=TRUE) # 4 x 4
panelDim(13, maxempty=2, plot=TRUE) # 5 x 3
panelDim(13, maxempty=1, plot=TRUE) # 7 x 2
panelDim(13, maxempty=0, plot=TRUE) # 13 x 1

panelDim(45, plot=TRUE) # no empty panels

# focus on aspect ratio of each panel (make it as square as possible):
panelDim(45, weight=c(1,3), plot=TRUE) # better aspect for each panel

# Orientation of plot:
panelDim(45, plot=TRUE) # good for portrait orientation of plot
panelDim(45, landscape=TRUE, plot=TRUE) # better if plot width > height

## Not run:
## Rcmd check --as-cran doesn't like to open external devices,
## so this example is excluded from running in the checks.
plot of several n with defaults
parallelCode 117

dev.new(record=TRUE)
for(i in 1:50) panelDim(i, plot=TRUE)

## End(Not run)

parallelCode code chunk for parallelization

Description
message a code chunk template for parallelization with progress bar on windows. On Linux, just
use pblapply(X, cl=8, FUN=fun)

Usage
parallelCode()

Author(s)
Berry Boessenkool, <[email protected]>, Aug 2017

Examples
parallelCode()

pdfpng Create pdf and png graph

Description
Create both a pdf and a png file with a graph, with custom size default values. To iteratively create
pdfs without closing and reopening the pdf viewer, you might want to use e.g. Sumatra, which
comes with Rstudio. It can be found e.g. in C:/Program Files/RStudio/bin/sumatra

Usage
pdfpng(expr, file, pdf = TRUE, png = TRUE, overwrite = FALSE,
open = TRUE, quiet = FALSE, tracewarnmes = !quiet, filargs = NULL,
width = 7, height = 5, units = "in", res = 500, seed = runif(1,
-1e+09, 1e+09), envlevel = 1, pdfargs = NULL, pngargs = NULL, ...)
118 pdfpng

Arguments
expr Expression creating the plot, can be included in curly braces.
file Character: Filename without pdf/png extension. Unless overwrite=TRUE, files
will not be overwritten, but "_1" will be appended instead, see newFilename. If
expr creates several plots, use file="fname%02d", otherwise the png will only
contain the last figure. Note: this overwrites files as the % notation is not cap-
tured by newFilename. You may also have to run dev.off().
pdf Logical: Create pdf? DEFAULT: TRUE
png Logical: Create png? DEFAULT: TRUE
overwrite Logical: Overwrite existing file? Can be a vector for pdf and png separately.
DEFAULT: FALSE (_n appended in filename)
open Logical: open file(s) after creation using openFile? DEFAULT: TRUE
quiet Logical: suppress file creation messages and expr execution error tracing? DE-
FAULT: FALSE
tracewarnmes Logical: trace warnings and messages in expr execution? Errors are always
traced. Default: !quiet
filargs List of other arguments passed to newFilename. DEFAULT: NULL
width, height Graph dimensions. DEFAULT: 7x5 inches
units, res Graph quality arguments passed only to png. DEFAULT: inches ("in"), 500 ppi
seed Seed passed to set.seed before each call. DEFAULT: runif(1,-1e9,1e9)
envlevel Environment level passed to eval.parent. Never needs to be changed, as far
as I can tell. DEFAULT: 1
pdfargs List of arguments only passed to pdf.
pngargs List of arguments only passed to png.
... Further arguments passed to both pdf and png

Value
Nothing

Author(s)
Berry Boessenkool, <[email protected]>, March 2017

See Also
pdf, png

Examples

## Not run: # excluded from CRAN checks, file opening not wanted
pdfpng( plot(rnorm(500), type="l") , file="dummyplot", png=FALSE)

## End(Not run)
popleaf 119

pdfpng({par(bg=8, las=1); plot(cumsum(rnorm(500)), type="l")},

file="dummyplot", res=100, open=FALSE)
pdfpng({par(bg=8, las=1); plot(cumsum(rnorm(500)), type="l")},
file="dummyplot", overwrite=c(TRUE,FALSE), open=FALSE)

# Nesting of functions is possible:

a <- list( cumsum(rnorm(2000)), cumsum(rnorm(20)) )
pdfpng(plot(a[[1]]), file="dummyplot", overwrite=TRUE, open=FALSE)
bfun <- function(b) pdfpng(plot(b,type="l"), file="dummyplot",
overwrite=TRUE, open=FALSE)
cfun <- function(c) bfun(c)
bfun(a[[1]])
sapply(a, function(d) cfun(d))

pdfpng(plot(-10:100, log="y"), "dummyplot",overwr=TRUE,png=FALSE, open=FALSE)

pdfpng({plot(1); plot(dummyobject)}, "dummyplot", overwrite=TRUE,
png=FALSE, open=FALSE)

unlink("dummyplot.pdf") ; unlink("dummyplot.png") ; unlink("dummyplot_1.png")

popleaf create leaflet popup box info

Description
combine data.frame columns into a leaflet popup-box compatible format

Usage
popleaf(df, sel = colnames(df))

Arguments
df Data.frame
sel Columns to be selected (Names or index or TRUE/FALSE vector). DEFAULT:
colnames(df)

Value
Vector with character strings

Author(s)
Berry Boessenkool, <[email protected]>, Apr 2017
120 pretty2

See Also
paste

Examples
dat <- data.frame(a=14:16, b=letters[14:16], c=LETTERS[14:16],
lat=c(52.58,53.45,52.4), lon=c(6.34,7.23,13.05))
popleaf(dat)
dat$display <- popleaf(dat, 1:4)

## Not run: # Excluded from CRAN checks

library(leaflet)
leaflet(dat) %>% addTiles() %>% addCircleMarkers(~lon, ~lat, popup=~display)

## End(Not run)

pretty2 Truncated pretty breakpoints

Description
pretty with no values outside of x range

Usage
pretty2(x, n = 5, force = FALSE, ...)

Arguments
x object with numeric values
n desired number of values in pretty. DEFAULT: 5
force Must output length equal n exactly? DEFAULT: FALSE
... all other arguments in pretty.

Details
calculates pretty(x), then removes the values that do not lie within range(x).
If force=TRUE, range(x) is reduced step by step in a while loop until the condition is met. This is
useful if you want exactly 2 labels on an axis. In order not to get stuck, the outer values are taken
if there are more than n values within range(x).

Author(s)
Berry Boessenkool, <[email protected]>, Aug 2014
quantileBands 121

See Also
pretty , logVals

Examples

k <- c(135, 155, 120, 105, 140, 130, 190, 110)

range(k)
pretty(k)
pretty2(k)

pretty(c(0.2, 0.9), n=2)

pretty2(c(0.2, 0.9), n=2)
pretty2(c(0.2, 0.9), n=2, force=TRUE)

quantileBands Quantile bands

Description
Quantile bands with optional smoothing, e.g. for visualizing simulations

Usage
quantileBands(mat, x = 1:ncol(mat), col = rgb(0, 0, 1, alpha = c(0.5, 0.7)),
add = FALSE, main = "Quantile Bands", ylab = "", xlab = "",
probs = 0:4/4, na.rm = FALSE, type = 7, smooth = NA, medargs = NULL,
meanargs = NULL, txi, textargs = NULL, ...)

Arguments
mat Matrix or data.frame with columns of data
x X-axis positions for each column. DEFAULT: 1:ncol(mat)
col Vector of colors for each quantile group, recycled reversely if necessary. DE-
FAULT: rgb(0,0,1, alpha=c(0.5, 0.7))
add Add to existing plot? Allows to add to highly customized plot. DEFAULT:
FALSE
main, xlab, ylab
plot labels. DEFAULT: "Quantile Bands", ""
probs Probabilities passed to quantile. DEFAULT: 0:4/4
na.rm Remove NAs before computing quantiles, median and mean? DEFAULT:
FALSE
type Which of the 9 quantile algorithms should be used. DEFAULT: 7
smooth If(!is.na), width passed to movAv smoothing quantiles. DEFAULT: NA
122 quantileBands

medargs List of arguments passed to lines drawing median. Not drawn if NULL. DE-
FAULT: NULL
meanargs List of arguments passed to lines drawing mean. Not drawn if NULL. DE-
FAULT: NULL
txi Text x position index (along columns of mat), recycled if necessary. NA to
suppress. INTERNAL DEFAULT: middle of the plot for all.
textargs List of arguments passed to text, like col, adj, ... DEFAULT: NULL
... Further arguments passed to polygon, like border, lty, ...

Value
Quantiles of each column, invisible. Smoothed if smooth is given!

Note
This is the first version and is not tested very well yet.

Author(s)
Berry Boessenkool, <[email protected]>, Sept 2014

See Also
quantile, quantileMean, ciBand, polygon, https://cran.r-project.org/package=fanplot

Examples

neff <- t(replicate(n=30, sapply(1:400, function(nn) max(rnorm(nn))) ))

qB <- quantileBands(neff, x=1:400)
qB[,1:9]
quantileBands(neff, smooth=19, meanargs=list(col=2), txi=NA)

library(RColorBrewer)

quantileBands(neff, smooth=35, ylab="max of rnorm(n)",

xlab="sample size (n)", probs=0:10/10, col=brewer.pal(5,"BuGn"),
medargs=list(lwd=2), meanargs=list(col=2, lty=1), txi=c(40,50,60),
main="Maximum is an unsaturated statistic:\n it rises with sample size")

neff2 <- t(replicate(n=50, sapply(1:400, function(nn) mean(rnorm(nn))) ))

quantileBands(neff2, x=1:400, smooth=35, ylab="mean of rnorm(n)",
xlab="sample size (n)", probs=0:10/10, col=brewer.pal(5,"BuGn"),
txi=c(40,50,60), textargs=list(col="yellow"), medargs=list(lwd=2),
meanargs=list(col=2, lty=1), main="Mean converges to true population mean")
quantileMean 123

quantileMean Average of R’s quantile methods

Description
Weighted average of R’s quantile methods

Usage
quantileMean(x, probs = seq(0, 1, 0.25), weights = rep(1, 9),
names = TRUE, truncate = 0, ...)

