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Met R

This package provides tools for analyzing meteorological data in R. It contains functions for reading meteorological file formats, plotting spatial weather data, and performing common calculations like wind components and geopotential heights. The package extends ggplot2 for improved plotting of scalar and vector fields.

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0% found this document useful (0 votes)

28 views95 pages

Met R

Uploaded by

Ary Giri

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Package ‘metR’

October 13, 2022

Type Package
Language en-GB
Title Tools for Easier Analysis of Meteorological Fields
Version 0.13.0
Description Many useful functions and extensions for dealing
with meteorological data in the tidy data framework. Extends 'ggplot2'
for better plotting of scalar and vector fields and provides commonly
used analysis methods in the atmospheric sciences.
License GPL-3

URL https://github.com/eliocamp/metR

BugReports https://github.com/eliocamp/metR/issues
Depends R (>= 2.10)
Imports checkmate, data.table, digest, Formula, formula.tools, ggplot2
(>= 3.0.0), grid, gtable, memoise, plyr, scales, sp, stringr,
purrr, isoband, lubridate
Suggests maps, maptools, covr, irlba, knitr, ncdf4, pkgdown, reshape2,
rmarkdown, testthat (>= 2.1.0), viridis, PCICt, gridExtra,
vdiffr, proj4, kriging, raster, rgdal, here, gsignal
ByteCompile yes
Encoding UTF-8
LazyData true
RoxygenNote 7.2.1
VignetteBuilder knitr
NeedsCompilation no
Author Elio Campitelli [cre, aut] (<https://orcid.org/0000-0002-7742-9230>)
Maintainer Elio Campitelli <[email protected]>
Repository CRAN
Date/Publication 2022-10-06 20:30:05 UTC

1
2 R topics documented:

R topics documented:
Anomaly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
as.discretised_scale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
as.path . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
ConvertLongitude . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
coriolis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
cut.eof . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
denormalise . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Derivate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
DivideTimeseries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
EOF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
EPflux . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
FitLm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
geom_arrow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
geom_contour2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
geom_contour_fill . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
geom_contour_tanaka . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
geom_label_contour . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
geom_relief . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
geom_streamline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
geopotential . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
GeostrophicWind . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
GetSMNData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
GetTopography . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
guide_vector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Impute2D . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
ImputeEOF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Interpolate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
is.cross . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
JumpBy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
logic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
Mag . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
MakeBreaks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
map_labels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
MaskLand . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
metR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Percentile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
ReadNetCDF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
reverselog_trans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
scale_divergent . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
scale_label_colour_continuous . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
scale_longitude . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
scale_mag . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
season . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
Smooth2D . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
spherical . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
standard_atmosphere . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Anomaly 3

stat_na . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
stat_subset . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
surface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
temperature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
thermodynamics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
Trajectory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
WaveFlux . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
waves . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
WrapCircular . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90

Index 92

Anomaly Anomalies

Description
Saves keystrokes for computing anomalies.

Usage
Anomaly(x, baseline = seq_along(x), ...)

Arguments
x numeric vector
baseline logical or numerical vector used for subsetting x before computing the mean
... other arguments passed to mean such as na.rm

Value
A numeric vector of the same length as x with each value’s distance to the mean.

See Also
Other utilities: JumpBy(), Mag(), Percentile(), logic

Examples
# Zonal temperature anomaly
library(data.table)
temperature[, .(lon = lon, air.z = Anomaly(air)), by = .(lat, lev)]
4 as.discretised_scale

as.discretised_scale Create discretised versions of continuous scales

Description
This scale allows ggplot to understand data that has been discretised with some procedure akin to
cut and access the underlying continuous values. For a scale that does the opposite (take continuous
data and treat them as discrete) see ggplot2::binned_scale().

Usage
as.discretised_scale(scale_function)

scale_fill_discretised(
...,
low = "#132B43",
high = "#56B1F7",
space = "Lab",
na.value = "grey50",
guide = ggplot2::guide_colorsteps(even.steps = FALSE, show.limits = TRUE),
aesthetics = "fill"
)

scale_fill_divergent_discretised(
...,
low = scales::muted("blue"),
mid = "white",
high = scales::muted("red"),
midpoint = 0,
space = "Lab",
na.value = "grey50",
guide = ggplot2::guide_colorsteps(even.steps = FALSE, show.limits = TRUE)
)

discretised_scale(
aesthetics,
scale_name,
palette,
name = ggplot2::waiver(),
breaks = ggplot2::waiver(),
labels = ggplot2::waiver(),
limits = NULL,
trans = scales::identity_trans(),
na.value = NA,
drop = FALSE,
guide = ggplot2::guide_colorsteps(even.steps = FALSE),
position = "left",
as.discretised_scale 5

rescaler = scales::rescale,
oob = scales::censor,
super = ScaleDiscretised
)

Arguments
scale_function a scale function (e.g. scale_fill_divergent)
... Arguments passed on to continuous_scale
scale_name The name of the scale that should be used for error messages as-
sociated with this scale.
palette A palette function that when called with a numeric vector with values
between 0 and 1 returns the corresponding output values (e.g., scales::area_pal()).
name The name of the scale. Used as the axis or legend title. If waiver(), the
default, the name of the scale is taken from the first mapping used for that
aesthetic. If NULL, the legend title will be omitted.
breaks One of:
• NULL for no breaks
• waiver() for the default breaks computed by the transformation object
• A numeric vector of positions
• A function that takes the limits as input and returns breaks as output
(e.g., a function returned by scales::extended_breaks()). Also ac-
cepts rlang lambda function notation.
minor_breaks One of:
• NULL for no minor breaks
• waiver() for the default breaks (one minor break between each major
break)
• A numeric vector of positions
• A function that given the limits returns a vector of minor breaks. Also
accepts rlang lambda function notation.
n.breaks An integer guiding the number of major breaks. The algorithm may
choose a slightly different number to ensure nice break labels. Will only
have an effect if breaks = waiver(). Use NULL to use the default number
of breaks given by the transformation.
labels One of:
• NULL for no labels
• waiver() for the default labels computed by the transformation object
• A character vector giving labels (must be same length as breaks)
• A function that takes the breaks as input and returns labels as output.
Also accepts rlang lambda function notation.
limits One of:
• NULL to use the default scale range
• A numeric vector of length two providing limits of the scale. Use NA to
refer to the existing minimum or maximum
6 as.discretised_scale

• A function that accepts the existing (automatic) limits and returns new
limits. Also accepts rlang lambda function notation. Note that setting
limits on positional scales will remove data outside of the limits. If
the purpose is to zoom, use the limit argument in the coordinate system
(see coord_cartesian()).
rescaler A function used to scale the input values to the range [0, 1]. This is
always scales::rescale(), except for diverging and n colour gradients
(i.e., scale_colour_gradient2(), scale_colour_gradientn()). The
rescaler is ignored by position scales, which always use scales::rescale().
Also accepts rlang lambda function notation.
oob One of:
• Function that handles limits outside of the scale limits (out of bounds).
Also accepts rlang lambda function notation.
• The default (scales::censor()) replaces out of bounds values with
NA.
• scales::squish() for squishing out of bounds values into range.
• scales::squish_infinite() for squishing infinite values into range.
trans For continuous scales, the name of a transformation object or the object
itself. Built-in transformations include "asn", "atanh", "boxcox", "date",
"exp", "hms", "identity", "log", "log10", "log1p", "log2", "logit", "modu-
lus", "probability", "probit", "pseudo_log", "reciprocal", "reverse", "sqrt"
and "time".
A transformation object bundles together a transform, its inverse, and meth-
ods for generating breaks and labels. Transformation objects are defined in
the scales package, and are called <name>_trans (e.g., scales::boxcox_trans()).
You can create your own transformation with scales::trans_new().
expand For position scales, a vector of range expansion constants used to add
some padding around the data to ensure that they are placed some distance
away from the axes. Use the convenience function expansion() to gen-
erate the values for the expand argument. The defaults are to expand the
scale by 5% on each side for continuous variables, and by 0.6 units on each
side for discrete variables.
position For position scales, The position of the axis. left or right for y
axes, top or bottom for x axes.
super The super class to use for the constructed scale
low, high Colours for low and high ends of the gradient.
space colour space in which to calculate gradient. Must be "Lab" - other values are
deprecated.
na.value Colour to use for missing values
guide Type of legend. Use "colourbar" for continuous colour bar, or "legend" for
discrete colour legend.
aesthetics Character string or vector of character strings listing the name(s) of the aes-
thetic(s) that this scale works with. This can be useful, for example, to ap-
ply colour settings to the colour and fill aesthetics at the same time, via
aesthetics = c("colour", "fill").
as.discretised_scale 7

mid colour for mid point

midpoint The midpoint (in data value) of the diverging scale. Defaults to 0.
scale_name The name of the scale that should be used for error messages associated with
this scale.
palette A palette function that when called with a numeric vector with values between
0 and 1 returns the corresponding output values (e.g., scales::area_pal()).
name The name of the scale. Used as the axis or legend title. If waiver(), the default,
the name of the scale is taken from the first mapping used for that aesthetic. If
NULL, the legend title will be omitted.
breaks One of:
• NULL for no breaks
• waiver() for the default breaks computed by the transformation object
• A numeric vector of positions
• A function that takes the limits as input and returns breaks as output (e.g.,
a function returned by scales::extended_breaks()). Also accepts rlang
lambda function notation.
labels One of:
• NULL for no labels
• waiver() for the default labels computed by the transformation object
• A character vector giving labels (must be same length as breaks)
• A function that takes the breaks as input and returns labels as output. Also
accepts rlang lambda function notation.
limits One of:
• NULL to use the default scale range
• A numeric vector of length two providing limits of the scale. Use NA to
refer to the existing minimum or maximum
• A function that accepts the existing (automatic) limits and returns new
limits. Also accepts rlang lambda function notation. Note that setting
limits on positional scales will remove data outside of the limits. If the
purpose is to zoom, use the limit argument in the coordinate system (see
coord_cartesian()).
trans For continuous scales, the name of a transformation object or the object itself.
Built-in transformations include "asn", "atanh", "boxcox", "date", "exp", "hms",
"identity", "log", "log10", "log1p", "log2", "logit", "modulus", "probability",
"probit", "pseudo_log", "reciprocal", "reverse", "sqrt" and "time".
A transformation object bundles together a transform, its inverse, and methods
for generating breaks and labels. Transformation objects are defined in the scales
package, and are called <name>_trans (e.g., scales::boxcox_trans()). You
can create your own transformation with scales::trans_new().
drop Should unused factor levels be omitted from the scale? The default, TRUE, uses
the levels that appear in the data; FALSE uses all the levels in the factor.
position For position scales, The position of the axis. left or right for y axes, top or
bottom for x axes.
8 as.discretised_scale

rescaler A function used to scale the input values to the range [0, 1]. This is always
scales::rescale(), except for diverging and n colour gradients (i.e., scale_colour_gradient2(),
scale_colour_gradientn()). The rescaler is ignored by position scales,
which always use scales::rescale(). Also accepts rlang lambda function
notation.
oob One of:
• Function that handles limits outside of the scale limits (out of bounds). Also
accepts rlang lambda function notation.
• The default (scales::censor()) replaces out of bounds values with NA.
• scales::squish() for squishing out of bounds values into range.
• scales::squish_infinite() for squishing infinite values into range.
super The super class to use for the constructed scale

Details
This scale makes it very easy to synchronise the breaks of filled contours and the breaks shown no
the colour guide. Bear in mind that when using geom_contour_fill(), the default fill aesthetic
(level_mid) is not discretised. To use this scale with that geom, you need to set aes(fill =
stat(level)).

Value
A function with the same arguments as scale_function that works with discretised values.

# Using the `level` compute aesthetic from `geom_contour_fill()`

# (or ggplot2::geom_contour_filled()), the default scale is discrete.
# This means that you cannot map colours to the underying numbers.
v <- ggplot(faithfuld, aes(waiting, eruptions, z = density))
v + geom_contour_fill(aes(fill = stat(level)))

v + geom_contour_fill(aes(fill = stat(level))) +
scale_fill_discretised()

# The scale can be customised the same as any continuous colour scale
v + geom_contour_fill(aes(fill = stat(level))) +
scale_fill_discretised(low = "#a62100", high = "#fff394")

# Setting limits explicitly will truncate the scale

# (if any limit is inside the range of the breaks but doesn't
as.path 9

# coincide with any range, it will be rounded with a warning)

v + geom_contour_fill(aes(fill = stat(level))) +
scale_fill_discretised(low = "#a62100", high = "#fff394",
limits = c(0.01, 0.028))

# Or extend it.
v + geom_contour_fill(aes(fill = stat(level))) +
scale_fill_discretised(low = "#a62100", high = "#fff394",
limits = c(0, 0.07))

v + geom_contour_fill(aes(fill = stat(level))) +
scale_fill_divergent_discretised(midpoint = 0.02)

# Existing continous scales can be "retrofitted" by changing the `super`

# and `guide` arguments.
v + geom_contour_fill(aes(fill = stat(level))) +
scale_fill_distiller(super = ScaleDiscretised)

# Unequal breaks will, by default, map to unequal spacing in the guide

v + geom_contour_fill(aes(fill = stat(level)), breaks = c(0, 0.005, 0.01, 0.02, 0.04)) +
scale_fill_discretised()

# You can change that by the `even.steps` argument on ggplot2::guide_colorsteps()

v + geom_contour_fill(aes(fill = stat(level)), breaks = c(0, 0.005, 0.01, 0.02, 0.04)) +
scale_fill_discretised(guide = guide_colorsteps(even.steps = TRUE, show.limits = TRUE))

as.path Interpolates between locations

Description
This is a helper function to quickly make an interpolated list of locations between a number of
locations

Usage
as.path(x, y, n = 10, path = TRUE)

Arguments
x, y numeric vectors of x and y locations. If one of them is of length 1, if will be
recycled.
n number of points to interpolate to
path either TRUE of a character vector with the name of the path.

Details
This function is mostly useful when combined with Interpolate
10 ConvertLongitude

Value
A list of components x and y with the list of locations and the path arguments

ConvertLongitude Converts between longitude conventions

Description
Converts longitude from [0, 360) to [-180, 180) and vice versa.

Usage
ConvertLongitude(lon, group = NULL, from = NULL)

Arguments
lon numeric vector of longitude
group optional vector of groups (the same length as longitude) that will be split on the
edges (see examples)
from optionally explicitly say from which convention to convert

Value
If group is missing, a numeric vector the same length of lon. Else, a list with vectors lon and
group.

Examples
library(ggplot2)
library(data.table)
data(geopotential)
ggplot(geopotential[date == date[1]], aes(lon, lat, z = gh)) +
geom_contour(color = "black") +
geom_contour(aes(x = ConvertLongitude(lon)))

map <- setDT(map_data("world"))

map[, c("lon", "group2") := ConvertLongitude(long, group, from = 180)]

ggplot(map, aes(lon, lat, group = group2)) +

geom_path()
coriolis 11

coriolis Effects of the Earth’s rotation

Description
Coriolis and beta parameters by latitude.

Usage
coriolis(lat)

f(lat)

coriolis.dy(lat, a = 6371000)

f.dy(lat, a = 6371000)

Arguments
lat latitude in degrees
a radius of the earth

Details
All functions use the correct sidereal day (24hs 56mins 4.091s) instead of the incorrect solar day
(24hs) for 0.3\ pedantry.

cut.eof Remove some principal components.

Description
Returns an eof object with just the n principal components.

Usage
## S3 method for class 'eof'
cut(x, n, ...)

Arguments
x an eof object
n which eofs to keep
... further arguments passed to or from other methods
12 Derivate

denormalise Denormalise eof matrices

Description
The matrices returned by EOF() are normalized. This function multiplies the left or right matrix by
the diagonal matrix to return it to proper units.

Usage
denormalise(eof, which = c("left", "right"))

denormalize(eof, which = c("left", "right"))

Arguments
eof an eof object.
which which side of the eof decomposition to denormalise

Derivate Derivate a discrete variable using finite differences

Description
Derivate a discrete variable using finite differences

Usage
Derivate(
formula,
order = 1,
cyclical = FALSE,
fill = FALSE,
data = NULL,
sphere = FALSE,
a = 6371000,
equispaced = TRUE
)

Laplacian(
formula,
cyclical = FALSE,
fill = FALSE,
data = NULL,
sphere = FALSE,
Derivate 13

a = 6371000,
equispaced = TRUE
)

Divergence(
formula,
cyclical = FALSE,
fill = FALSE,
data = NULL,
sphere = FALSE,
a = 6371000,
equispaced = TRUE
)

Vorticity(
formula,
cyclical = FALSE,
fill = FALSE,
data = NULL,
sphere = FALSE,
a = 6371000,
equispaced = TRUE
)

Arguments
formula a formula indicating dependent and independent variables
order order of the derivative
cyclical logical vector of boundary condition for each independent variable
fill logical indicating whether to fill values at the boundaries with forward and back-
wards differencing
data optional data.frame containing the variables
sphere logical indicating whether to use spherical coordinates (see details)
a radius to use in spherical coordinates (defaults to Earth’s radius)
equispaced logical indicating whether points are equispaced or not.

Details
∂nx
Each element of the return vector is an estimation of ∂y n by centred finite differences.
If sphere = TRUE, then the first two independent variables are assumed to be longitude and latitude
(in that order) in degrees. Then, a correction is applied to the derivative so that they are in the
same units as a.
Using fill = TRUE will degrade the solution near the edges of a non-cyclical boundary. Use with
caution.
Laplacian(), Divergence() and Vorticity() are convenient wrappers that call Derivate() and
make the appropriate sums. For Divergence() and Vorticity(), formula must be of the form vx
+ vy ~ x + y (in that order).
14 DivideTimeseries

Value
If there is one independent variable and one dependent variable, a numeric vector of the same length
as the dependent variable. If there are two or more independent variables or two or more dependent
variables, a list containing the directional derivatives of each dependent variables.

See Also
Other meteorology functions: EOF(), GeostrophicWind(), WaveFlux(), thermodynamics, waves

Examples
theta <- seq(0, 360, length.out = 20)*pi/180
theta <- theta[-1]
x <- cos(theta)
dx_analytical <- -sin(theta)
dx_finitediff <- Derivate(x ~ theta, cyclical = TRUE)[[1]]

plot(theta, dx_analytical, type = "l")

points(theta, dx_finitediff, col = "red")

# Curvature (Laplacian)
# Note the different boundary conditions for each dimension
variable <- expand.grid(lon = seq(0, 360, by = 3)[-1],
lat = seq(-90, 90, by = 3))
variable$z <- with(variable, cos(lat*pi/180*3) + sin(lon*pi/180*2))
variable <- cbind(
variable,
as.data.frame(Derivate(z ~ lon + lat, data = variable,
cyclical = c(TRUE, FALSE), order = 2)))
library(ggplot2)
ggplot(variable, aes(lon, lat)) +
geom_contour(aes(z = z)) +
geom_contour(aes(z = z.ddlon + z.ddlat), color = "red")

# The same as
ggplot(variable, aes(lon, lat)) +
geom_contour(aes(z = z)) +
geom_contour(aes(z = Laplacian(z ~ lon + lat, cyclical = c(TRUE, FALSE))),
color = "red")

DivideTimeseries Divides long timeseries for better reading

Description
Long timeseries can be compressed to the point of being unreadable when plotted on a page. This
function takes a ggplot object of a timeseries and divides it into panels so that the time dimension
gets stretched for better readability.
EOF 15

Usage

DivideTimeseries(g, x, n = 2, xlab = "x", ylab = "y")

Arguments

g ggplot object
x The vector that was used in g for the x axis (must be of class Date)
n Number of panels
xlab x axis label
ylab y axis label

Value

Draws a plot.