Arguments
x Numeric vector whose sample quantiles are wanted
probs Numeric vector of probabilities with values in [0,1]. DEFAULT: seq(0, 1, 0.25)
weights Numeric vector of length 9 with weight for each quantile method. Recycled
if shorter. DEFAULT: unweighted mean. DEFAULT: rep(1,9)
names If TRUE, the resulting vector has a names attribute. DEFAULT: TRUE
truncate Number between 0 and 1. Censored quantile: fit to highest values only (truncate
lower proportion of x). Probabilities are adjusted accordingly. DEFAULT: 0
... further arguments passed to quantile, except for type

Details
weights are internally normalized to sum 1

Value
numeric named vector, as returned by apply

Author(s)
Berry Boessenkool, <[email protected]>, Sept 2014

See Also
quantile

Examples

exDat <- rnorm(30,sd=5)

quantile(exDat, probs=c(0.9, 0.99), type=1)
quantile(exDat, probs=c(0.9, 0.99), type=2)
round( sapply(1:9, function(m) quantile(exDat, probs=0.9, type=m)) , 3)
# and now the unweighted average:
124 quantileMean

quantileMean(exDat, probs=c(0.9, 0.99))

quantileMean(exDat, probs=0.9)
# say I trust type 2 and 3 especially and want to add a touch of 7:
quantileMean(exDat, probs=c(0.9, 0.99), weights=c(1,5,5,0,1,1,3,1,1))

# quantile sample size dependency simulation:

qbeta(p=0.999, 2, 9) # dist with Q99.9% = 0.62
betaPlot(2, 9, cumulative=FALSE)
abline(v=qbeta(p=0.999, 2, 9), col=6, lwd=3)
qm <- function(size) quantileMean(rbeta(size, 2,9), probs=0.999, names=FALSE)
n30 <- replicate(n=500, expr=qm(30))
n1000 <- replicate(n=500, expr=qm(1000))
lines(density(n30)) # with small sample size, high quantiles are systematically
lines(density(n1000), col=3) # underestimated. for Q0.999, n must be > 1000

## Not run:
# #Excluded from CRAN Checks because of the long computing time
# median of 500 simulations:
qmm <- function(size, truncate=0) median(replicate(n=500,
expr=quantileMean(rbeta(size, 2,9), probs=0.999, names=FALSE, truncate=truncate)))

n <- seq(10, 1000, length=30)

medians <- sapply(n, qmm) # medians of regular quantile average
plot(n, medians, type="l", las=1)
abline(h=qbeta(p=0.999, 2, 9), col=6) # real value
# with truncation:
medians_trunc <- sapply(n, qmm, truncate=0.8) # only top 20% used for quantile estimation
lines(n, medians_trunc, col=2) # censored quantiles don't help!
# In small samples, rare high values do not occur on average

# Parametrical quantiles can avoid sample size dependency!

if(!require(devtools)) install.packages("devtools")
devtools::install_github("brry/extremeStat")
library("extremeStat")
library2("pbapply")

distLquantile(rbeta(1000, 2,9), probs=0.999, plot=TRUE, nbest=10) # 10 distribution functions

distLquantile(rbeta(1000, 2,9), probs=0.999, plot=TRUE, nbest=10) # that seem to work well
select <- c("wei","wak","pe3","ln3","kap","gno","gev","gum","gpa","gam")

pqmm <- function(size, truncate=0, plot=FALSE) median(replicate(n=50,

expr=mean(distLquantile(rbeta(size, 2,9), probs=0.999, type=select,
plot=plot, nbest=10, progbars=FALSE, time=FALSE, truncate=truncate))))

#dev.new(record=TRUE)
#pqmm(30, plot=TRUE)

# medians of parametrical quantile estimation

###suppressMessages(pmedians <- pbsapply(n, pqmm) ) # takes several minutes
write.table(pmedians, file="../inst/extdata/pmedians.txt", row.names=FALSE, col.names=FALSE)
pmedians <- read.table("../inst/extdata/pmedians.txt")[,1]
rainbow2 125

plot(n, medians, type="l", ylim=c(0.4, 0.7), las=1)

abline(h=qbeta(p=0.999, 2, 9), col=6) # real value
lines(n, medians_trunc, col=2) # censored quantiles don't help!
lines(n, pmedians, col=4) # overestimated, but not dependent on n
# with truncation, only top 20% used for quantile estimation
suppressMessages(pmedians_trunc <- pbsapply(n[-1], pqmm, truncate=0.8))
lines(n[-1], pmedians_trunc, col=6) # much better!
# Good for this beta distribution. I don't know how it scales to other dists.

## End(Not run)

rainbow2 Rainbow from blue to red

Description
Reversed rainbow with different defaults, resulting in a color vector from blue (good) to red (bad)

Usage
rainbow2(n = 10, s = 1, v = 1, start = 0, end = 0.7, alpha = 1)

Arguments
n number of colors. DEFAULT: 10
s, v saturation and value as in rainbow. DEFAULT: 1
start start color. DEFAULT: 0
end end color. DEFAULT: 0.7
alpha transparency. DEFAULT: 1)

Value
A character vector of color names.

Author(s)
Berry Boessenkool, <[email protected]>, Sept 2014

See Also
seqPal for a better palette, rainbow

Examples

plot(1:10, pch=16, cex=2, col=rainbow2(10))

126 removeSpace

removeSpace Remove white spaces from strings

Description
Remove leading and/or trailing white space from character strings

Usage
removeSpace(x, begin = TRUE, end = TRUE, all = FALSE, ...)

Arguments
x Character string, can be a vector
begin Logical. Remove leading spaces at the beginning of the character string? DE-
FAULT: TRUE
end Logical. Remove trailing spaces at the end? DEFAULT: TRUE
all Logical. Remove all spaces anywhere in the string? DEFAULT: FALSE
... Further arguments passed to sub or gsub, like ignore.case, perl, fixed, useBytes.

Value
Character string (vector)

Note
If all arguments are FALSE, the string is returned unchanged.
Not extensively tested yet, please mail me any problems...

Author(s)
Berry Boessenkool, <[email protected]>, Dec 2014

See Also
sub

Examples

s <- c("space at end ", " white at begin", " both ", " special ^ ")
removeSpace(s)

# To add space, use:

x <- c("ab","abcde")
format(x)
format(x, justify="centre")
format(x, width=9)
rescale 127

rescale shift and scale a vector

Description
rescale a numeric vector: map values linearly onto a given range

Usage
rescale(x, from = 0, to = 1)

Arguments
x Numerical vector of values to be mapped to a given range
from output minimum. DEFAULT: 0
to output maximum. DEFAULT: 1

Value
numeric vector, rescaled onto output range

Author(s)
Berry Boessenkool, <[email protected]>, Jan 2016

References
http://stackoverflow.com/a/18303620

See Also
scales::rescale

Examples

rescale(10:15, 135, 200)

rescale(10:15, 200, 135)
rescale(10:15, to=c(1,5))

values <- rbeta(1e3, shape1=4, shape2=35)

hist(rescale(values, 135, 200), breaks=25, col=3)
128 round0

round0 Round numbers with leading and trailing zeros

Description
Round numbers and add leading + trailing zeros

Usage
round0(x, digits = 0, pre = 2, width = digits + pre + ifelse(digits == 0,
0, 1), flag = 0, ...)

Arguments
x Value(s)
digits Number of digits (after decimal separator) to keep. DEFAULT: 0
pre Minimum number of characters before the decimal separator. DEFAULT: 2
width Total width (number of characters including dot). DEFAULT: digits+pre (+1 if
needed)
flag Flag. Could be "" for spaces. DEFAULT: "0"
... Further arguments passed to formatC, except for "format".

Value
Character string vector

Author(s)
Berry Boessenkool, <[email protected]>, Jun 2017

See Also
formatC, sprintf

Examples
round0( pi*10^(-3:5), 2)
stopifnot(round0(17.3, 2) == "17.30")
round0(7.3)
round0(c(7.3,777.1234), 2)
round0(c(0.2,7.3,12.8), 2, pre=1)
round0(c(0.2,7.3,12.8), 1, pre=3, flag="") # spaces instead of zeros
roundedRect 129

roundedRect Rectangles with rounded corners

Description
Draw rectangles with rounded corners via polygon

Usage
roundedRect(xleft, ybottom, xright, ytop, rounding = 0.25, bothsame = TRUE,
aspcorrect = bothsame, devcorrect = bothsame, corfactor = 1.3,
factorpoints = FALSE, corners = 1:4, npoints = 200, plot = TRUE, ...)

Arguments
xleft, ybottom, xright, ytop
Single numbers with the outer end locations of the rectangle.
rounding Proportion of the box to round. Recommended to be between 0 and 1. DE-
FAULT: 0.25
bothsame Set the visual amount of rounding to the same in both x and y direction? If
TRUE (the default), the proportion relates to the shortest rectangle side. This is
visually correct only if aspcorrect and devcorrect are both left at TRUE and
corfactor is set correctly. bothsame DEFAULT: TRUE
aspcorrect Correct for graph aspect ratio? DEFAULT: bothsame
devcorrect Correct for device aspect ratio? DEFAULT: bothsame
corfactor Aspect correction factor. I found this by trial and error. More elegant solutions
are welcome! DEFAULT 1.3, works well for 7x5 (width x height) graphs
factorpoints Logical: plot points at inset locations to determine the exact value for corfactor
by measuring on screen. DEFAULT: FALSE
corners Vector with integers indicating which corners to round. Starting bottom left,
going clockwise. Zero to suppress rounding. DEFAULT: 1:4
npoints Total number of vertices for the corners. DEFAULT: 200
plot Logical. Plot the polygon? FALSE to only compute coordinates. DEFAULT:
TRUE
... Further arguments passed to polygon, like col, border, ...

Value
Final coordinates, invisible

Author(s)
Berry Boessenkool, <[email protected]>, Dec 2017
130 runAxis

See Also
textField

Examples
plot(1:10) ; rect(4,2,7,8, border=8)
roundedRect(4,2,7,8, rounding=0.1)
roundedRect(4,2,7,8, rounding=0.25) # default
roundedRect(4,2,7,8, rounding=0.5)
roundedRect(4,2,7,8, rounding=-0.1, border="red")
roundedRect(4,2,7,8, rounding=1.1, border="blue")
roundedRect(2,2,8,4, rounding=0.5) # in long boxes, 0.5 is max
roundedRect(2,2,8,4, rounding=0.5, bothsame=FALSE, corfactor=1, border=3)

plot(1:10) ; rect(4,2,7,8, border=8)

roundedRect(4,2,7,8, corners=c(2,4))

plot(1:10, asp=1) ; rect(4,2,7,8, border=8)

roundedRect(4,2,7,8)
roundedRect(4,2,7,8, aspcorrect=FALSE, border="red") # results depend on asp

plot(1:10, asp=1.5) ; rect(4,2,7,8, border=8)

roundedRect(4,2,7,8)
roundedRect(4,2,7,8, aspcorrect=FALSE, border="red") # results depend on asp

plot(1:10, asp=1) ; rect(4,2,7,8, border=8)

roundedRect(4,2,7,8) # difference only visible if rect is clearly not a square:
roundedRect(4,2,7,8, bothsame=FALSE, border="red")
roundedRect(4,2,7,8, bothsame=FALSE, aspcorrect=TRUE, border="blue")

## Not run: # aspect correction factor determination

rrtest <- function(...) roundedRect(10,0.5, 35,15, border=2, factorpoints=TRUE)
pdfpng({plot(1:40 ); rrtest();
plot(1:40, ylim=c(0,15) ); rrtest();
plot(1:40, ylim=c(0,15), asp=1); rrtest();
roundedRect(2,0, 8,15, factorpoints=TRUE);
roundedRect(15,10, 25,16, npoints=200)},
file="dummytest", png=F, overwrite=T)

## End(Not run)

runAxis Label axis with typical running times

Description
Label a numerical axis (in minutes) with time units that are typical for running times (10 sec inter-
vals)
seasonality 131

Usage
runAxis(t = 3 * 60, int1 = 10, int2 = 5, side = 1, linarg = NULL, ...)