See Also

Other ggplot2 helpers: MakeBreaks(), WrapCircular(), geom_arrow(), geom_contour2(), geom_contour_fill(),

geom_label_contour(), geom_relief(), geom_streamline(), guide_colourstrip(), map_labels,
reverselog_trans(), scale_divergent, scale_longitude, stat_na(), stat_subset()

Examples

library(ggplot2)
library(data.table)
gdata <- geopotential[lat == -30 & lon == 0]
g <- ggplot(gdata, aes(date, gh)) +
geom_line() +
geom_smooth() +
scale_x_date(date_breaks = "1 year", date_labels = "%b")
DivideTimeseries(g, gdata$date, n = 2, "Date", "Max Temperature")

EOF Empirical Orthogonal Function

Description

Computes Singular Value Decomposition (also known as Principal Components Analysis or Em-
pirical Orthogonal Functions).
16 EOF

Usage
EOF(
formula,
n = 1,
data = NULL,
B = 0,
probs = c(lower = 0.025, mid = 0.5, upper = 0.975),
rotate = FALSE,
suffix = "PC",
fill = NULL,
engine = NULL
)

Arguments
formula a formula to build the matrix that will be used in the SVD decomposition (see
Details)
n which singular values to return (if NULL, returns all)
data a data.frame
B number of bootstrap samples used to estimate confidence intervals. Ignored if
<= 1.
probs the probabilities of the lower and upper values of estimated confidence intervals.
If named, it’s names will be used as column names.
rotate if TRUE, scores and loadings will be rotated using varimax
suffix character to name the principal components
fill value to infill implicit missing values or NULL if the data is dense.
engine function to use to compute SVD. If NULL it uses irlba::irlba (if installed) if the
largest singular value to compute is lower than half the maximum possible value,
otherwise it uses base::svd. If the user provides a function, it needs to be a drop-
in replacement for base::svd (the same arguments and output format).

Details
Singular values can be computed over matrices so formula denotes how to build a matrix from the
data. It is a formula of the form VAR ~ LEFT | RIGHT (see Formula::Formula) in which VAR is
the variable whose values will populate the matrix, and LEFT represent the variables used to make
the rows and RIGHT, the columns of the matrix. Think it like "VAR as a function of LEFT and
RIGHT". The variable combination used in this formula must identify an unique value in a cell.
So, for example, v ~ x + y | t would mean that there is one value of v for each combination of x, y
and t, and that there will be one row for each combination of x and y and one row for each t.
In the result, the left and right vectors have dimensions of the LEFT and RIGHT part of the formula,
respectively.
It is much faster to compute only some singular vectors, so is advisable not to set n to NULL. If the
irlba package is installed, EOF uses irlba::irlba instead of base::svd since it’s much faster.
The bootstrapping procedure follows Fisher et.al. (2016) and returns the standard deviation of each
singular value.
EOF 17

Value
An eof object which is just a named list of data.tables

left data.table with left singular vectors

right data.table with right singular vectors
sdev data.table with singular values, their explained variance, and, optionally, quantiles estimated
via bootstrap

There are some methods implemented

• summary
• screeplot and the equivalent autoplot
• cut.eof
• predict

References
Fisher, A., Caffo, B., Schwartz, B., & Zipunnikov, V. (2016). Fast, Exact Bootstrap Principal
Component Analysis for p > 1 million. Journal of the American Statistical Association, 111(514),
846–860. doi:10.1080/01621459.2015.1062383

See Also
Other meteorology functions: Derivate(), GeostrophicWind(), WaveFlux(), thermodynamics,
waves

Examples
# The Antarctic Oscillation is computed from the
# monthly geopotential height anomalies weigthed by latitude.
library(data.table)
data(geopotential)
geopotential <- copy(geopotential)
geopotential[, gh.t.w := Anomaly(gh)*sqrt(cos(lat*pi/180)),
by = .(lon, lat, month(date))]

eof <- EOF(gh.t.w ~ lat + lon | date, 1:5, data = geopotential,

B = 100, probs = c(low = 0.1, hig = 0.9))

# Inspect the explained variance of each component

summary(eof)
screeplot(eof)

# Keep only the 1st.

aao <- cut(eof, 1)

# AAO field
library(ggplot2)
ggplot(aao$left, aes(lon, lat, z = gh.t.w)) +
geom_contour(aes(color = ..level..)) +
18 EPflux

coord_polar()

# AAO signal
ggplot(aao$right, aes(date, gh.t.w)) +
geom_line()

# standard deviation, % of explained variance and

# confidence intervals.
aao$sdev

# Reconstructed fields based only on the two first

# principal components
field <- predict(eof, 1:2)

# Compare it to the real field.

ggplot(field[date == date[1]], aes(lon, lat)) +
geom_contour_fill(aes(z = gh.t.w), data = geopotential[date == date[1]]) +
geom_contour2(aes(z = gh.t.w, linetype = factor(-sign(stat(level))))) +
scale_fill_divergent()

EPflux Computes Eliassen-Palm fluxes.

Description
Computes Eliassen-Palm fluxes.

Usage
EPflux(lon, lat, lev, t, u, v)

Arguments
lon longitudes in degrees.
lat latitudes in degrees.
lev pressure levels.
t temperature in Kelvin.
u zonal wind in m/s.
v meridional wind in m/s.

Value
A data.table with columns Flon, Flat and Flev giving the zonal, meridional and vertical compo-
nents of the EP Fluxes at each longitude, latitude and level.
FitLm 19

References
Plumb, R. A. (1985). On the Three-Dimensional Propagation of Stationary Waves. Journal of the
Atmospheric Sciences, 42(3), 217–229. doi:10.1175/15200469(1985)042<0217:OTTDPO>2.0.CO;2
Cohen, J., Barlow, M., Kushner, P. J., & Saito, K. (2007). Stratosphere–Troposphere Coupling and
Links with Eurasian Land Surface Variability. Journal of Climate, 20(21), 5335–5343. doi:10.1175/
2007JCLI1725.1

FitLm Fast estimates of linear regression

Description
Computes a linear regression with stats::.lm.fit and returns the estimate and, optionally, standard
error for each regressor.

Usage
FitLm(y, ..., weights = NULL, se = FALSE, r2 = se)

ResidLm(y, ..., weights = NULL)

Detrend(y, time = seq_along(y))

Arguments
y numeric vector of observations to model
... numeric vectors of variables used in the modelling
weights numerical vector of weights (which doesn’t need to be normalised)
se logical indicating whether to compute the standard error
r2 logical indicating whether to compute r squared
time time vector to use for detrending. Only necessary in the case of irregularly
sampled timeseries

Value
FitLm returns a list with elements
term the name of the regressor
estimate estimate of the regression
std.error standard error
df degrees of freedom
r.squared Percent of variance explained by the model (repeated in each term)
adj.r.squared r.squared‘ adjusted based on the degrees of freedom)
ResidLm and Detrend returns a vector of the same length
If there’s no complete cases in the regression, NAs are returned with no warning.
20 geom_arrow

Examples
# Linear trend with "signficant" areas shaded with points
library(data.table)
library(ggplot2)
system.time({
regr <- geopotential[, FitLm(gh, date, se = TRUE), by = .(lon, lat)]
})

ggplot(regr[term != "(Intercept)"], aes(lon, lat)) +

geom_contour(aes(z = estimate, color = ..level..)) +
stat_subset(aes(subset = abs(estimate) > 2*std.error), size = 0.05)

# Using stats::lm() is much slower and with no names.

## Not run:
system.time({
regr <- geopotential[, coef(lm(gh ~ date))[2], by = .(lon, lat)]
})

## End(Not run)

geom_arrow Arrows

Description
Parametrization of ggplot2::geom_segment either by location and displacement or by magnitude
and angle with default arrows. geom_arrow() is the same as geom_vector() but defaults to pre-
serving the direction under coordinate transformation and different plot ratios.

Usage
geom_arrow(
mapping = NULL,
data = NULL,
stat = "arrow",
position = "identity",
...,
start = 0,
direction = c("ccw", "cw"),
pivot = 0.5,
preserve.dir = TRUE,
min.mag = 0,
skip = 0,
skip.x = skip,
skip.y = skip,
arrow.angle = 15,
arrow.length = 0.5,
geom_arrow 21

arrow.ends = "last",
arrow.type = "closed",
arrow = grid::arrow(arrow.angle, grid::unit(arrow.length, "lines"), ends = arrow.ends,
type = arrow.type),
lineend = "butt",
na.rm = FALSE,
show.legend = NA,
inherit.aes = TRUE
)

geom_vector(
mapping = NULL,
data = NULL,
stat = "arrow",
position = "identity",
...,
start = 0,
direction = c("ccw", "cw"),
pivot = 0.5,
preserve.dir = FALSE,
min.mag = 0,
skip = 0,
skip.x = skip,
skip.y = skip,
arrow.angle = 15,
arrow.length = 0.5,
arrow.ends = "last",
arrow.type = "closed",
arrow = grid::arrow(arrow.angle, grid::unit(arrow.length, "lines"), ends = arrow.ends,
type = arrow.type),
lineend = "butt",
na.rm = FALSE,
show.legend = NA,
inherit.aes = TRUE
)

value must be a data.frame, and will be used as the layer data. A function
can be created from a formula (e.g. ~ head(.x, 10)).
stat The statistical transformation to use on the data for this layer, as a string.
position Position adjustment, either as a string, or the result of a call to a position adjust-
ment function.
... Other arguments passed on to layer(). These are often aesthetics, used to set
an aesthetic to a fixed value, like colour = "red" or size = 3. They may also
be parameters to the paired geom/stat.
start starting angle for rotation in degrees
direction direction of rotation (counter-clockwise or clockwise)
pivot numeric indicating where to pivot the arrow where 0 means at the beginning and
1 means at the end.
preserve.dir logical indicating whether to preserve direction or not
min.mag minimum magnitude for plotting vectors
skip, skip.x, skip.y
numeric specifying number of gridpoints not to draw in the x and y direction
arrow.length, arrow.angle, arrow.ends, arrow.type
parameters passed to grid::arrow
arrow specification for arrow heads, as created by arrow().
lineend Line end style (round, butt, square).
na.rm If FALSE, the default, missing values are removed with a warning. If TRUE,
missing values are silently removed.
show.legend logical. Should this layer be included in the legends? NA, the default, includes if
any aesthetics are mapped. FALSE never includes, and TRUE always includes. It
can also be a named logical vector to finely select the aesthetics to display.
inherit.aes If FALSE, overrides the default aesthetics, rather than combining with them.
This is most useful for helper functions that define both data and aesthetics and
shouldn’t inherit behaviour from the default plot specification, e.g. borders().

Details
Direction and start allows to work with different standards. For the meteorological standard, for
example, use star = -90 and direction = "cw".

Aesthetics
geom_vector understands the following aesthetics (required aesthetics are in bold)
• x
• y
• either mag and angle, or dx and dy
• alpha
• colour
• linetype
• size
• lineend
geom_arrow 23

See Also
Other ggplot2 helpers: DivideTimeseries(), MakeBreaks(), WrapCircular(), geom_contour2(),
geom_contour_fill(), geom_label_contour(), geom_relief(), geom_streamline(), guide_colourstrip(),
map_labels, reverselog_trans(), scale_divergent, scale_longitude, stat_na(), stat_subset()

Examples
library(data.table)
library(ggplot2)

data(seals)
# If the velocity components are in the same units as the axis,
# geom_vector() (or geom_arrow(preserve.dir = TRUE)) might be a better option
ggplot(seals, aes(long, lat)) +
geom_arrow(aes(dx = delta_long, dy = delta_lat), skip = 1, color = "red") +
geom_vector(aes(dx = delta_long, dy = delta_lat), skip = 1) +
scale_mag()

data(geopotential)
geopotential <- copy(geopotential)[date == date[1]]
geopotential[, gh.z := Anomaly(gh), by = .(lat)]
geopotential[, c("u", "v") := GeostrophicWind(gh.z, lon, lat)]

(g <- ggplot(geopotential, aes(lon, lat)) +

geom_arrow(aes(dx = dlon(u, lat), dy = dlat(v)), skip.x = 3, skip.y = 2,
color = "red") +
geom_vector(aes(dx = dlon(u, lat), dy = dlat(v)), skip.x = 3, skip.y = 2) +
scale_mag(max_size = 2, guide = "none"))

# A dramatic illustration of the difference between arrow and vector

g + coord_polar()

# When plotting winds in a lat-lon grid, a good way to have both

# the correct direction and an interpretable magnitude is to define
# the angle by the longitud and latitude displacement and the magnitude
# by the wind velocity. That way arrows are always parallel to streamlines
# and their magnitude are in the correct units.
ggplot(geopotential, aes(lon, lat)) +
geom_contour(aes(z = gh.z)) +
geom_vector(aes(angle = atan2(dlat(v), dlon(u, lat))*180/pi,
mag = Mag(v, u)), skip = 1, pivot = 0.5) +
scale_mag()

# Sverdrup transport
library(data.table)
b <- 10
d <- 10
grid <- as.data.table(expand.grid(x = seq(1, d, by = 0.5),
y = seq(1, b, by = 0.5)))
grid[, My := -sin(pi*y/b)*pi/b]
grid[, Mx := -pi^2/b^2*cos(pi*y/b)*(d - x)]
24 geom_contour2

ggplot(grid, aes(x, y)) +

geom_arrow(aes(dx = Mx, dy = My))

# Due to limitations in ggplot2 (see: https://github.com/tidyverse/ggplot2/issues/4291),

# if you define the vector with the dx and dy aesthetics, you need
# to explicitly add scale_mag() in order to show the arrow legend.

ggplot(grid, aes(x, y)) +

geom_arrow(aes(dx = Mx, dy = My)) +
scale_mag()

# Alternative, use Mag and Angle.

ggplot(grid, aes(x, y)) +
geom_arrow(aes(mag = Mag(Mx, My), angle = Angle(Mx, My)))

geom_contour2 2d contours of a 3d surface

Description
Similar to ggplot2::geom_contour but it can label contour lines, accepts accepts a function as the
breaks argument and and computes breaks globally instead of per panel.

Usage
geom_contour2(
mapping = NULL,
data = NULL,
stat = "contour2",
position = "identity",
...,
lineend = "butt",
linejoin = "round",
linemitre = 1,
breaks = MakeBreaks(),
bins = NULL,
binwidth = NULL,
global.breaks = TRUE,
na.rm = FALSE,
na.fill = FALSE,
skip = 1,
margin = grid::unit(c(1, 1, 1, 1), "pt"),
label.placer = label_placer_flattest(),
show.legend = NA,
inherit.aes = TRUE
)
geom_contour2 25

stat_contour2(
mapping = NULL,
data = NULL,
geom = "contour2",
position = "identity",
...,
breaks = MakeBreaks(),
bins = NULL,
binwidth = NULL,
kriging = FALSE,
global.breaks = TRUE,
na.rm = FALSE,
na.fill = FALSE,
show.legend = NA,
inherit.aes = TRUE
)

binwidth Distance between breaks.

global.breaks Logical indicating whether breaks should be computed for the whole data or
for each grouping.
na.rm If FALSE, the default, missing values are removed with a warning. If TRUE,
missing values are silently removed.
na.fill How to fill missing values.
• FALSE for letting the computation fail with no interpolation
• TRUE for imputing missing values with Impute2D
• A numeric value for constant imputation
• A function that takes a vector and returns a numeric (e.g. mean)
skip number of contours to skip for labelling (e.g. skip = 1 will skip 1 contour line
between labels).
margin the margin around labels around which contour lines are clipped to avoid over-
lapping.
label.placer a label placer function. See label_placer_flattest().
show.legend logical. Should this layer be included in the legends? NA, the default, includes if
any aesthetics are mapped. FALSE never includes, and TRUE always includes. It
can also be a named logical vector to finely select the aesthetics to display.
inherit.aes If FALSE, overrides the default aesthetics, rather than combining with them.
This is most useful for helper functions that define both data and aesthetics and
shouldn’t inherit behaviour from the default plot specification, e.g. borders().
geom The geometric object to use display the data
kriging Logical indicating whether to perform ordinary kriging before contouring. Use
this if you want to use contours with irregularly spaced data.

Aesthetics
geom_contour2 understands the following aesthetics (required aesthetics are in bold):
Aesthetics related to contour lines:
• x
• y
• z
• alpha
• colour
• group
• linetype
• size
• weight
Aesthetics related to labels:
• label
geom_contour2 27

• label_colour
• label_alpha
• label_size
• family
• fontface

Computed variables
level height of contour

See Also
Other ggplot2 helpers: DivideTimeseries(), MakeBreaks(), WrapCircular(), geom_arrow(),
geom_contour_fill(), geom_label_contour(), geom_relief(), geom_streamline(), guide_colourstrip(),
map_labels, reverselog_trans(), scale_divergent, scale_longitude, stat_na(), stat_subset()
Other ggplot2 helpers: DivideTimeseries(), MakeBreaks(), WrapCircular(), geom_arrow(),
geom_contour_fill(), geom_label_contour(), geom_relief(), geom_streamline(), guide_colourstrip(),
map_labels, reverselog_trans(), scale_divergent, scale_longitude, stat_na(), stat_subset()

Examples
library(ggplot2)

# Breaks can be a function.

ggplot(reshape2::melt(volcano), aes(Var1, Var2)) +
geom_contour2(aes(z = value, color = ..level..),
breaks = AnchorBreaks(130, binwidth = 10))

# Add labels by supplying the label aes.

ggplot(reshape2::melt(volcano), aes(Var1, Var2)) +
geom_contour2(aes(z = value, label = ..level..))

ggplot(reshape2::melt(volcano), aes(Var1, Var2)) +

geom_contour2(aes(z = value, label = ..level..),
skip = 0)

# Use label.placer to control where contours are labelled.

ggplot(reshape2::melt(volcano), aes(Var1, Var2)) +
geom_contour2(aes(z = value, label = ..level..),
label.placer = label_placer_n(n = 2))

# Use the rot_adjuster argument of the placer function to

# control the angle. For example, to fix it to some angle:
ggplot(reshape2::melt(volcano), aes(Var1, Var2)) +
geom_contour2(aes(z = value, label = ..level..),
skip = 0,
label.placer = label_placer_flattest(rot_adjuster = 0))
28 geom_contour_fill

geom_contour_fill Filled 2d contours of a 3d surface

Description

While ggplot2’s geom_contour can plot nice contours, it doesn’t work with the polygon geom. This
stat makes some small manipulation of the data to ensure that all contours are closed and also com-
putes a new aesthetic int.level, which differs from level (computed by ggplot2::geom_contour)
in that represents the value of the z aesthetic inside the contour instead of at the edge. It also
computes breaks globally instead of per panel, so that faceted plots have all the same binwidth.

Usage

geom_contour_fill(
mapping = NULL,
data = NULL,
stat = "ContourFill",
position = "identity",
...,
breaks = MakeBreaks(),
bins = NULL,
binwidth = NULL,
kriging = FALSE,
global.breaks = TRUE,
na.fill = FALSE,
show.legend = NA,
inherit.aes = TRUE
)

stat_contour_fill(
mapping = NULL,
data = NULL,
geom = "polygon",
position = "identity",
...,
breaks = MakeBreaks(),
bins = NULL,
binwidth = NULL,
global.breaks = TRUE,
kriging = FALSE,
na.fill = FALSE,
show.legend = NA,
inherit.aes = TRUE
)
geom_contour_fill 29

Arguments
mapping Set of aesthetic mappings created by aes() or aes_(). If specified and inherit.aes
= TRUE (the default), it is combined with the default mapping at the top level of
the plot. You must supply mapping if there is no plot mapping.
data The data to be displayed in this layer. There are three options:
If NULL, the default, the data is inherited from the plot data as specified in the
call to ggplot().
A data.frame, or other object, will override the plot data. All objects will be
fortified to produce a data frame. See fortify() for which variables will be
created.
A function will be called with a single argument, the plot data. The return
value must be a data.frame, and will be used as the layer data. A function
can be created from a formula (e.g. ~ head(.x, 10)).
stat The statistical transformation to use on the data for this layer, as a string.
position Position adjustment, either as a string, or the result of a call to a position adjust-
ment function.
... Other arguments passed on to layer(). These are often aesthetics, used to set
an aesthetic to a fixed value, like colour = "red" or size = 3. They may also
be parameters to the paired geom/stat.
breaks numeric vector of breaks
bins Number of evenly spaced breaks.
binwidth Distance between breaks.
kriging Logical indicating whether to perform ordinary kriging before contouring. Use
this if you want to use contours with irregularly spaced data.
global.breaks Logical indicating whether breaks should be computed for the whole data or
for each grouping.
na.fill How to fill missing values.
• FALSE for letting the computation fail with no interpolation
• TRUE for imputing missing values with Impute2D
• A numeric value for constant imputation
• A function that takes a vector and returns a numeric (e.g. mean)
show.legend logical. Should this layer be included in the legends? NA, the default, includes if
any aesthetics are mapped. FALSE never includes, and TRUE always includes. It
can also be a named logical vector to finely select the aesthetics to display.
inherit.aes If FALSE, overrides the default aesthetics, rather than combining with them.
This is most useful for helper functions that define both data and aesthetics and
shouldn’t inherit behaviour from the default plot specification, e.g. borders().
geom The geometric object to use display the data

Aesthetics
geom_contour_fill understands the following aesthetics (required aesthetics are in bold):
30 geom_contour_tanaka

• x
• y
• alpha
• colour
• group
• linetype
• size
• weight

Computed variables
level An ordered factor that represents bin ranges.
level_d Same as level, but automatically uses scale_fill_discretised()
level_low,level_high,level_mid Lower and upper bin boundaries for each band, as well the mid
point between the boundaries.