Arguments
t Maximum time in minutes
int1 Primary interval (for labels)
int2 Secondary interval (for lines)
side Side of the plot to draw axis (1,2,3,4 = bottom, left, top, right)
linarg List of arguments passed to abline
... Further arguments passed to axis

Value
List with the positions and labels

Author(s)
Berry Boessenkool, <[email protected]>, Jun 2016

See Also
logAxis, monthAxis

Examples
plot(1:200, xaxt="n")
runAxis(t=200, int1=20, int2=10)

seasonality Seasonality analysis

Description
Examine time series for seasonality of high (low) values

Usage
seasonality(dates, values, data, drange = NA, vrange = NA, shift = 0,
janline = TRUE, hlines = FALSE, nmax = 0, maxargs = NULL, plot = 1,
add = FALSE, nmin = 100, probs = c(0, 25, 50, 75, 95, 99.9)/100,
width = 3, text = TRUE, texti = seq(200, 20, length.out =
length(probs)), textargs = NULL, months = substr(month.abb, 1, 1),
slab = "Month", tlab = "Year", vlab = NA, xlim = NA, ylim = NA,
xaxs = NA, yaxs = NA, main = "Seasonality", adj = 0.2, mar = c(3, 3,
4, 1), mgp = c(1.7, 0.7, 0), keeppar = TRUE, legend = TRUE,
legargs = NULL, returnall = FALSE, quiet = FALSE, ...)
132 seasonality

Arguments
dates Dates in ascending order. Can be character strings or strptime results, as ac-
cepted (and coerced) by as.Date
values Values to be mapped in color with colPoints
data Optional: data.frame with the column names as given by dates and values
drange Optional date range (analogous to xlim), can be a vector like dates. Can also be
numerical years, in which case "-01-01" is appended. DEFAULT: NA (computed
from dates internally)
vrange Optional value range (analogous to ylim), can be a vector like values. DE-
FAULT: NA (computed from values internally)
shift Number of days to move the year-break to. E.g. shift=61 for German hydrolog-
ical year (Nov to Oct). DEFAULT: 0
janline Logical: Should horizontal line be plotted at January 1st if shift!=0? DE-
FAULT: TRUE
hlines Draw horizontal background lines in plot 1? Either FALSE (the default), TRUE
to draw gray background lines at each month start, or a list of arguments passed
to abline with owa. DEFAULT: FALSE
nmax Number of annual maxima to be marked, plotted and returned. Currently, only
0 and 1 are implemented. DEFAULT: 0
maxargs List of arguments passed to lines for annual maxima, e.g. maxargs=list(type="l", col="red", lty=
DEFAULT: NULL (several internal defaults are used, but can be overridden)
plot Integer specifying the type of plot. Can be a vector to produce several plots.
0: none, only return the data.frame with annual maxima.
1: color coded doy (day of the year) over year (the default).
2: Color coded spiral graph with spiralDate.
3: Spaghetti line plot with discharge over doy, one line per year.
4: probs quantileMean over doy, with optional aggregation window (width)
around each doy.
5: Annmax over time for crude trend analysis.
DEFAULT: 1
add Logical. Add to existing plot? DEFAULT: FALSE
nmin Minimum number of values that must be present per (hydrological) year to be
plotted in plot type 5. DEFAULT: 100
probs Probabilities passed to quantileMean for plot=4. DEFAULT: c(0,25,50,75,95,99)/100
width Numeric: window width for plot=4. Used as sd in gaussian weighting. Support
(number of values around a DOY passed to quantile function at least once) is
ca 4.9*width. The value at doy itself is used 10 times. Larger values of width
require more computing time. DEFAULT: 3
text Logical. Call textField if plot=4? DEFAULT: TRUE
texti Numerical (vector): indices at which to label the lines. DEFAULT: seq(200,20,length.out=length(probs))
textargs List of arguments passed to textField for plot=4. DEFAULT: NULL
months Labels for the months. DEFAULT: J,F,M,A,M,J,J,A,S,O,N,D
seasonality 133

slab, tlab, vlab

Labels for the season, time (year) and values used on the axes and title of
colPointsLegend. DEFAULT: "Month", "Year", substitute(values)
xlim, ylim Limits of x and y axis. DEFAULT: NA (specified internally per plot type)
xaxs, yaxs x and y Axis style, see par. Use "r" for regular 4% expansion, "i" for in range
only. DEFAULT: NA (specified internally per plot type)
main, adj Graph title and offset to the left (adj passed to title). DEFAULT: "Seasonal-
ity", 0.2
mar, mgp Parameters specifying plot margin size and labels placement. DEFAULT: c(3,3,4,1),
c(1.7,0.7,0) (Changed for plot 3:5 if not given)
keeppar Logical: Keep the margin parameters? If FALSE, they are reset to the previous
values. DEFAULT: TRUE
legend Logical. Should a legend be drawn? DEFAULT: TRUE
legargs List of arguments passed as legargs to colPoints. DEFAULT: NULL (inter-
nally, plots 3 and 5 have density=F as default)
returnall Logical: return all relevant output as a list instead of only annmax data.frame?
DEFAULT: FALSE
quiet Logical: suppress progress stuff and colPoints messages? DEFAULT: FALSE
... Further arguments passed to colPoints like pch, main, xaxs, but not Range (use
vrange). Passed to spiralDate if plot=2, like add, format, lines.

Value
The output is always invisible, don’t forget to assign it. If returnall=FALSE: Data.frame with year,
number of nonNA entries, max value + doy of annual maxima. Please note that the column year
does not match the calendrical year if shift!=0.
if returnall=TRUE: a list with annmax (df from above) as well as:
data: data.frame(doy, values, year) and optionally:
plot1, plot3, plot4, plot5: outputs from colPoints
plot2: output list from spiralDate
and other elements depending on plot type, like data3, data4, probs4, width4.

Author(s)
Berry Boessenkool, <[email protected]>, Jul-Oct 2016

See Also
spiralDate, colPoints, https://waterdata.usgs.gov/nwis

Examples
# browseURL("http://nrfa.ceh.ac.uk/data/station/meanflow/39072")
qfile <- system.file("extdata/discharge39072.csv", package="berryFunctions")
Q <- read.table(qfile, skip=19, header=TRUE, sep=",", fill=TRUE)[,1:2]
rm(qfile)
colnames(Q) <- c("date","discharge")
134 seqPal

Q$date <- as.Date(Q$date)

Q$discharge[450:581] <- NA
plot(Q, type="l")
seas <- seasonality(date, discharge, data=Q, shift=100, main="NRFA: Thames\nRoyal Windsor Park")
head(seas)
# notice how n for nonmissing values is lower in the first hydrological year,
# which includes parts of two consecutive calendarical years.

# Be careful with your interpretation. This looks normal up to 2007, but then BAM!:
seasonality(date, discharge, data=Q[Q$date<as.Date("2007-07-15"),], plot=3, shift=100, nmax=1)
seasonality(date, discharge, data=Q[Q$date<as.Date("2007-08-15"),], plot=3, shift=100, nmax=1)

# Shift is important. You don't want to have this event included twice:
seasonality(date, discharge, data=Q[850:950,], plot=3, nmax=1, quiet=TRUE, shift=100)

## Not run: # excluded from CRAN checks because it is slow

seasonality(date, discharge, data=Q, plot=2) # most floods in winter
seasonality(date, discharge, data=Q, plot=5, vlab="Dude, look at annual max Q!")
seasonality(date, discharge, data=Q, plot=5, shift=100)
s <- seasonality(date, discharge, data=Q, plot=4, shift=100, width=3, returnall=TRUE)
str(s, max.lev=1)

seasonality(date, discharge, data=Q, plot=3:4, add=0:1, ylim=lim0(400), shift=117)

seasonality(date, discharge, data=Q, plot=4, add=TRUE, lwd=3, shift=117, width=3)

## End(Not run)

## Not run:
dev.new(noRStudioGD=TRUE, record=TRUE) # large graph on 2nd monitor
par(mfrow=c(2,2))
seasonality(date, discharge, data=Q, plot=(1:5)[-4], shift=100)
seasonality(date, discharge, data=Q, plot=(1:5)[-4], lwd=2)
seasonality(date, discharge, data=Q, plot=(1:5)[-4], nmax=1, shift=100)
seasonality(date, discharge, data=Q, plot=(1:5)[-4], col=divPal(100, ryb=TRUE))
dev.off()

## End(Not run)

seqPal Sequential color palette

Description
Sequential color palette from yellow to red or yellow to blue or custom colors.

Usage
seqPal(n = 12, reverse = FALSE, alpha = 1, extr = FALSE, yb = FALSE,
yr = FALSE, gb = FALSE, b = FALSE, colors = NULL, logbase = 1, ...)
seqPal 135

Arguments
n Number of colors. DEFAULT: 12
reverse Reverse colors? DEFAULT: FALSE
alpha Transparency (0=transparent, 1=fully colored). DEFAULT: 1
extr Should colors span possible range more extremely? If TRUE, it has very light
yellow and very dark blue values included, using the result from RColorBrewer::brewer.pal(9, "YlGnB
DEFAULT: FALSE
yb Should colors be in yellow-blue instead of the internal (nice) default? DE-
FAULT: FALSE
yr Should colors be in yellow-red instead of the default? DEFAULT: FALSE
gb Should colors be in green-blue instead of the default? DEFAULT: FALSE
b Should colors be in an increasingly saturated blue? DEFAULT: FALSE
colors If not NULL, a color vector used in colorRampPalette. DEFAULT: NULL
logbase If !=1, this is passed to classify and logSpaced. DEFAULT: 1
... Further arguments passed to colorRamp

Value
Character string vector with color names

Author(s)
Berry Boessenkool, <[email protected]>, Jan 2016

See Also
showPal, divPal, addAlpha, colorRampPalette, package RColorBrewer

Examples

plot(rep(1,12), pch=16, cex=5, col=seqPal(12), xaxt="n")

showPal()

# nonlinear color scale (use colPoints + see classify for more options):
v <- rescale(volcano^30)
image(v, col=seqPal(1000), asp=1); colPointsLegend(v, nbins=1000)
image(v, col=seqPal(1000, logbase=1.007), asp=1)
colPointsLegend(v, col=seqPal(1000, logbase=1.007))

plot( rep(1, 1000), pch=15, cex=3, col=seqPal(1000), ylim=c(0.99, 1.01), ylab="logbase", las=1)
for(b in seq(0.99, 1.01, len=30))
points(rep(b, 1000), pch=15, cex=1, col=seqPal(1000, logbase=b))
136 seqR

seqR seq with a range argument

Description
sequence given by range or vector of values.

Usage
seqR(range, from = 1, to = 1, extend = 0, ...)

Arguments
range vector with 2 values (1st taken as from, 2nd as to) or more (the result is then
always ascending).
from start value of sequence. DEFAULT:1
to end value of sequence. DEFAULT:1
extend Factor f passed to extendrange. DEFAULT:0
... further arguments passed to seq.

Value
Numeric vector.

Author(s)
Berry Boessenkool, <[email protected]>, Feb 2014

See Also
seq, range, http://r.789695.n4.nabble.com/seq-range-argument-td4684627.html

Examples

seqR(range=c(12,6), by=-2)
m <- c(41, 12, 38, 29, 50, 39, 22)
seqR(m, len=6)
# Takes min and max of range if the vector has more than two elements.

seqR(range=c(12,6), by=-2, extend=0.1)

# internaly calls extendrange with f=extend
showPal 137

showPal show color palettes

Description
Plot examples of the sequential and diverging color palettes in this package. Do not use rainbow:
https://eagereyes.org/basics/rainbow-color-map

Usage
showPal(cex = 4, ...)

Arguments
cex Character EXpansion size (width of color bar). DEFAULT: 4
... Arguments passed to par

Author(s)
Berry Boessenkool, <[email protected]>, Apr 2016

See Also
seqPal, divPal, package RColorBrewer

Examples
showPal()

smallPlot Inset small plot within figure

Description
multipanel-compatible inset plot with margins, background and border Adding points after smallPlot
is called may be incorrect if the original function messes with the graph margins, see the note in
colPointsLegend.