See Also
Other ggplot2 helpers: DivideTimeseries(), MakeBreaks(), WrapCircular(), geom_arrow(),
geom_contour2(), geom_label_contour(), geom_relief(), geom_streamline(), guide_colourstrip(),
map_labels, reverselog_trans(), scale_divergent, scale_longitude, stat_na(), stat_subset()

Examples
library(ggplot2)
surface <- reshape2::melt(volcano)
ggplot(surface, aes(Var1, Var2, z = value)) +
geom_contour_fill() +
geom_contour(color = "black", size = 0.1)

ggplot(surface, aes(Var1, Var2, z = value)) +

geom_contour_fill(aes(fill = stat(level)))

ggplot(surface, aes(Var1, Var2, z = value)) +

geom_contour_fill(aes(fill = stat(level_d)))

geom_contour_tanaka Illuminated contours

Description
Illuminated contours (aka Tanaka contours) use varying brightness and width to create an illusion
of relief. This can help distinguishing between concave and convex areas (local minimums and
maximums), specially in black and white plots or to make photocopy safe plots with divergent
colour palettes, or to render a more aesthetically pleasing representation of topography.
geom_contour_tanaka 31

Usage
geom_contour_tanaka(
mapping = NULL,
data = NULL,
stat = "Contour2",
position = "identity",
...,
breaks = NULL,
bins = NULL,
binwidth = NULL,
sun.angle = 60,
light = "white",
dark = "gray20",
range = c(0.01, 0.5),
smooth = 0,
na.rm = FALSE,
show.legend = NA,
inherit.aes = TRUE
)

binwidth Distance between breaks.

sun.angle angle of the sun in degrees counterclockwise from 12 o’ clock
light, dark valid colour representing the light and dark shading
range numeric vector of length 2 with the minimum and maximum size of lines
smooth numeric indicating the degree of smoothing of illumination and size. Larger
na.rm If FALSE, the default, missing values are removed with a warning. If TRUE,
missing values are silently removed.
show.legend logical. Should this layer be included in the legends? NA, the default, includes if
any aesthetics are mapped. FALSE never includes, and TRUE always includes. It
can also be a named logical vector to finely select the aesthetics to display.
inherit.aes If FALSE, overrides the default aesthetics, rather than combining with them.
This is most useful for helper functions that define both data and aesthetics and
shouldn’t inherit behaviour from the default plot specification, e.g. borders().

Aesthetics
geom_contour_tanaka understands the following aesthetics (required aesthetics are in bold)

• x
• y
• z
• linetype

Examples
library(ggplot2)
library(data.table)
# A fresh look at the boring old volcano dataset
ggplot(reshape2::melt(volcano), aes(Var1, Var2)) +
geom_contour_fill(aes(z = value)) +
geom_contour_tanaka(aes(z = value)) +
theme_void()

# If the transition between segments feels too abrupt,

# smooth it a bit with smooth
ggplot(reshape2::melt(volcano), aes(Var1, Var2)) +
geom_contour_fill(aes(z = value)) +
geom_contour_tanaka(aes(z = value), smooth = 1) +
theme_void()

data(geopotential)
geo <- geopotential[date == unique(date)[4]]
geo[, gh.z := Anomaly(gh), by = lat]

# In a monochrome contour map, it's impossible to know which areas are

# local maximums or minimums.
ggplot(geo, aes(lon, lat)) +
geom_contour2(aes(z = gh.z), color = "black", xwrap = c(0, 360))
geom_label_contour 33

# With tanaka contours, they are obvious.

ggplot(geo, aes(lon, lat)) +
geom_contour_tanaka(aes(z = gh.z), dark = "black",
xwrap = c(0, 360)) +
scale_fill_divergent()

# A good divergent color palette has the same luminosity for positive
# and negative values.But that means that printed in grayscale (Desaturated),
# they are indistinguishable.
(g <- ggplot(geo, aes(lon, lat)) +
geom_contour_fill(aes(z = gh.z), xwrap = c(0, 360)) +
scale_fill_gradientn(colours = c("#767676", "white", "#484848"),
values = c(0, 0.415, 1)))

# Tanaka contours can solve this issue.

g + geom_contour_tanaka(aes(z = gh.z))

geom_label_contour Label contours

Description
Draws labels on contours built with ggplot2::stat_contour.

Usage
geom_label_contour(
mapping = NULL,
data = NULL,
stat = "text_contour",
position = "identity",
...,
min.size = 5,
skip = 1,
label.placer = label_placer_flattest(),
parse = FALSE,
nudge_x = 0,
nudge_y = 0,
label.padding = grid::unit(0.25, "lines"),
label.r = grid::unit(0.15, "lines"),
label.size = 0.25,
na.rm = FALSE,
show.legend = NA,
inherit.aes = TRUE
)
34 geom_label_contour

geom_text_contour(
mapping = NULL,
data = NULL,
stat = "text_contour",
position = "identity",
...,
min.size = 5,
skip = 1,
rotate = TRUE,
label.placer = label_placer_flattest(),
parse = FALSE,
nudge_x = 0,
nudge_y = 0,
stroke = 0,
check_overlap = FALSE,
na.rm = FALSE,
show.legend = NA,
inherit.aes = TRUE
)

nudge_x, nudge_y
Horizontal and vertical adjustment to nudge labels by. Useful for offsetting text
from points, particularly on discrete scales. Cannot be jointly specified with
position.
label.padding Amount of padding around label. Defaults to 0.25 lines.
label.r Radius of rounded corners. Defaults to 0.15 lines.
label.size Size of label border, in mm.
na.rm If FALSE, the default, missing values are removed with a warning. If TRUE,
missing values are silently removed.
show.legend logical. Should this layer be included in the legends? NA, the default, includes if
any aesthetics are mapped. FALSE never includes, and TRUE always includes. It
can also be a named logical vector to finely select the aesthetics to display.
inherit.aes If FALSE, overrides the default aesthetics, rather than combining with them.
This is most useful for helper functions that define both data and aesthetics and
shouldn’t inherit behaviour from the default plot specification, e.g. borders().
rotate logical indicating whether to rotate text following the contour.
stroke numerical indicating width of stroke relative to the size of the text. Ignored if
less than zero.
check_overlap If TRUE, text that overlaps previous text in the same layer will not be plotted.
check_overlap happens at draw time and in the order of the data. Therefore
data should be arranged by the label column before calling geom_text(). Note
that this argument is not supported by geom_label().

Details
Is best used with a previous call to ggplot2::stat_contour with the same parameters (e.g. the same
binwidth, breaks, or bins). Note that while geom_text_contour() can angle itself to follow the
contour, this is not the case with geom_label_contour().

Aesthetics
geom_text_contour understands the following aesthetics (required aesthetics are in bold):

• x
• y
• label
• alpha
• angle
• colour
• stroke.color
• family
• fontface
• group
36 geom_relief

• hjust
• lineheight
• size
• vjust

See Also
Other ggplot2 helpers: DivideTimeseries(), MakeBreaks(), WrapCircular(), geom_arrow(),
geom_contour2(), geom_contour_fill(), geom_relief(), geom_streamline(), guide_colourstrip(),
map_labels, reverselog_trans(), scale_divergent, scale_longitude, stat_na(), stat_subset()

Examples
library(ggplot2)
v <- reshape2::melt(volcano)
g <- ggplot(v, aes(Var1, Var2)) +
geom_contour(aes(z = value))
g + geom_text_contour(aes(z = value))

g + geom_text_contour(aes(z = value), stroke = 0.2)

g + geom_text_contour(aes(z = value), stroke = 0.2, stroke.colour = "red")

g + geom_text_contour(aes(z = value, stroke.colour = ..level..), stroke = 0.2) +

scale_colour_gradient(aesthetics = "stroke.colour", guide = "none")

g + geom_text_contour(aes(z = value), rotate = FALSE)

g + geom_text_contour(aes(z = value),
label.placer = label_placer_random())

g + geom_text_contour(aes(z = value),
label.placer = label_placer_n(3))

g + geom_text_contour(aes(z = value),
label.placer = label_placer_flattest())

g + geom_text_contour(aes(z = value),
label.placer = label_placer_flattest(ref_angle = 90))

geom_relief Relief Shading

Description
geom_relief() simulates shading caused by relief. Can be useful when plotting topographic data
because relief shading might give a more intuitive impression of the shape of the terrain than contour
lines or mapping height to colour. geom_shadow() projects shadows.
geom_relief 37

Usage
geom_relief(
mapping = NULL,
data = NULL,
stat = "identity",
position = "identity",
...,
sun.angle = 60,
raster = TRUE,
interpolate = TRUE,
shadow = FALSE,
na.rm = FALSE,
show.legend = NA,
inherit.aes = TRUE
)

geom_shadow(
mapping = NULL,
data = NULL,
stat = "identity",
position = "identity",
...,
sun.angle = 60,
range = c(0, 1),
skip = 0,
raster = TRUE,
interpolate = TRUE,
na.rm = FALSE,
show.legend = NA,
inherit.aes = TRUE
)

position Position adjustment, either as a string, or the result of a call to a position adjust-
ment function.
... Other arguments passed on to layer(). These are often aesthetics, used to set
an aesthetic to a fixed value, like colour = "red" or size = 3. They may also
be parameters to the paired geom/stat.
sun.angle angle from which the sun is shining, in degrees counterclockwise from 12 o’
clock
raster if TRUE (the default), uses ggplot2::geom_raster, if FALSE, uses ggplot2::geom_tile.
interpolate If TRUE interpolate linearly, if FALSE (the default) don’t interpolate.
shadow if TRUE, adds also a layer of geom_shadow()
na.rm If FALSE, the default, missing values are removed with a warning. If TRUE,
missing values are silently removed.
show.legend logical. Should this layer be included in the legends? NA, the default, includes if
any aesthetics are mapped. FALSE never includes, and TRUE always includes. It
can also be a named logical vector to finely select the aesthetics to display.
inherit.aes If FALSE, overrides the default aesthetics, rather than combining with them.
This is most useful for helper functions that define both data and aesthetics and
shouldn’t inherit behaviour from the default plot specification, e.g. borders().
range transparency range for shadows
skip data points to skip when casting shadows

Details
light and dark must be valid colours determining the light and dark shading (defaults to "white"
and "gray20", respectively).

Aesthetics
geom_relief() and geom_shadow() understands the following aesthetics (required aesthetics are
in bold)

• x
• y
• z
• light
• dark
• sun.angle

See Also
Other ggplot2 helpers: DivideTimeseries(), MakeBreaks(), WrapCircular(), geom_arrow(),
geom_contour2(), geom_contour_fill(), geom_label_contour(), geom_streamline(), guide_colourstrip(),
map_labels, reverselog_trans(), scale_divergent, scale_longitude, stat_na(), stat_subset()
geom_streamline 39

Examples
## Not run:
library(ggplot2)
ggplot(reshape2::melt(volcano), aes(Var1, Var2)) +
geom_relief(aes(z = value))

## End(Not run)

geom_streamline Streamlines

Description
Streamlines are paths that are always tangential to a vector field. In the case of a steady field, it’s
identical to the path of a massless particle that moves with the "flow".

Usage
geom_streamline(
mapping = NULL,
data = NULL,
stat = "streamline",
position = "identity",
...,
L = 5,
min.L = 0,
res = 1,
S = NULL,
dt = NULL,
xwrap = NULL,
ywrap = NULL,
skip = 1,
skip.x = skip,
skip.y = skip,
n = NULL,
nx = n,
ny = n,
jitter = 1,
jitter.x = jitter,
jitter.y = jitter,
arrow.angle = 6,
arrow.length = 0.5,
arrow.ends = "last",
arrow.type = "closed",
arrow = grid::arrow(arrow.angle, grid::unit(arrow.length, "lines"), ends = arrow.ends,
type = arrow.type),
lineend = "butt",
40 geom_streamline

na.rm = TRUE,
show.legend = NA,
inherit.aes = TRUE
)

stat_streamline(
mapping = NULL,
data = NULL,
geom = "streamline",
position = "identity",
...,
L = 5,
min.L = 0,
res = 1,
S = NULL,
dt = NULL,
xwrap = NULL,
ywrap = NULL,
skip = 1,
skip.x = skip,
skip.y = skip,
n = NULL,
nx = n,
ny = n,
jitter = 1,
jitter.x = jitter,
jitter.y = jitter,
arrow.angle = 6,
arrow.length = 0.5,
arrow.ends = "last",
arrow.type = "closed",
arrow = grid::arrow(arrow.angle, grid::unit(arrow.length, "lines"), ends = arrow.ends,
type = arrow.type),
lineend = "butt",
na.rm = TRUE,
show.legend = NA,
inherit.aes = TRUE
)

fortified to produce a data frame. See fortify() for which variables will be
created.
A function will be called with a single argument, the plot data. The return
value must be a data.frame, and will be used as the layer data. A function
can be created from a formula (e.g. ~ head(.x, 10)).
stat The statistical transformation to use on the data for this layer, as a string.
position Position adjustment, either as a string, or the result of a call to a position adjust-
ment function.
... Other arguments passed on to layer(). These are often aesthetics, used to set
an aesthetic to a fixed value, like colour = "red" or size = 3. They may also
be parameters to the paired geom/stat.
L, typical length of a streamline in x and y units
min.L minimum length of segments to show
res, resolution parameter (higher numbers increases the resolution)
S optional numeric number of timesteps for integration
dt optional numeric size "timestep" for integration
xwrap, ywrap vector of length two used to wrap the circular dimension.
skip, skip.x, skip.y
numeric specifying number of gridpoints not to draw in the x and y direction
n, nx, ny optional numeric indicating the number of points to draw in the x and y direction
(replaces skip if not NULL)
jitter, jitter.x, jitter.y
amount of jitter of the starting points
arrow.length, arrow.angle, arrow.ends, arrow.type
parameters passed to grid::arrow
arrow specification for arrow heads, as created by arrow().
lineend Line end style (round, butt, square).
na.rm If FALSE, the default, missing values are removed with a warning. If TRUE,
missing values are silently removed.
show.legend logical. Should this layer be included in the legends? NA, the default, includes if
any aesthetics are mapped. FALSE never includes, and TRUE always includes. It
can also be a named logical vector to finely select the aesthetics to display.
inherit.aes If FALSE, overrides the default aesthetics, rather than combining with them.
This is most useful for helper functions that define both data and aesthetics and
shouldn’t inherit behaviour from the default plot specification, e.g. borders().
geom The geometric object to use display the data

Details
Streamlines are computed by simple integration with a forward Euler method. By default, stat_streamline()
computes dt and S from L, res, the resolution of the grid and the mean magnitude of the field. S
is then defined as the number of steps necessary to make a streamline of length L under an uniform
mean field and dt is chosen so that each step is no larger than the resolution of the data (divided by
42 geom_streamline

the res parameter). Be aware that this rule of thumb might fail in field with very skewed distribution
of magnitudes.
Alternatively, L and/or res are ignored if S and/or dt are specified explicitly. This not only makes
it possible to fine-tune the result but also divorces the integration parameters from the properties of
the data and makes it possible to compare streamlines between different fields.
The starting grid is a semi regular grid defined, either by the resolution of the field and the skip.x
and skip.y parameters o the nx and ny parameters, jittered by an amount proportional to the reso-
lution of the data and the jitter.x and jitter.y parameters.
It might be important that the units of the vector field are compatible to the units of the x and y di-
mensions. For example, passing dx and dy in m/s on a longitude-latitude grid will might misleading
results (see spherical).
Missing values are not permitted and the field must be defined on a regular grid, for now.

Aesthetics
stat_streamline understands the following aesthetics (required aesthetics are in bold)

• x
• y
• dx
• dy
• alpha
• colour
• linetype
• size

Computed variables
step step in the simulation
dx dx at each location of the streamline
dy dy at each location of the streamline

See Also
Other ggplot2 helpers: DivideTimeseries(), MakeBreaks(), WrapCircular(), geom_arrow(),
geom_contour2(), geom_contour_fill(), geom_label_contour(), geom_relief(), guide_colourstrip(),
map_labels, reverselog_trans(), scale_divergent, scale_longitude, stat_na(), stat_subset()

Examples
## Not run:
library(data.table)
library(ggplot2)
data(geopotential)

geopotential <- copy(geopotential)[date == date[1]]

geopotential 43

geopotential[, gh.z := Anomaly(gh), by = .(lat)]

geopotential[, c("u", "v") := GeostrophicWind(gh.z, lon, lat)]

(g <- ggplot(geopotential, aes(lon, lat)) +

geom_contour2(aes(z = gh.z), xwrap = c(0, 360)) +
geom_streamline(aes(dx = dlon(u, lat), dy = dlat(v)), L = 60,
xwrap = c(0, 360)))

# The circular parameter is particularly important for polar coordinates

g + coord_polar()

# If u and v are not converted into degrees/second, the resulting

# streamlines have problems, specially near the pole.
ggplot(geopotential, aes(lon, lat)) +
geom_contour(aes(z = gh.z)) +
geom_streamline(aes(dx = u, dy = v), L = 50)

# The step variable can be mapped to size or alpha to

# get cute "drops". It's important to note that ..dx.. (the calculated variable)
# is NOT the same as dx (from the data).
ggplot(geopotential, aes(lon, lat)) +
geom_streamline(aes(dx = dlon(u, lat), dy = dlat(v), alpha = ..step..,
color = sqrt(..dx..^2 + ..dy..^2), size = ..step..),
L = 40, xwrap = c(0, 360), res = 2, arrow = NULL,
lineend = "round") +
scale_size(range = c(0, 0.6))

# Using topographic information to simulate "rivers" from slope

topo <- GetTopography(295, -55+360, -30, -42, res = 1/20) # needs internet!
topo[, c("dx", "dy") := Derivate(h ~ lon + lat)]
topo[h <= 0, c("dx", "dy") := 0]

# See how in this example the integration step is too coarse in the
# western montanous region where the slope is much higher than in the
# flatlands of La Pampa at in the east.
ggplot(topo, aes(lon, lat)) +
geom_relief(aes(z = h), interpolate = TRUE, data = topo[h >= 0]) +
geom_contour(aes(z = h), breaks = 0, color = "black") +
geom_streamline(aes(dx = -dx, dy = -dy), L = 10, skip = 3, arrow = NULL,
color = "#4658BD") +
coord_quickmap()

## End(Not run)

geopotential Geopotential height

Description
Monthly geopotential field at 700hPa south of 20°S from January 1990 to December 2000.
44 GeostrophicWind

Usage
geopotential

Format
A data.table with 53224 rows and 5 variables.
lon longitude in degrees
lat latitude in degrees
lev level in hPa
gh geopotential height in meters
date date

Source
https://psl.noaa.gov/data/gridded/data.ncep.reanalysis.derived.pressure.html

GeostrophicWind Calculate geostrophic winds

Description
Geostrophic wind from a geopotential height field.

Usage
GeostrophicWind(gh, lon, lat, cyclical = "guess", g = 9.81, a = 6371000)

Arguments
gh geopotential height
lon longitude in degrees
lat latitude in degrees
cyclical boundary condition for longitude (see details)
g acceleration of gravity
a Earth’s radius

Details
If cyclical = "guess" (the default) the function will try to guess if lon covers the whole globe
and set cyclical conditions accordingly. For more predictable results, set the boundary condition
explicitly.

Value
A named list with vectors for the zonal and meridional component of geostrophic wind.
GetSMNData 45

See Also

Other meteorology functions: Derivate(), EOF(), WaveFlux(), thermodynamics, waves

Examples
data(geopotential)
geopotential <- data.table::copy(geopotential)
geopotential[date == date[1], c("u", "v") := GeostrophicWind(gh, lon, lat)]
library(ggplot2)
ggplot(geopotential[date == date[1]], aes(lon, lat)) +
geom_contour(aes(z = gh)) +
geom_vector(aes(dx = u, dy = v), skip = 2) +
scale_mag()

GetSMNData Get Meteorological data

Description

Downloads minimum and maximum temperature station data from Argentina’s National Weather
Service’s public access. Data availability is not guaranteed so you are encouraged to check it on the
website.