Usage
smallPlot(expr, x1 = 0.05, x2 = 0.7, y1 = 0.5, y2 = 1, outer = FALSE,
xpd = NA, mar = c(3, 3, 1, 1), mgp = c(1.8, 0.8, 0), bg = par("bg"),
border = par("fg"), las = 1, resetfocus = TRUE, colwise = FALSE, ...)
138 smallPlot

Arguments
expr expression creating a plot. Can be code within braces.
x1, x2, y1, y2 Position of small plot, relative to current figure region [0:1]. DEFAULT: x: 0.05-
0.7, y: 0.5-1
outer Logical. Should inset plot be placed in the device outer margin region instead of
relative to the current figure region? Useful in multipanel plots with par(oma).
outer here does not have exactly the same meaning as in title. DEFAULT:
FALSE
xpd Plotting and notation clipped to plot region (if xpd=FALSE), figure region (TRUE)
or device region (xpd=NA). DEFAULT: NA
mar Margin vector in (approximate) number of lines. It is internally multiplied with
strheight to convert it to relative units [0:1], thus the behaviour is a bit different
from par(mar). It’s recycled, so you can use mar=0. DEFAULT: c(3,3,1,1)
mgp MarGinPlacement: distance of xlab/ylab, numbers and line from plot margin, as
in par, but with different defaults. DEFAULT: c(1.8, 0.8, 0)
bg Background. DEFAULT: par("bg")
border Border around inset plot. DEFAULT: par("fg")
las LabelAxisStyle. DEFAULT: 1
resetfocus Reset focus to original plot? Specifies where further low level plot commands
are directed to. DEFAULT: TRUE
colwise Logical: Continue next plot below current plot? If you had par(mfcol=...),
you must use colwise=TRUE, otherwise the next plot will be to the right of the
current plot (as with par(mfrow=...)). DEFAULT: FALSE
... further arguments passed to par. This may mess things up - please tell me
for which arguments! You can do par(las=1, las=2) (the last will be set),
so smallPlot(plot(1), new=FALSE) works, but may not yield the intended
result.

Value
parameters of small plot, invisible.

Warning
setting mai etc does not work!

Author(s)
Berry Boessenkool, <[email protected]>, 2014-2016

See Also
colPointsLegend for an example of usage. subplot and add.scatter for alternative solutions to
this problem that do not set margins.
smallPlot 139

Examples

# Basic usage:
op <- par(no.readonly=TRUE) # original parameters
plot(1:10)
smallPlot(plot(5:1, ylab="Yo man!"), bg="lightgreen" )
smallPlot(plot(5:1), x1=0.5,x2=1, y1=0.3,y2=0.6, bg="yellow", yaxt="n")
# if R warns "figure margins too large", try dragging the plot viewer bigger

# select focus for further add-on's:

points(2, 2, pch="+", cex=2, col=2) # main window
smallPlot( plot(5:1), bg="lightblue", resetfocus=FALSE )
mtext("dude")
points(2, 2, pch="+", cex=2, col=2) # smallPlot window
par(op)

# More par settings:

plot(1:10)
smallPlot( plot(50:1), bg=6, mai=c(0.2, 0.3, 0.1, 0.1)) # screws up
smallPlot( plot(5:1), bg=8, ann=FALSE)
smallPlot(plot(10:50), bg="transparent") # old plot is kept

# complex graphics in code chunks:

plot(1:100)
smallPlot( {plot(5:1, ylab="Rocky label"); lines(c(2,4,3));
legend("topright", "BerryRocks!", lwd=3) }, bg="white")

# multiple figure situations

par(op)
par(mfcol=c(3,4))
plot(1:10)
plot(1:10)
smallPlot(plot(5:1), bg="lightblue")
plot(1:10)
smallPlot(plot(5:1), bg="bisque", colwise=TRUE) # if mfcol (not mfrow) was set
plot(1:10)

# Outer margins (e.g. to add legends to multi-panel plots)

par(op)
par(mfrow=c(3,2), oma=c(0,5,0,0), mar=c(0,0,1,0)+0.5)
for(i in 0:5*4) image(volcano+i, zlim=c(90,200), xaxt="n", yaxt="n",
main=paste("volcano +", i))
smallPlot(plot(1:10), x1=0,x2=0.25, y1=0.5,y2=1, bg="green", mar=1)
smallPlot(plot(1:10), x1=0,x2=0.25, y1=0.5,y2=1, bg="green", mar=1, outer=TRUE)
colPointsLegend(90:200, horizontal=FALSE, x1=0, col=heat.colors(12), outer=TRUE,
labelpos=5, density=FALSE, title="", cex=2, lines=FALSE)

# Further testing with mfrow and mfcol

par(op)
old_plt <- par("plt")
140 smoothLines

par(mfcol=c(3,4))
new_plt <- par("plt")
plot(1:10)
plot(1:10)
smallPlot(plot(5:1), bg="lightblue", colwise=TRUE)
points(3, 2, pch="+", cex=2, col=2)
plot(1:10) # canot keep mfcol, only mfrow, if colwise is left FALSE.
smallPlot(plot(5:1), bg="bisque", resetfocus=FALSE )
points(3, 2, pch="+", cex=2, col=2)
plot(1:10) # in smallPlot space
par(plt=old_plt)
plot(1:10) # too large
smallPlot(plot(5:1), bg="palegreen")
points(3, 2, pch="+", cex=2, col=2, xpd=NA) # not drawn with default xpd
par(plt=new_plt)
plot(1:10) # canot keep mfcol, only mfrow, if colwise is left FALSE.
smallPlot(plot(5:1), bg="yellow")
points(3, 2, pch="+", cex=2, col=2) # everything back to normal
par(op)

# if layout is used instead of par(mfrow), it is difficult to add graphs

# after using smallPlot
lay <- matrix(c(1,1,1,1,2,2,3,3,2,2,3,3,4,4,5,5), ncol=4)
layout.show(layout(lay))
layout(lay)
plot(1:10)
plot(1:10)
smallPlot(plot(1:10), mar=c(1,3,1,0), x1=0,x2=0.2, y1=0.2,y2=0.8, bg=4, outer=TRUE)
# plot(1:10) # now in a weird location (par("mfrow") is 4x4 after layout)

smoothLines draw smoothed lines

Description
draw smoothed lines with an n-level partially transparent haze

Usage
smoothLines(x, y, lwd = 1, col = 1, n = 5, alpha = 0.1, ...)

Arguments
x numerical. x-coordinates. x can be a matrix, then the y coordinates are taken
from the second column
y numerical. y-coordinates
lwd single integer. line width
col color. DEFAULT: 1 (black)
sortDF 141

n single integer. number of transparent lines overlayed with sinking line widths.
DEFAULT: 5
alpha Transparency of color. DEFAULT: 0.1 (very transparent)
... further arguments as in lines

Value
none, draws lines

Author(s)
Berry Boessenkool, <[email protected]>, 2011/2012

See Also
lines, col2rgb, rgb

Examples

x <- 1:5 ; y <- c(0.31, 0.45, 0.84, 0.43, 0.25)

plot(x,y)
smoothLines(x,y)
#png("smoothLines.png")
par(mar=c(2,2,2,0)+.5)
plot(1:100, las=1, type="n", main="usage of smoothLines(x,y, lwd, col, n, alpha ...)")
abline(h=0:10*10, v=0:10*10, col=6); box()
for(i in 0:9) { smoothLines(x=c(0,10,25,35), y=c(i*10, i*10, i*10+12, i*10+7), lwd=i)
text(25, i*10+5, paste("n=5,lwd=", i, sep="")) }
for(i in 0:9) { smoothLines(x=c(40,50,65,75), y=c(i*10, i*10, i*10+12, i*10+7), n=i)
text(65, i*10+5, paste("n=",i,",lwd=1", sep="")) }
for(i in 0:9/20) { smoothLines(x=c(80,90,105), y=c(i*200, i*200+12, i*200+12), alpha=i)
text(90, i*200+10, paste("alpha=", i, sep=""), adj=0) }
text(5,10, "default", adj=c(0.5,-0.2)); text(45,50, "default", adj=c(0.5,-0.2))

#dev.off()

sortDF sort dataframes by column

Description
sort a data.frame by column - basically just a wrapper for order

Usage
sortDF(df, col, decreasing = TRUE, ...)
142 spiralDate

Arguments
df Data.frame to be sorted
col Column (index or (un)quoted name) to be sorted by
decreasing Logical: should highest value be on top? DEFAULT: TRUE (unlike order!)
... Further arguments passed to order, like eg na.last or method

Value
data.frame

Author(s)
Berry Boessenkool, <[email protected]>, June 2015

See Also
sort, order

Examples
sortDF(USArrests[USArrests$Murder>11,], Assault)
sortDF(USArrests[USArrests$Murder>11,], "Assault") # safer within functions
sortDF(USArrests[USArrests$Murder>11,], 3)

spiralDate Spiral graph of time series

Description
Plot seasonality of (daily) time series along spiral

Usage
spiralDate(dates, values, data, drange = NA, vrange = NA,
months = substr(month.abb, 1, 1), add = FALSE, shift = 0, prop = NA,
zlab = substitute(values), format = "%Y", nint = 1, ...)

Arguments
dates Dates in ascending order. Can be character strings or strptime results, as ac-
cepted (and coerced) by as.Date
values Values to be mapped in color with colPoints along seasonal spiral
data Optional: data.frame with the column names as given by dates and values
drange Optional date range (analogous to xlim), can be a vector like dates. DEFAULT:
NA
spiralDate 143

vrange Optional value range (analogous to ylim), can be a vector like values. DE-
FAULT: NA
months Labels for the months. DEFAULT: J,F,M,A,M,J,J,A,S,O,N,D
add Add to existing plot? DEFAULT: FALSE
shift Number of days to move January 1st clockwise. DEFAULT: 0
prop Proportion of the data to be actually plotted, used in spiralDateAnim. DE-
FAULT: NA (ignored)
zlab Title of colPointsLegend
format Format of date labels see details in strptime. DEFAULT: "%Y"
nint Number of interpolation segments between points, only used if lines=TRUE
(passed to colPoints). DEFAULT: 1 (with long time series, the colPoints de-
fault of 30 is too high!)
... Further arguments passed to colPoints, but not Range (use vrange)

Value
invisible data.frame with date, vals, and the plotting coordinates

Author(s)
Berry Boessenkool, <[email protected]>, May 2016

See Also
seasonality, colPoints, as.Date

Examples
# synthetic seasonal Data
set.seed(42)
fakeData <- data.frame(time = as.Date("1985-01-01")+0:5000,
vals = cumsum(rnorm(5001))+50 )
fakeData$vals <- fakeData$vals + sin(0:5000/366*2*pi)*max(abs(fakeData$vals))

sp <- spiralDate(time,vals, data=fakeData)

tail(sp)
spiralDate(time,vals, data=fakeData, drange=as.Date(c("1980-01-01", "2004-11-15")), lines=TRUE)

par(mfrow=c(1,3), mar=c(3,3,6,1), mgp=c(2,0.6,0), las=1)

colPoints(time,vals,vals, data=fakeData, col=divPal(100), add=FALSE, legend=FALSE,
lines=TRUE, pch=NA, nint=1, lwd=2)
title(main="classical time series\nworks badly for long time series\nshows trends well")

seasonality(time, vals, fakeData, col=divPal(100), mar=c(3,3,6,1), legend=FALSE, main="", shift=61)

title(main="yearly time series\nday of year over time\nfails for cyclicity over all year")

spiralDate(time,vals, data=fakeData, col=divPal(100), legargs=list(y1=0.7,y2=0.8))

title(main="spiral graph\nshows cyclic values nicely
trends are harder to detect\nrecent values = more visual weight")
144 spiralDateAnim

par(mfrow=c(1,1))

# Data with missing values:

fakeData[1300:1500, 2] <- NA
spiralDate(time,vals, data=fakeData, lines=TRUE) # no problem
# Missing data:
fakeData <- na.omit(fakeData)
spiralDate(time,vals, data=fakeData, lines=TRUE) # problematic for lines
spiralDate(time,vals, data=fakeData, pch=3) # but not for points

## Real data:
#library2("waterData")
#data(exampleWaterData)
#spiralDate(dates, val, data=q05054000LT, lines=TRUE, lwd=3)

spiralDateAnim Animated spiral graph

Description
Animation of (daily) time series along spiral

Usage
spiralDateAnim(dates, values, data, steps = 100, sleep = 0,
progbar = TRUE, ...)