Usage

GetSMNData(
date,
type = c("hourly", "daily", "radiation"),
bar = FALSE,
cache = TRUE,
file.dir = tempdir()
)

Arguments

date date vector of dates to fetch data

type type of data to retrieve
bar logical object indicating whether to show a progress bar
cache logical indicating if the results should be saved on disk
file.dir optional directory where to save and/or retrieve data
46 GetSMNData

Value

For type = "hourly", a data.frame with observations of

date date
t temperature in degrees celsius
rh relative humidity in %
slp sea level pressure in hPa
dir wind direction in clockwise degrees from 6 o’clock
V wind magnitude in m/s
station station name

For type = "daily", a data.frame with observations of

date date
tmax maximum daily temperature in degrees celsius
tmin minimum daily temperature in degrees celsius
station station name

For type = "radiation", a data.frame with observations of

date date
global global radiation in W/m^2
diffuse diffuse radiation in W/m^2
station station name

Source

https://ssl.smn.gob.ar/dpd/pron5d-calendario.php

Examples
## Not run:
dates <- seq.Date(lubridate::today() - 30, lubridate::today(), by = "1 day")
data <- GetSMNData(dates, type = "daily", bar = TRUE)

library(ggplot2)
ggplot(subset(data, station == "BASE BELGRANO II"),
aes(date, (tmax + tmin)/2)) +
geom_line()

## End(Not run)
GetTopography 47

GetTopography Get topographic data

Description
Retrieves topographic data from ETOPO1 Global Relief Model (see references).

Usage
GetTopography(
lon.west,
lon.east,
lat.north,
lat.south,
resolution = 3.5,
cache = TRUE,
file.dir = tempdir(),
verbose = interactive()
)

Arguments
lon.west, lon.east, lat.north, lat.south
latitudes and longitudes of the bounding box in degrees
resolution numeric vector indicating the desired resolution (in degrees) in the lon and lat
directions (maximum resolution is 1 minute)
cache logical indicating if the results should be saved on disk
file.dir optional directory where to save and/or retrieve data
verbose logical indicating whether to print progress

Details
Very large requests can take long and can be denied by the NOAA server. If the function fails, try
with a smaller bounding box or coarser resolution.
Longitude coordinates must be between 0 and 360.

Value
A data table with height (in meters) for each longitude and latitude.

References
Source: Amante, C. and B.W. Eakins, 2009. ETOPO1 1 Arc-Minute Global Relief Model: Proce-
dures, Data Sources and Analysis. NOAA Technical Memorandum NESDIS NGDC-24. National
Geophysical Data Center, NOAA. doi:10.7289/V5C8276M
48 guide_vector

Examples
## Not run:
topo <- GetTopography(280, 330, 0, -60, resolution = 0.5)
library(ggplot2)
ggplot(topo, aes(lon, lat)) +
geom_raster(aes(fill = h)) +
geom_contour(aes(z = h), breaks = 0, color = "black", size = 0.3) +
scale_fill_gradient2(low = "steelblue", high = "goldenrod2", mid = "olivedrab") +
coord_quickmap()

## End(Not run)

guide_vector Reference arrow for magnitude scales

Description

Draws a reference arrow. Highly experimental.

Usage

guide_vector(
title = ggplot2::waiver(),
title.position = NULL,
title.theme = NULL,
title.hjust = NULL,
title.vjust = NULL,
label = TRUE,
label.position = NULL,
label.theme = NULL,
label.hjust = NULL,
label.vjust = NULL,
keywidth = NULL,
keyheight = NULL,
direction = NULL,
default.unit = "cm",
override.aes = list(),
nrow = NULL,
ncol = NULL,
byrow = FALSE,
reverse = FALSE,
order = 0,
...
)
guide_vector 49

Arguments
title A character string or expression indicating a title of guide. If NULL, the title is
not shown. By default (waiver()), the name of the scale object or the name
specified in labs() is used for the title.
title.position A character string indicating the position of a title. One of "top" (default for a
vertical guide), "bottom", "left" (default for a horizontal guide), or "right."
title.theme A theme object for rendering the title text. Usually the object of element_text()
is expected. By default, the theme is specified by legend.title in theme() or
theme.
title.hjust A number specifying horizontal justification of the title text.
title.vjust A number specifying vertical justification of the title text.
label logical. If TRUE then the labels are drawn. If FALSE then the labels are invisible.
label.position A character string indicating the position of a label. One of "top", "bottom"
(default for horizontal guide), "left", or "right" (default for vertical guide).
label.theme A theme object for rendering the label text. Usually the object of element_text()
is expected. By default, the theme is specified by legend.text in theme().
label.hjust A numeric specifying horizontal justification of the label text.
label.vjust A numeric specifying vertical justification of the label text.
keywidth A numeric or a grid::unit() object specifying the width of the legend key.
Default value is legend.key.width or legend.key.size in theme().
keyheight A numeric or a grid::unit() object specifying the height of the legend key.
Default value is legend.key.height or legend.key.size in theme().
direction A character string indicating the direction of the guide. One of "horizontal" or
"vertical."
default.unit A character string indicating grid::unit() for keywidth and keyheight.
override.aes A list specifying aesthetic parameters of legend key. See details and examples.
nrow The desired number of rows of legends.
ncol The desired number of column of legends.
byrow logical. If FALSE (the default) the legend-matrix is filled by columns, otherwise
the legend-matrix is filled by rows.
reverse logical. If TRUE the order of legends is reversed.
order positive integer less than 99 that specifies the order of this guide among multiple
guides. This controls the order in which multiple guides are displayed, not the
contents of the guide itself. If 0 (default), the order is determined by a secret
algorithm.
... ignored.

Impute2D Impute missing values by linear or constant interpolation

Description
Provides methods for (soft) imputation of missing values.

Usage
Impute2D(formula, data = NULL, method = "interpolate")

Arguments
formula a formula indicating dependent and independent variables (see Details)
data optional data.frame with the data
method "interpolate" for interpolation, a numeric for constant imputation or a function
that takes a vector and returns a number (like mean)

Details
This is "soft" imputation because the imputed values are not supposed to be representative of the
missing data but just filling for algorithms that need complete data (in particular, contouring). The
method used if method = "interpolate" is to do simple linear interpolation in both the x and y
direction and then average the result.
This is the imputation method used by geom_contour_fill().

ImputeEOF Impute missing values

Description
Imputes missing values via Data Interpolating Empirical Orthogonal Functions (DINEOF).

Usage
ImputeEOF(
formula,
max.eof = NULL,
data = NULL,
min.eof = 1,
tol = 0.01,
max.iter = 10000,
validation = NULL,
verbose = interactive()
)
ImputeEOF 51

Arguments
formula a formula to build the matrix that will be used in the SVD decomposition (see
Details)
max.eof, min.eof
maximum and minimum number of singular values used for imputation
data a data.frame
tol tolerance used for determining convergence
max.iter maximum iterations allowed for the algorithm
validation number of points to use in cross-validation (defaults to the maximum of 30 or
10% of the non NA points)
verbose logical indicating whether to print progress

Value
A vector of imputed values with attributes eof, which is the number of singular values used in the
final imputation; and rmse, which is the Root Mean Square Error estimated from cross-validation.

References
Beckers, J.-M., Barth, A., and Alvera-Azcárate, A.: DINEOF reconstruction of clouded images
including error maps – application to the Sea-Surface Temperature around Corsican Island, Ocean
Sci., 2, 183-199, doi:10.5194/os21832006, 2006.

Examples
library(data.table)
data(geopotential)
geopotential <- copy(geopotential)
geopotential[, gh.t := Anomaly(gh), by = .(lat, lon, month(date))]

# Add gaps to field

geopotential[, gh.gap := gh.t]
set.seed(42)
geopotential[sample(1:.N, .N*0.3), gh.gap := NA]

max.eof <- 5 # change to a higher value

52 Interpolate

geopotential[, gh.impute := ImputeEOF(gh.gap ~ lat + lon | date, max.eof,

verbose = TRUE, max.iter = 2000)]

library(ggplot2)
ggplot(geopotential[date == date[1]], aes(lon, lat)) +
geom_contour(aes(z = gh.t), color = "black") +
geom_contour(aes(z = gh.impute))

# Scatterplot with a sample.

na.sample <- geopotential[is.na(gh.gap)][sample(1:.N, .N*0.1)]
ggplot(na.sample, aes(gh.t, gh.impute)) +
geom_point()

# Estimated RMSE
attr(geopotential$gh.impute, "rmse")
# Real RMSE
geopotential[is.na(gh.gap), sqrt(mean((gh.t - gh.impute)^2))]

Interpolate Bilinear interpolation

Description
Interpolates values using bilinear interpolation.

Usage
Interpolate(formula, x.out, y.out, data = NULL, grid = TRUE, path = FALSE)

Arguments
formula a formula indicating dependent and independent variables (see Details)
x.out, y.out x and y values where to interpolate (see Details)
data optional data.frame with the data
grid logical indicating if x.out and y.out define a regular grid.
path a logical or character indicating if the x.out and y.out define a path. If character,
it will be the name of the column returning the order of said path.

Details
formula must be of the form VAR1 | VAR2 ~ X + Y where VAR1, VAR2, etc... are the names of
the variables to interpolate and X and Y the names of the x and y values, respectively. It is also
possible to pass only values of x, in which case, regular linear interpolation is performed and y.out,
if exists, is ignored with a warning.
is.cross 53

If grid = TRUE, x.out and y.out must define the values of a regular grid. If grid = FALSE, they
define the locations where to interpolate. Both grid and path cannot be set to TRUE and the value
of path takes precedence.
x.out can be a list, in which case, the first two elements will be interpreted as the x and y values
where to interpolate and it can also have a path element that will be used in place of the path
argument. This helps when creating a path with as.path (see Examples)

Value
A data.frame with interpolated values and locations

Examples
library(data.table)
data(geopotential)
geopotential <- geopotential[date == date[1]]
# new grid
x.out <- seq(0, 360, by = 10)
y.out <- seq(-90, 0, by = 10)

# Interpolate values to a new grid

interpolated <- geopotential[, Interpolate(gh ~ lon + lat, x.out, y.out)]

# Add values to an existing grid

geopotential[, gh.new := Interpolate(gh ~ lon + lat, lon, lat,
data = interpolated, grid = FALSE)$gh]

# Interpolate multiple values

geopotential[, c("u", "v") := GeostrophicWind(gh, lon, lat)]
interpolated <- geopotential[, Interpolate(u | v ~ lon + lat, x.out, y.out)]

# Interpolate values following a path

lats <- c(-34, -54, -30) # start and end latitudes
lons <- c(302, 290, 180) # start and end longituded
path <- geopotential[, Interpolate(gh ~ lon + lat, as.path(lons, lats))]

is.cross Cross pattern

Description
Reduces the density of a regular grid using a cross pattern.