Arguments
dates, values, data
Input as in spiralDate
steps Number of steps (images) in animation. DEFAULT: 100
sleep Pause time between frames, in seconds, passed to Sys.sleep. DEFAULT: 0
progbar Should a progress bar be drawn? Useful if you have a large dataset or many
steps. DEFAULT: TRUE
... Further arguments passed to spiralDate

Author(s)
Berry Boessenkool, <[email protected]>, May 2016

See Also
spiralDate, linLogHist
superPos 145

Examples

set.seed(42)
x <- as.Date("1985-01-01")+0:5000
y <- cumsum(rnorm(5001))+50
y <- y + sin(0:5000/366*2*pi)*max(abs(y))/2
plot(x,y)

spiralDateAnim(x,y, steps=10, sleep=0.01) # 0.05 might be smoother...

spiralDateAnim(x,y, steps=20)

## Not run:
## Rcmd check --as-cran doesn't like to open external devices such as pdf,
## so this example is excluded from running in the checks.
pdf("spiralDateAnimation.pdf")
spiralDateAnim(x,y, main="Example Transition", col=divPal(100), format=" ")
dev.off()

# if you have FFmpeg installed, you can use the animation package like this:
library2(animation)
saveVideo(spiralDateAnim(x,y, steps=300), video.name="spiral_anim.mp4", interval=0.1,
ffmpeg="C:/Program Files/R/ffmpeg/bin/ffmpeg.exe")

## End(Not run)

superPos superposition of discharge, unit hydrograph

Description
superposition of precipitation along unit hydrograph (to simulate Q from P)

Usage
superPos(P, UH)

Arguments
P Vector with precipitation values
UH Vector with discrete values of the Unit Hydrograph. This can be any UH sum-
ming to one, not just the storage cascade model.

Value
Vector of streamflow values
146 superPos

Author(s)
Berry Boessenkool, <[email protected]>, July 2013

See Also
lsc where superPos is used, unitHydrograph

Examples

N <- c(9,5,2,14,1,3) # [mm/hour]

UH <- c(0, 0.1, 0.4, 0.3, 0.1, 0.1) # [1/h]
sum(UH) # sum must be 1

superPos(N, UH)
# If catchment area = 34 km^2 and precipitation is homogenous:
superPos(N/10^3, UH) * 34*10^6 / 3600 # m^3/s # Add baseflow and you're done...

SP <- data.frame(Prec=c(N, 0,0,0,0,0),

P1=c( UH*N[1], 0,0,0,0,0),
P2=c(0, UH*N[2], 0,0,0,0),
P3=c(0,0, UH*N[3], 0,0,0),
P4=c(0,0,0, UH*N[4], 0,0),
P5=c(0,0,0,0, UH*N[5], 0),
P6=c(0,0,0,0,0, UH*N[6] ),
runoff=superPos(N, UH))
SP # SuperPosition

SPcum <- t( apply(SP[2:7], 1, cumsum) )

plot(N, type="h", col=2:7, lwd=3, xlim=c(1, 10), ylim=c(30,0), lend=1)

par(new=TRUE)
plot(1, type="n", ylim=c(0, 15), xlim=c(1, 10), axes=FALSE, ann=FALSE)
axis(4, las=1)
polygon(x=c(1:11, 11:1), y=c(SPcum[,1], rep(0, 11)), col=2)
for(i in 2:6) polygon(x=c(1:11, 11:1), y=c(SPcum[,i], rev(SPcum[,i-1])), col=i+1)
text(3.5, 1, "Shape of UH")
lines( superPos(N, UH), lwd=3)

plot(UH, type="o", ylim=lim0(0.4), las=1)

lines(UH, type="h" )

# Effect of distribution of Prec:

P_a <- c(1,2,3,4,5,6,7,8)
P_b <- c(4,4,4,4,4,4,4,4,4)
P_c <- c(8,7,6,5,4,3,2,1)
sum(P_a) ; sum(P_b) ; sum(P_c)

UH_1 <- unitHydrograph(n=2, k=2.3, t=1:25)

UH_2 <- unitHydrograph(n=5.5, k=1.8, t=1:25)
tableColVal 147

par(mfrow=c(2,3), mar=c(2,3,2,1), las=1)

plot(P_a, type="h", col=3, lwd=3, ylim=c(0,8), main="Precipitation a")
plot(P_b, type="h", col=4, lwd=3, ylim=c(0,8), main="Precipitation b")
plot(P_c, type="h", col=5, lwd=3, ylim=c(0,8), main="Precipitation c")
#
plot(UH_1, type="l", main="unit hydrograph", ylab="",xlab="Zeit")
lines(UH_2, col=2)
text(c(7,14), c(0.12, 0.07), c("UH_1","UH_2"), col=1:2)
abline(h=0)
#
plot( superPos(P=P_a, UH=UH_1), col=3, ylim=c(0,5), type="l",
main="Discharge", ylab="Q [m^3/s]")
lines(superPos(P=P_b, UH=UH_1), col=4)
lines(superPos(P=P_c, UH=UH_1), col=5)
legend("topright", c("P a","P b", "P c"), title="with UH_1", col=3:5, lty=1)
#
plot( superPos(P=P_a, UH=UH_2), col=3, ylim=c(0,5), type="l",
main="Discharge", ylab="Q [m^3/s]")
lines(superPos(P=P_b, UH=UH_2), col=4)
lines(superPos(P=P_c, UH=UH_2), col=5)
legend("topright", c("P a","P b", "P c"), title="with UH_2", col=3:5, lty=1)

tableColVal Table with values with value-dependent colored backgrounds in pdf

Description
Table with numbers and corresponding color in the background of each cell. (heatmap)

Usage
tableColVal(mat, main = deparse(substitute(mat)), nameswidth = 0.3,
namesheight = 0.1, palette = seqPal(100), Range = range(mat, finite =
TRUE), digits = 2, ..., classargs = NULL, cellargs = NULL,
colargs = NULL, rowargs = NULL, mainargs = NULL)

Arguments
mat Matrix with values and row/column names
main Title for topleft space. DEFAULT: name of mat object.
nameswidth Relative width of row names at the left, as a percentage of plot. DEFAULT: 0.3
namesheight Relative height of column names at the top. DEFAULT: 0.1
palette Color palette for the heatmap. DEFAULT: seqPal(100)
Range Range mapped to color palette. DEFAULT: range(mat)
digits Number of digits rounded to for writing. DEFAULT: 2
... Further arguments passed to all text like cex, col, srt, ...
148 tableColVal

classargs List of arguments specifying how to call classify, e.g. method. DEFAULT:
NULL
cellargs, colargs, rowargs, mainargs
List of arguments passed to text only for the cells, column labels, row labels or
title, respectively. DEFAULTS: NULL

Details
Create tables with corresponding color in the background of each cell. (heatmap)

Value
List of locations in plot.

Author(s)
Berry Boessenkool, <[email protected]>, Nov 2012 + Nov 2016

See Also
pdf, heatmap

Examples

Bsp <- matrix(c(21,23,26,27, 18,24,25,28, 14,17,23,23, 16,19,21,25), ncol=4, byrow=TRUE)

colnames(Bsp) <- paste0("Measure", LETTERS[1:4])
rownames(Bsp) <- paste("prod", 8:11, sep="_")
Bsp

( tableColVal(Bsp) )
tableColVal(Bsp, nameswidth=0.1) # relative to plot width
tableColVal(Bsp, namesheight=0.5, srt=45)
tableColVal(Bsp, namesheight=0.5, colargs=c(srt=45))

tableColVal(Bsp, cellargs=list(cex=2), col="red")

tableColVal(Bsp, Range=c(10,40))
tableColVal(Bsp, Range=c(20,40))
tableColVal(Bsp, palette=heat.colors(12))
tableColVal(Bsp, palette=c(2,4,7), main="more\nstuff")

Bsp2 <- matrix(rexp(30), ncol=6, byrow=TRUE)

( tableColVal(Bsp2) )
tableColVal(Bsp2, digits=4)
colPointsLegend(Bsp2, horizontal=FALSE, x1=0.05, x2=0.15, y1=0.1, y2=0.8, title="")

## Not run:
## Rcmd check --as-cran doesn't like to open external devices such as pdf,
## so this example is excluded from running in the checks.
pdf("TableColVal.pdf", height=5); tableColVal(Bsp); dev.off()
openFile("TableColVal.pdf")
unlink("TableColVal.pdf")
textField 149

## End(Not run)

textField Write text to plot with halo underneath

Description
Write text to plot. A field the size of each label is drawn beneath it, so the text can be read easily
even if there are many points in the plot. Fields can be rectangular, elliptic or rectangular with
rounded edges.

Usage
textField(x, y, labels = seq_along(x), fill = "white", border = NA,
expression = NA, margin = 0.3, field = "rounded", nv = 500,
rounding = 0.25, rrarg = NULL, lty = par("lty"), lwd = par("lwd"),
cex = par("cex"), xpd = par("xpd"), adj = par("adj"), pos = NULL,
offset = 0.5, quiet = TRUE, ...)

Arguments
x X coordinates, if necessary, they are recycled
y Y coordinates
labels labels to be placed at the coordinates, as in text. DEFAULT: seq_along(x)
fill fill is recycled if necessary. With a message when quiet = FALSE. DEFAULT:
"white"
border ditto for border. DEFAULT: NA
expression If TRUE, labels are converted to expression for better field positioning through
expression bounding boxes. If NA, it is set to TRUE for labels without line
breaks (Newlines, "\n"). If FALSE, no conversion happens. DEFAULT: NA
margin added field space around words (multiple of em/ex). DEFAULT: 0.3
field ’rectangle’, ’ellipse’, or ’rounded’, partial matching is performed. DEFAULT:
"rounded"
nv number of vertices for field = "ellipse" or "rounded". low: fast drawing. high:
high resolution in vector graphics as pdf possible. DEFAULT: 500
rounding between 0 and 0.5: portion of height that is cut off rounded at edges when field
= "rounded". DEFAULT: 0.25
rrarg List of arguments passed to roundedRect. DEFAULT: NULL
lty line type. DEFAULT: par("lty")
lwd line width. DEFAULT: par("lwd")
cex character expansion. DEFAULT: par("cex")
150 textField

xpd expand text outside of plot region ("figure")?. DEFAULT: par("xpd")

adj vector of length one or two. DEFAULT: par("adj")
pos in ’text’, pos overrides adj values. DEFAULT: NULL
offset I want the field to still be drawn with adj, but have it based on pos. DEFAULT:
0.5
quiet Suppress warning when Arguments are recycled? DEFAULT: TRUE
... further arguments passed to strwidth and text, like font, vfont, family

Details
Specifying pos and offset will currently change the position of the text, but not of the field.
srt is not supported yet.
lend, ljoin and lmitre can not be specified for rect, to keep argument number low.
density (crosshatch etc.) is not supported, as this would distract from the text. # Search Engine
Keywords: R Text visible on top R labeling with color underneath R Creating text with a halo R
Text with shadow

Value
None

Author(s)
Berry Boessenkool, <[email protected]>, April 2013 + March 2014

References
with inspiration taken from ordilabel in package vegan and thanks to Jari Oksanen for his com-
ments

See Also
text, roundedRect; shadowtext in package TeachingDemos, see http://blog.revolutionanalytics.
com/2009/05/make-text-stand-out-with-outlines.html, and http://stackoverflow.com/
questions/25631216.
s.label in package ade4, which is not so versatile and doesn’t work with logarithmic axes

Examples

# TextFields with mixed field shapes ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

set.seed(13); plot(cumsum(rnorm(100)), type="l", main="berryFunctions::textField")
for(i in 2:7) lines(cumsum(rnorm(100)), col=i)
textField(40, 4, "default")
textField(40, 0, "some options", col=2, fill=4, margin=c(-0.4, 0.9), font=2)
# Ellipsis (looks better in vector graphics like pdf):
textField(80, 2, "field='ellipse'", field="ell", mar=c(0.5, 2.3), border=5)
# Rectangular field with edges rounded:
textField(60,-3, "field='Rounded'", field="rounded", fill="orange", cex=1.7)
TFtest 151

# Field type can be abbreviated (partial matching), margin may need adjustment:
textField(90, 5, "short", field="ell", fill=7, border=4, mar=-0.4)

# Rounded can also vectorized:

textField(30, c(2,0,-2,-4,-6), paste("rounding =",seq(0,0.6,len=5)), field="round",
fill=(2:6), mar=1, rounding=seq(0,0.6,len=5), border=1)
# turn off warning about recycling:
textField(80, c(-5,-6.5), c("Ja", "Nein"), field="round", fill=6:8, quiet=TRUE)

set.seed(007); plot(rnorm(1e4)) ; abline(v=0:5*2e3, col=8)

# Default settings:
textField(5000, 0, "Here's some good text")
# right-adjusted text (the field box still extends 'margin' stringwidths em):
textField(2000, -1, "Some more (smores!)", cex=1.5, adj=0, col=2)
# Field color, no extra margin beyond baseline (excluding descenders):
textField(2000, -2, "more yet", col=2, fill="blue", margin=0)
# margin can be one number for both x and y direction ... :
textField(1000, 2, "Up we go", fill=7, margin=1.4)
# ... or two (x and y different), even negative:
textField(5000, 2, "to the right", col=2, fill=4, margin=c(-0.4, 0.9))
# Fonts can be set as well:
textField(5000, 1, "And boldly down in bold font", font=2, border=3)
# Text can expand outsinde of the plot region (figure) into the margins:
textField(11000, -2, "Hi, I'm a long block of text", adj=1, fill="red")
textField(11000, -3, "You're not outside the plot!", adj=1, xpd=TRUE, fill="red")
# And most parameters can be vectorized, while x/y are recycled:
textField(3000, c(-3, -3.7), c("0", "good"), border=c("red",3), lty=1:2)

# textField even works on logarithmic axes:

mylabel <- c("This","is (g)","the","ever-\n great","Sparta")
plot(10^runif(5000, -1,2), log="y", col=8)
textField(1000, c(100,20,4,2,0.5), mylabel, fill=2, mar=0, expression=FALSE)
textField(2500, c(100,20,4,2,0.5), mylabel, fill=4, mar=0, expression=TRUE)
textField(4000, c(100,20,4,2,0.5), mylabel, fill=3, mar=0)
textField(c(1,2.5,4)*1000, 0.2, paste("expression=\n", c("FALSE","TRUE","NA")))

# In most devices, vertical adjustment is slightly off when the character string
# contains no descenders. The default is for centered text: adj = c(0.5, NA).
# For drawing the field, adj[2] is in this case set to 0.5.
# Text positioning is different for NA than for 0.5, see details of ?text
# I'm working on it through expression, which does not work with newlines yet

TFtest Test logical expressions

152 TFtest

Description

Check if logical expressions return what you expect with a truth table

Usage

TFtest(..., na = TRUE)

Arguments

... Expression(s) with logical operators to be evaluated, with single letters for vari-
ables. Each expression is to be separated with a comma
na Logical: should NAs be included in the truth table? DEFAULT: TRUE

Details

This is a nice way to check operator precedence, see Syntax

Value

Truth table as data.frame with TRUE and FALSE (and NA) combinations

Author(s)

Berry Boessenkool, <[email protected]>, Mrz 2016

See Also

logical

Examples

TFtest(!a & !b)

TFtest(!a & !b, a&b, !(a&b))
TFtest(!a & !b | c)
TFtest(!a & !b | c, na=FALSE)
TFtest(!a)
TFtest(a&b|c, (a&b)|c, a&(b|c), na=FALSE) # AND has precedence over OR
timeAxis 153

timeAxis Label date axis

Description
Labels date axes at sensible intervals in the time domain of weeks to decades.

Usage
timeAxis(side = 1, timeAxis = NA, origin = "1970-01-01",
startyear = NULL, stopyear = NULL, n = 5, npm = NULL, npy = NA,
format = "%d.%m.\n%Y", yformat = "%Y", labels = format.Date(d,
format), ym = FALSE, mcex = 0.6, mmgp = c(3, 0, 0), midyear = FALSE,
midmonth = FALSE, midargs = NULL, mgp = c(3, 1.5, 0), cex.axis = 1,
tick = TRUE, tcl = par("tcl"), las = 1, ...)

Arguments
side Which axis are to be labeled? (can be several). DEFAULT: 1
timeAxis Logical indicating whether the axis is POSIXct, not date. DEFAULT: NA, mean-
ing axis value >1e5
origin Origin foras.Date and as.POSIXct. DEFAULT: "1970-01-01"
startyear Integer. starting year. DEFAULT: NULL = internally computed from par("usr")
stopyear Ditto for ending year. DEFAULT: NULL
n Approximate number of labels that should be printed (as in pretty). DEFAULT:
5
npm Number of labels per month, overrides n. DEFAULT: NULL = internally com-
puted.
npy Number of labels per year, overrides npm and n. DEFAULT: NA
format Format of date, see details in strptime. DEFAULT: "%d.%m.\n%Y"
yformat Format of year if ym=TRUE. Use yformat=" " (with space) to suppress year
labeling. DEFAULT: "%Y"
labels labels. DEFAULT: format.Date(d, format)
ym Label months with first letter at the center of the month and year at center below.
Sets midyear and midmonth to TRUE. Uses labels and format for the years,
but ignores them for the months. DEFAULT: FALSE
mcex cex.axis for month labels if ym=TRUE. DEFAULT: 0.6
mmgp mgp for month labels if ym=TRUE. DEFAULT: 3,0,0
midyear Place labels in the middle of the year? if TRUE, format default is "%Y". DE-
FAULT: FALSE
midmonth Place labels in the middle of the month? if TRUE, format default is "%m\n%Y".
DEFAULT: FALSE
154 timeAxis

midargs List of arguments passed to axis for the year-start lines without labels. DE-
FAULT: NULL
mgp MarGinPlacement, see par. The second value is for label distance to axis. DE-
FAULT: c(3,1.5,0)
cex.axis Character EXpansion (letter size). DEFAULT: 1
tick Draw tick lines? DEFAULT: TRUE
tcl Tick length (negative to go below axis) in text line height units like mgp[2]
Changed to -2.5 for year borders if ym=TRUE. DEFAULT: par("tcl")
las LabelAxisStyle for orientation of labels. DEFAULT: 1 (upright)
... Further arguments passed to axis, like lwd, col.ticks, hadj, lty, ...

Value
The dates that were labeled

Author(s)
Berry Boessenkool, <[email protected]>, Feb 2015, update labels and midyear Dec 2015

See Also
monthLabs for the numbercrunching itself, axis.Date with defaults that are less nice.

Examples

set.seed(007) # for reproducibility

Date1 <- as.Date("2013-09-25")+sort(sample(0:150, 30))
plot(Date1, cumsum(rnorm(30)), type="l", xaxt="n", ann=FALSE)
timeAxis(side=1)
timeAxis(1, npm=2, cex.axis=0.5, col.axis="red") # fix number of labels per month

DateYM <- as.Date("2013-04-25")+0:500

plot(DateYM, cumsum(rnorm(501)), type="l", xaxt="n", ann=FALSE)

monthAxis() # see more examples there - it largely replaces timeAxis!!!

plot(Date1, cumsum(rnorm(30)), type="l", xaxt="n", ann=FALSE)

timeAxis(labels=FALSE, col.ticks=2)
timeAxis(1, format=" ") # equivalent to axis(labels=FALSE)
timeAxis(1)
d <- timeAxis(1, labels=letters[1:24], mgp=c(3,2.5,0))
d # d covers the full year, thus is longer than n=5

Date2 <- as.Date("2011-07-13")+sort(sample(0:1400, 50))

plot(Date2, cumsum(rnorm(50)), type="l", xaxt="n", ann=FALSE)
timeAxis(npy=12, format=" ") # fix number of labels per year
timeAxis(tcl=-0.8, lwd.ticks=2, format="%Y/%m", mgp=c(3,1,0))
timeAxis(format="", mgp=c(3,2,0)) # International Date format YYYY-mm-dd
timer 155

plot(Date2, cumsum(rnorm(50)), type="l", xaxt="n", ann=FALSE)

timeAxis(midyear=TRUE)
abline(v=monthLabs(npm=1), col=8)

Date3 <- as.Date("2011-07-13")+sort(sample(0:1200, 50))

plot(Date3, cumsum(rnorm(50)), type="l", xaxt="n", ann=FALSE)
timeAxis(1, n=4, font=2)
timeAxis(1, col.axis=3) # too many labels with default n=5

monthAxis(side=3) # again: use monthAxis, it is usually nicer!

# mid-year labels:
plot(Date3, cumsum(rnorm(50)), type="l", xaxt="n", ann=FALSE)
timeAxis(midyear=TRUE, midargs=list(tcl=-1.2))

# mid-month labels:
plot(Date1, cumsum(rnorm(30)), type="l", xaxt="n", ann=FALSE)
timeAxis(midmonth=TRUE)

# Time axis instead of date axis:

plot(as.POSIXct(Sys.time()+c(0,10)*24*3600), 1:2, xaxt="n")
timeAxis(n=3)
timeAxis()

timer Timer alarm

Description
Beeps in a given interval and gives a progress bar in the console

Usage
timer(interval = 20, n = 15, write = FALSE)

Arguments
interval alarm interval in seconds. DEFAULT: 20
n number of alarm signals to be given. DEFAULT: 15
write Should the actual estimated time be written for overhead computing time control
purposes? DEFAULT: FALSE

Details
defaults to practice useR lightning talks: 15 slides, each shown 20 secs, change automatically

Value
none
156 toupper1

Author(s)
Berry Boessenkool, <[email protected]>, June 2015

References
http://user2015.math.aau.dk/lightning_talks

See Also
alarm, Sys.sleep, txtProgressBar

Examples

## Not run: ## Skip time consuming checks on CRAN

timer(interval=0.5, n=3)
timer(interval=0.2, n=8, write=TRUE) # a slight deviation occurs for a large n
timer() # to practice lightning talks at useR! conferences

## End(Not run)

toupper1 capitalize words

Description
capitalizes the first letter of character strings using toupper

Usage
toupper1(x)

Arguments
x Character vector

Details
Basically just a one-liner using toupper

Value
character string vector

Author(s)
Berry Boessenkool, <[email protected]>, Jul 2016
traceCall 157

See Also

toupper, substr

Examples
toupper1("berry")
toupper1(c("berRy","likes to code"))

traceCall call stack of a function

Description

trace the call stack e.g. for error checking and format output for do.call levels

Usage

traceCall(skip = 0, prefix = "\nCall stack: ", suffix = "\n",

vigremove = TRUE)

Arguments

skip Number of levels to skip in traceback

prefix Prefix prepended to the output character string. DEFAULT: "\nCall stack: "
suffix Suffix appended to the end of the output. DEFAULT: "\n"
vigremove Logical: remove call created using devtools::build_vignettes()? DEFAULT:
TRUE

Value

Character string with the call stack

Author(s)

Berry Boessenkool, <[email protected]>, Sep 2016 + March 2017

See Also

tryStack, checkFile for example usage

158 truncMessage

Examples
lower <- function(a, s) {warning(traceCall(s), "stupid berry warning: ", a+10); a}
upper <- function(b, skip=0) lower(b+5, skip)
upper(3)
upper(3, skip=1) # traceCall skips last level (warning)
upper(3, skip=4) # now the stack is empty
d <- tryStack(upper("four"), silent=TRUE)
inherits(d, "try-error")
cat(d)

lower <- function(a,...) {warning(traceCall(1, prefix="in ", suffix=": "),

"How to use traceCall in functions ", call.=FALSE); a}
upper(3)

truncMessage truncate message parts

Description
truncate long vectors for messages

Usage
truncMessage(x, ntrunc = 3, prefix = "s", midfix = " ", altnix = "'",
sep = ", ")

Arguments
x Character vector
ntrunc Integer: number of elements printed before truncation. DEFAULT: 3
prefix Character: Prefix added if length(x)>1. DEFAULT: "s"
midfix Character: string added after prefix OR before first altnix. DEFAULT: " "
altnix Character: Alternative string padded around x if length(x)==1. DEFAULT: "’"
sep Character: Separator between elements. DEFAULT: ", "

Value
Character string

Author(s)
Berry Boessenkool, <[email protected]>, Nov 2016

See Also
message
tryStack 159

Examples
truncMessage("hi")
message("listing name", truncMessage( "hi" ), ".")
message("listing name", truncMessage(paste0("hi",1:10)), ".")
truncMessage(paste0("hi",1:10), ntrunc=1)
truncMessage(paste0("hi",1:10), ntrunc=2, prefix="", midfix="")
truncMessage(paste0("hi",1:10), ntrunc=8, prefix="files _ ")

tryStack try an expression, returning the error stack

Description
As in try, the result of an expression if it works. If it fails, execution is not halted, but an invisible
try-error class object is returned and (unless silent=TRUE) a message catted to the console.
Unlike try, tryStack also returns the calling stack to trace errors and warnings and ease debugging.

Usage
tryStack(expr, silent = FALSE, warn = TRUE, short = TRUE, file = "",
removetry = TRUE, skip = NULL)

Arguments
expr Expression to try, potentially wrapped in curly braces if spanning several com-
mands.
silent Logical: Should printing of error message + stack be suppressed? Does not
affect warnings and messages. DEFAULT: FALSE
warn Logical: trace warnings and messages also? They are still handled like regu-
lar warnings / messages unless file !="", when they are catted into that file.
DEFAULT: TRUE
short Logical: should trace be abbreviated to upper -> middle -> lower? If NA, it is
set to TRUE for warnings and messages, FALSE for errors. DEFAULT: TRUE
file File name passed to cat. If given, Errors will be appended to the file after
two empty lines. if warn=T and file!="", warnings and messages will not be
shown, but also appended to the file. This is useful in lapply simulation runs.
DEFAULT: "" (catted to the console)
removetry Logical: should all stack entries matching typical tryCatch expressions be re-
moved? Unless the call contains customized tryCatch code, this can be left to
the DEFAULT: TRUE
skip Character string(s) to be removed from the stack. e.g. "eval(expr, p)". Use
short=F to find exact matches. DEFAULT: NULL
160 tryStack

Value
Value of expr if evaluated successfully. If not, an invisible object of class "try-error" as in try with
the stack in object[2]. For nested tryStack calls, object[3], object[4] etc. will contain "–
empty error stack –"

Author(s)
Berry Boessenkool, <[email protected]>, Nov 2016

See Also
try, traceCall, http://r.789695.n4.nabble.com/Stack-trace-td4021537.html, http://
stackoverflow.com/questions/15282471/get-stack-trace-on-trycatched-error-in-r, http:
//stackoverflow.com/questions/1975110/printing-stack-trace-and-continuing-after-error-occurs-in-r,
http://stackoverflow.com/questions/16879821/save-traceback-on-error-using-trycatch

Examples

# Functions -----

lower <- function(a) {message("fake message, a = ", a); a+10}

middle <- function(b) {plot(b, main=b) ; warning("fake warning, b = ", b); lower(b) }
upper <- function(c) {cat("printing c:", c, "\n") ; middle(c)}
d <- upper(42)
d
rm(d)

# Classical error management with try -----

## Not run: ## intentional error

d <- upper("42") # error, no d creation
traceback() # calling stack, but only in interactive mode

## End(Not run)

d <- try(upper("42"), silent=TRUE) # d created

cat(d) # with error message, but no traceback
inherits(d, "try-error") # use for coding

# way cooler with tryStack -----

d <- tryStack(upper("42") ) # like try, but with traceback, even for warnings
cat(d)
d <- tryStack(upper("42"), silent=TRUE, warn=0) # don't trace warnings
d <- tryStack(upper("42"), short=FALSE)

tryStack(upper(42)) # returns normal output, but warnings are easier to debug

# Note: you can also set options(showWarnCalls=TRUE)
tryStack 161

stopifnot(inherits(d, "try-error"))
stopifnot(tryStack(upper(42))==52)

## Not run: ## file writing not wanted by CRAN checks

d <- tryStack(upper("42"), silent=TRUE, file="log.txt")
openFile("log.txt")
unlink("log.txt")

## End(Not run)

op <- options(warn=2)
d <- try(upper("42") )
cat(d)
d <- tryStack(upper("42") )
d <- tryStack(upper("42"), warn=FALSE)
cat(d)
options(op) ; rm(op)

# Nested calls -----

f <- function(k) tryStack(upper(k), silent=TRUE)

d <- f(42) ; cat("-----\n", d, "\n-----\n") ; rm(d)
d <- f("42") ; cat("-----\n", d, "\n-----\n") ; rm(d)
d <- tryStack(f(4) ) ; cat("-----\n", d, "\n-----\n") ; rm(d)
# warnings in nested calls are printed twice, unless warn=0
d <- tryStack(f(4), warn=0) # could also be set within 'f'

d <- tryStack(f("4")) ; cat("-----\n", d, "\n-----\n")

d[1:3] ; rm(d)
# empty stack at begin - because of tryStack in f, no real error happened in f

# Other tests -----

cat( tryStack(upper("42")) )
f <- function(k) tryStack(stop("oh oh"))
d <- f(42) ; cat("-----\n", d, "\n-----\n") ; rm(d) # level 4 not helpful, but OK

# stuff with base::try

f <- function(k) try(upper(k), silent=TRUE)
d <- f(42) ; cat("-----\n", d, "\n-----\n") ; rm(d)
d <- f("42") ; cat("-----\n", d, "\n-----\n") ; rm(d) # regular try output

f2 <- function(k) tryStack(f(k), warn=0, silent=TRUE)

d <- f2(42) ; cat("-----\n", d, "\n-----\n") ; rm(d)
d <- f2("42") ; cat("-----\n", d, "\n-----\n") ; rm(d) # try -> no error.
# -> Use tryCatch and you can nest those calls. note that d gets longer.
162 unitHydrograph

unitHydrograph Unit Hydrograph

Description
Calculate continuous unit hydrograph with given n and k (in the framework of the linear storage
cascade)

Usage
unitHydrograph(n, k, t, force = FALSE)

Arguments
n Numeric. Number of storages in cascade.
k Numeric. Storage coefficient [1/s] (resistance to let water run out). High damp-
ing = slowly reacting landscape = high soil water absorbtion = high k.
t Numeric, possibly a vector. Time [s].
force Logical: Force the integral of the hydrograph to be 1? DEFAULT: FALSE

Value
Vector with the unit hydrograph along t

Note
The sum under the UH should always be 1 (if t is long enough). This needs yet to be checked...

Author(s)
Berry Boessenkool, <[email protected]>, July 2013

See Also
lsc on how to estimate n and k for a given discharge dataset. deconvolution.uh in the package
hydromad, http://hydromad.catchment.org

Examples

Time <- 0:100

plot(Time, unitHydrograph(n=2, k=3, t=Time), type="l", las=1,
main="Unit Hydrograph - linear storage cascade")
lines(Time, unitHydrograph(n=2, k=8, t=Time), col=2)
lines(Time, unitHydrograph(n=5.5,k=8, t=Time), col=4)
text(c(12, 20, 50), c(0.1, 0.04, 0.025), c("n=2, k=3","n=2, k=8","n=5.5, k=8"),
col=c(1,2,4), adj=0)
yearSample 163

# try several parameters (e.g. in Monte Carlo Simulation to estimate

# sensitivity of model towards slight differences/uncertainty in parameters):
nreps <- 1e3 # 5e4 eg on faster computers
n <- rnorm(nreps, mean=2, sd=0.8); n <- n[n>0]
k <- rnorm(nreps, mean=8, sd=1.1); k <- k[k>0]
UH <- sapply(1:nreps, function(i) unitHydrograph(n=n[i], k=k[i], t=Time))
UHquant <- apply(UH, 1, quantile, probs=0:10/10, na.rm=TRUE)
if(interactive()) View(UHquant)

plot(Time, unitHydrograph(n=2, k=8, t=Time), type="l", ylim=c(0, 0.06), las=1)

# uncertainty intervals as semi-transparent bands:
for(i in 1:5)
polygon(x=c(Time, rev(Time)), y=c(UHquant[i,], rev(UHquant[12-i,])),
col=rgb(0,0,1, alpha=0.3), lty=0)

lines(Time, UHquant[6,], col=4)

lines(Time, unitHydrograph(n=2, k=8, t=Time))

# Label a few bands for clarity:

points(rep(24,3), UHquant[c(2,5,9),25], pch="+")
for(i in 1:3) text(25, UHquant[c(2,5,9)[i],25],
paste("Q", c(10,40,80)[i], sep=""), adj=-0.1, cex=0.7)
# And explain what they mean:
Explain <- "Q80: 80% of the 50000 simulations are smaller than this value"
legend("topright", bty="n", legend=Explain)

# Some n and k values are cut off at the left, that explains the shift from the
# median of simulations relative to the n2k8 line.

yearSample Nonrandom year with sample

Description
Nerdy way to wish someone a happy new year by using sample

Usage
yearSample(year)

Arguments
year 4 digit numerical year.

Details
Nerdy way to wish someone a happy new year, eg:
Have a great
set.seed(1244); sample(0:9,4,T)
164 yearSample

Value
cats command into the console that can be copypasted to anyone’s R script.

Author(s)
Berry Boessenkool, <[email protected]>, April 2014

See Also
nameSample to impress with "randomly" finding a name, set.seed, sample, letters

Examples

yearSample(2016)
# Have a nerdy
set.seed(12353); sample(0:9, 4, replace=TRUE)
Index

∗Topic IO insertRows, 64
combineFiles, 34 l2array, 67
compareFiles, 36 panelDim, 115
dupes, 43 ∗Topic character
getName, 55 combineFiles, 34
na9, 106 compareFiles, 36
∗Topic aplot convertUmlaut, 37
ciBand, 18 dupes, 43
circle, 20 getName, 55
colPoints, 27 googleLink2pdf, 59
colPointsHist, 30 nameSample, 107
colPointsLegend, 32 removeSpace, 126
expReg, 45 toupper1, 156
funnelPlot, 48 truncMessage, 158
legendmt, 72 ∗Topic chron
linReg, 80 monthAxis, 94
locArrow, 82 monthLabs, 96
locLine, 83 spiralDate, 142
logAxis, 84 spiralDateAnim, 144
logHist, 86 timeAxis, 153
logVals, 88 timer, 155
monthAxis, 94 ∗Topic classif
mReg, 100 classify, 21
popleaf, 119 ∗Topic color
quantileBands, 121 addAlpha, 5
roundedRect, 129 addFade, 6
runAxis, 130 colPoints, 27
seasonality, 131 colPointsHist, 30
smallPlot, 137 colPointsLegend, 32
smoothLines, 140 divPal, 41
spiralDate, 142 rainbow2, 125
spiralDateAnim, 144 seqPal, 134
textField, 149 showPal, 137
timeAxis, 153 spiralDate, 142
∗Topic arith spiralDateAnim, 144
approx2, 10 ∗Topic connection
logSpaced, 87 funTinn, 53
sortDF, 141 ∗Topic datagen
∗Topic array seqR, 136

165
166 INDEX

∗Topic distribution openFile, 112

betaPlot, 12 packagePath, 114
betaPlotComp, 13 pdfpng, 117
groupHist, 60 ∗Topic hplot
normPlot, 110 betaPlot, 12
∗Topic documentation betaPlotComp, 13
berryFunctions-package, 4 ciBand, 18
createFun, 38 climateGraph, 23
dataStr, 40 colPoints, 27
exTime, 47 expReg, 45
∗Topic dplot funnelPlot, 48
addAlpha, 5 groupHist, 60
addFade, 6 horizHist, 62
approx2, 10 linLogHist, 75
divPal, 41 linLogTrans, 77
groupHist, 60 linReg, 80
lim0, 74 lsc, 90
linLogHist, 75 mReg, 100
linLogTrans, 77 normPlot, 110
logAxis, 84 smallPlot, 137
logHist, 86 spiralDate, 142
logVals, 88 spiralDateAnim, 144
monthAxis, 94 superPos, 145
panelDim, 115 tableColVal, 147
pretty2, 120 unitHydrograph, 162
quantileBands, 121 ∗Topic htest
rainbow2, 125 ci, 17
seqPal, 134 ∗Topic iplot
showPal, 137 locArrow, 82
smallPlot, 137 locLine, 83
timeAxis, 153 ∗Topic list
∗Topic dynamic l2array, 67
linLogHist, 75 l2df, 70
linLogTrans, 77 ∗Topic logic
∗Topic error between, 15
is.error, 66 TFtest, 151
traceCall, 157 ∗Topic manip
tryStack, 159 headtail, 61
∗Topic file insertRows, 64
checkFile, 16 l2array, 67
combineFiles, 34 l2df, 70
compareFiles, 36 movAv, 97
createPres, 39 movAvLines, 99
dupes, 43 rescale, 127
lsMem, 93 sortDF, 141
na9, 106 ∗Topic misc
newFilename, 108 addRows, 7
normalizePathCP, 109 insertRows, 64
INDEX 167

∗Topic multivariate addAlpha, 5, 6, 42, 99, 100, 135

mReg, 100 addFade, 5, 6
∗Topic nonlinear addRows, 7, 65
exp4p, 44 alarm, 155, 156
mReg, 100 all.equal, 8
∗Topic optimize almost.equal, 8
lsc, 90 anhang, 9
panelDim, 115 apply, 123
∗Topic package approx, 10
berryFunctions-package, 4 approx2, 10, 19
instGit, 65 around, 11
library2, 73 arrows, 82
∗Topic print as.Date, 94, 96, 97, 132, 142, 143, 153
dataStr, 40 as.POSIXct, 94, 153
∗Topic programming axis, 14, 63, 64, 84, 94, 95, 120, 131, 153, 154
is.error, 66 axis.Date, 95, 154
lsMem, 93
owa, 113 barplot, 63, 64
traceCall, 157 berryFunctions
tryStack, 159 (berryFunctions-package), 4
∗Topic regression berryFunctions-package, 4
exp4p, 44 betaPlot, 12, 14, 111
expReg, 45 betaPlotComp, 13, 13
linReg, 80 between, 15
mReg, 100 browseURL, 52
∗Topic smooth
movAv, 97 capture.output, 48
movAvLines, 99 cat, 107, 159, 164
∗Topic spatial checkFile, 16, 112, 157
distance, 40 ci, 17
∗Topic ts ciBand, 10, 18, 122
gof, 57 circle, 20
lsc, 90 classify, 21, 27, 28, 88, 135, 148
movAv, 97 climateGraph, 23
movAvLines, 99 col2rgb, 5, 6, 141
superPos, 145 colorRamp, 6, 42, 135
unitHydrograph, 162 colorRampPalette, 42, 135
∗Topic univar colors, 5, 6
gof, 57 colPoints, 22, 23, 27, 31–34, 132, 133, 142,
quantileBands, 121 143
quantileMean, 123 colPointsHist, 28, 30, 34
sortDF, 141 colPointsLegend, 27, 28, 32, 32, 133, 137,
∗Topic utilities 138, 143
exTime, 47 combineFiles, 34, 36
timer, 155 compareFiles, 35, 36, 43
convertUmlaut, 37
abind, 68 cor, 58
abline, 28, 45, 46, 75, 77, 80–85, 131, 132 createFun, 38, 39
add.scatter, 138 createPres, 39
168 INDEX

curve, 74 image, 27
inherits, 67
data, 40 insertRows, 7, 64
data.frame, 7 install.packages, 66, 73
dataStr, 40 instGit, 65
Date, 94 is.character, 52
dbeta, 12–14 is.error, 66
decompose, 98
density, 33 kge (gof), 57
distance, 40
divPal, 41, 135, 137 l2array, 67, 70
dnorm, 111 l2df, 68, 69
dupes, 36, 43 legend, 44–46, 49, 72, 80, 81, 102, 113
legendmt, 72
edit, 53 letters, 107, 164
eval.parent, 118 library, 73
example, 48 library2, 73
exp4p, 44, 101 lim0, 74
expReg, 45, 81 lines, 12, 100, 111, 132, 141
extendrange, 74, 136 linLogHist, 75, 77, 144
exTime, 47 linLogTrans, 76, 77
linReg, 47, 80
file.exists, 16, 109
lm, 45, 47, 58, 80, 81, 103
filter, 98
locArrow, 82
findInterval, 15
locator, 82, 83
format, 84, 88, 89
locLine, 82, 83
formatC, 128
loess, 98
funnelPlot, 48
log, 87, 88
funSource, 9, 38, 51, 66
log10, 85, 87, 89
funTinn, 53
logAxis, 46, 76, 84, 86, 89, 131
getColumn, 53 logHist, 86
getElement, 54 logical, 152
getName, 55 logSpaced, 22, 87, 135
getwd, 115 logVals, 75, 77, 78, 84, 85, 88, 121
glm, 103 ls, 93
gof, 57 lsc, 90, 146, 162
gofNA (gof), 57 lsMem, 93
googleLink2pdf, 59
matrix, 7
groupHist, 60, 116
mean, 121, 122
gsub, 37, 59, 126
median, 121, 122
head, 36, 61, 62 message, 40, 47, 67, 73, 113, 158, 159
headtail, 61 min, 15
heatmap, 148 model.frame, 101
help, 47, 68 monthAxis, 94, 131
hist, 31, 60, 61, 63, 64, 75, 76, 86 monthLabs, 95, 96, 154
horizHist, 62 movAv, 97, 99, 100, 121
movAvLines, 99
iconv, 37 mReg, 45, 47, 81, 100
INDEX 169

na9, 106 rect, 129

nameSample, 107, 164 removeSpace, 126
newFilename, 35, 39, 108, 110, 118 require2 (library2), 73
nndist, 41 rescale, 127
normalizePath, 109, 110 rgb, 5, 141
normalizePathCP, 109 rmse, 91
normPlot, 13, 110 rmse (gof), 57
nse, 91 rollapply, 98
nse (gof), 57 round0, 128
roundedRect, 129, 149, 150
object.size, 93 rsquare (gof), 57
openFile, 39, 112, 118 runAxis, 130
optim, 45, 57, 101, 103
options, 89 sample, 107, 164
order, 142 sapply, 70
owa, 113, 132 scan, 35
seasonality, 131, 143
packagePath, 38, 114 segments, 28
panelDim, 115 seq, 87, 136
par, 12, 14, 19, 28, 31, 33, 44, 46, 49, 60, 74, seqPal, 27, 33, 42, 125, 134, 137, 147
75, 77, 80, 81, 84, 94, 101, 111, 133, seqR, 80, 136
137, 138, 153, 154 set.seed, 107, 118, 164
parallelCode, 117 setwd, 39
paste, 35, 97, 106, 120 showNonASCII, 37
pdf, 47, 117, 118, 148 showPal, 42, 135, 137
pdfpng, 117 signif, 82
plot, 12, 14, 19, 28, 44, 46, 49, 81, 87, 90, sin, 20
111, 113 smallPlot, 27, 28, 31–34, 137
plot.default, 74 smooth, 98
png, 117, 118 smoothLines, 140
points, 19, 28 sort, 142
polygon, 12, 18–21, 24, 45, 111, 122, 129 sortDF, 12, 141
popleaf, 119 spiralDate, 132, 133, 142, 144
POSIXct, 94, 153 spiralDateAnim, 143, 144
predict.lm, 46, 47, 80 split, 60
pretty, 120, 121, 153 sprintf, 128
pretty2, 120 stop, 16, 67
prettyNum, 88 str, 40
strheight, 138
quantile, 121–123 strptime, 94, 132, 142, 143, 153
quantileBands, 19, 121 strsplit, 59
quantileMean, 122, 123, 132 strwidth, 33, 150
sub, 126
rainbow, 125 subplot, 138
rainbow2, 125 subset, 54
range, 120, 136 substitute, 28, 54, 56
rbind, 7 substr, 157
read.table, 106 superPos, 91, 145
readLines, 36 suppressMessages, 48
170 INDEX

suppressWarnings, 48
symbols, 21
Syntax, 152
Sys.sleep, 75, 77, 144, 156
system.time, 48
system2, 9, 38, 112

t.test, 17, 18
tableColVal, 147
tail, 61
tapply, 60, 61
tempfile, 47
text, 33, 122, 147–150
textField, 14, 130, 132, 149
TFtest, 151
timeAxis, 95, 97, 153
timer, 155
title, 133, 138
toupper, 156, 157
toupper1, 156
traceback, 157
traceCall, 157, 160
truncMessage, 158
try, 67, 159, 160
tryCatch, 159
tryStack, 157, 159
txtProgressBar, 156

unitHydrograph, 91, 146, 162

View, 11, 12

warning, 16, 159

which, 11
write, 35

xy.coords, 46, 81

yearSample, 107, 163