Usage
is.cross(x, y, skip = 0)

cross(x, y)
54 JumpBy

Arguments
x, y x and y points that define a regular grid.
skip how many points to skip. Greater value reduces the final point density.

Value
is.cross returns a logical vector indicating whether each point belongs to the reduced grid or not.
cross returns a list of x and y components of the reduced density grid.

Examples
# Basic usage
grid <- expand.grid(x = 1:10, y = 1:10)
cross <- is.cross(grid$x, grid$y, skip = 2)

with(grid, plot(x, y))

with(grid, points(x[cross], y[cross], col = "red"))

# Its intended use is to highlight areas with geom_subset()

# with reduced densnity. This "hatches" areas with temperature
# over 270K
library(ggplot2)
ggplot(temperature[lev == 500], aes(lon, lat)) +
geom_raster(aes(fill = air)) +
stat_subset(aes(subset = air > 270 & is.cross(lon, lat)),
geom = "point", size = 0.1)

JumpBy Skip observations

Description
Skip observations

Usage
JumpBy(x, by, start = 1, fill = NULL)

Arguments
x vector
by numeric interval between elements to keep
start index to start from
fill how observations are skipped
logic 55

Details
Mostly useful for labelling only every byth element.

Value
A vector of the same class as x and, if fill is not null, the same length.

See Also
Other utilities: Anomaly(), Mag(), Percentile(), logic

Examples
x <- 1:50
JumpBy(x, 2) # only odd numbers
JumpBy(x, 2, start = 2) # only even numbers
JumpBy(x, 2, fill = NA) # even numbers replaced by NA
JumpBy(x, 2, fill = 6) # even numbers replaced by 6

logic Extended logical operators

Description
Extended binary operators for easy subsetting.

Usage
x %~% target

Similar(x, target, tol = Inf)

Arguments
x, target numeric vectors
tol tolerance for similarity

Details
%~% can be thought as a "similar" operator. It’s a fuzzy version of %in% in that returns TRUE for the
element of x which is the (first) closest to any element of target.
Similar is a functional version of %~% that also has a tol parameter that indicates the maximum
allowed tolerance.

Value
A logical vector of the same length of x.
56 Mag

See Also
Other utilities: Anomaly(), JumpBy(), Mag(), Percentile()

Examples
set.seed(198)
x <- rnorm(100)
x[x %~% c(0.3, 0.5, 1)]

# Practical use case: vertical cross-section at

# approximately 36W between 50S and 50N.
cross.lon <- -34 + 360
library(ggplot2)
library(data.table)
ggplot(temperature[lon %~% cross.lon & lat %between% c(-50, 50)],
aes(lat, lev)) +
geom_contour(aes(z = air))

Mag Magnitude and angle of a vector

Description
Computes the magnitude of a vector of any dimension. Or angle (in degrees) in 2 dimensions.

Usage
Mag(...)

Angle(x, y)

Arguments
... numeric vectors of coordinates or list of coordinates
x, y, x and y directions of the vector

Details
Helpful to save keystrokes and gain readability when computing wind (or any other vector quantity)
magnitude.

Value
Mag: A numeric vector the same length as each element of ... that is (x2 + y 2 + ...). Angle: A
p

numeric vector of the same length as x and y that is atan2(y, x)*180/pi.

MakeBreaks 57

See Also
Other utilities: Anomaly(), JumpBy(), Percentile(), logic
Other utilities: Anomaly(), JumpBy(), Percentile(), logic

Examples
Mag(10, 10)
Angle(10, 10)
Mag(10, 10, 10, 10)
Mag(list(10, 10, 10, 10))

# There's no vector recicling!

## Not run:
Mag(1, 1:2)

## End(Not run)

MakeBreaks Functions for making breaks

Description
Functions that return functions suitable to use as the breaks argument in ggplot2’s continuous
scales and in geom_contour_fill.

Usage
MakeBreaks(binwidth = NULL, bins = 10, exclude = NULL)

AnchorBreaks(anchor = 0, binwidth = NULL, exclude = NULL, bins = 10)

Arguments
binwidth width of breaks
bins number of bins, used if binwidth = NULL
exclude a vector of breaks to exclude
anchor anchor value

Details
MakeBreaks is essentially an export of the default way ggplot2::stat_contour makes breaks.
AnchorBreaks makes breaks starting from an anchor value and covering the range of the data
according to binwidth.
58 map_labels

Value
A function that takes a range as argument and a binwidth as an optional argument and returns a
sequence of equally spaced intervals covering the range.

See Also
Other ggplot2 helpers: DivideTimeseries(), WrapCircular(), geom_arrow(), geom_contour2(),
geom_contour_fill(), geom_label_contour(), geom_relief(), geom_streamline(), guide_colourstrip(),
map_labels, reverselog_trans(), scale_divergent, scale_longitude, stat_na(), stat_subset()

Examples

my_breaks <- MakeBreaks(10)

my_breaks(c(1, 100))
my_breaks(c(1, 100), 20) # optional new binwidth argument ignored

MakeBreaks()(c(1, 100), 20) # but is not ignored if initial binwidth is NULL

# One to one mapping between contours and breaks

library(ggplot2)
binwidth <- 20
ggplot(reshape2::melt(volcano), aes(Var1, Var2, z = value)) +
geom_contour(aes(color = ..level..), binwidth = binwidth) +
scale_color_continuous(breaks = MakeBreaks(binwidth))

#Two ways of getting the same contours. Better use the second one.
ggplot(reshape2::melt(volcano), aes(Var1, Var2, z = value)) +
geom_contour2(aes(color = ..level..), breaks = AnchorBreaks(132),
binwidth = binwidth) +
geom_contour2(aes(color = ..level..), breaks = AnchorBreaks(132, binwidth)) +
scale_color_continuous(breaks = AnchorBreaks(132, binwidth))

map_labels Label longitude and latitude

Description
Provide easy functions for adding suffixes to longitude and latitude for labelling maps.

Usage
LonLabel(lon, east = "°E", west = "°W", zero = "°")

LatLabel(lat, north = "°N", south = "°S", zero = "°")

MaskLand 59

Arguments
lon longitude in degrees
east, west, north, south, zero
text to append for each quadrant
lat latitude in degrees

Details
The default values are for Spanish.

See Also
Other ggplot2 helpers: DivideTimeseries(), MakeBreaks(), WrapCircular(), geom_arrow(),
geom_contour2(), geom_contour_fill(), geom_label_contour(), geom_relief(), geom_streamline(),
guide_colourstrip(), reverselog_trans(), scale_divergent, scale_longitude, stat_na(),
stat_subset()

Examples

LonLabel(0:360)

MaskLand Mask

Description
Creates a mask

Usage
MaskLand(lon, lat, mask = "world", wrap = c(0, 360))

Arguments
lon a vector of longitudes in degrees in 0-360 format
lat a vector of latitudes in degrees
mask the name of the dataset (that will be load with map) for creating the mask
wrap the longitude range to be used for a global mask

Value
A logical vector of the same length as lat and lon where TRUE means that the point is inside one of
the polygons making up the map. For a global map (the default), this means that the point is over
land.
60 metR

Examples

# Make a sea-land mask

mask <- temperature[lev == 1000, .(lon = lon, lat = lat, land = MaskLand(lon, lat))]
temperature <- temperature[mask, on = c("lon", "lat")]

# Take the temperature difference between land and ocean

diftemp <- temperature[,
.(tempdif = mean(air[land == TRUE]) - mean(air[land == FALSE])),
by = .(lat, lev)]
library(ggplot2)
ggplot(diftemp, aes(lat, lev)) +
geom_contour(aes(z = tempdif, color = ..level..)) +
scale_y_level() +
scale_x_latitude() +
scale_color_divergent()

# Mean temperature in the USA

usatemp <- temperature[, usa := MaskLand(lon, lat, mask = "usa")][
, .(air = weighted.mean(air, cos(lat*pi/180))), by = .(usa, lev)][
usa == TRUE]

ggplot(usatemp, aes(lev, air)) +

geom_line() +
scale_x_level() +
coord_flip()

metR metR: Tools for Easier Analysis of Meteorological Fields

Description
Many useful functions and extensions for dealing with meteorological data in the tidy data frame-
work. Extends ’ggplot2’ for better plotting of scalar and vector fields and provides commonly used
analysis methods in the atmospheric sciences.

Overview
Conceptually it’s divided into visualization tools and data tools. The former are geoms, stats and
scales that help with plotting using ggplot2, such as stat_contour_fill or scale_y_level, while the
later are functions for common data processing tools in the atmospheric sciences, such as Derivate
or EOF; these are implemented to work in the data.table paradigm, but also work with regular data
frames.
To get started, check the vignettes:

• Visualization Tools: vignette("Visualization-tools", package = "metR")

• Working with Data: vignette("Working-with-data", package = "metR")
Percentile 61

Author(s)

Maintainer: Elio Campitelli <[email protected]> (ORCID)

See Also

Useful links:

• https://github.com/eliocamp/metR
• Report bugs at https://github.com/eliocamp/metR/issues

Percentile Percentiles

Description

Computes percentiles.

Usage

Percentile(x)

Arguments

x numeric vector

Value

A numeric vector of the same length as x with the percentile of each value of x.

See Also

Other utilities: Anomaly(), JumpBy(), Mag(), logic

Examples
x <- rnorm(100)
p <- Percentile(x)
62 ReadNetCDF

ReadNetCDF Read NetCDF files.

Description
Using the ncdf4-package package, it reads a NetCDF file. The advantage over using ncvar_get
is that the output is a tidy data.table with proper dimensions.

Usage
ReadNetCDF(
file,
vars = NULL,
out = c("data.frame", "vector", "array"),
subset = NULL,
key = FALSE
)

GlanceNetCDF(file, ...)

Arguments
file source to read from. Must be one of:
• A string representing a local file with read access.
• A string representing a URL readable by ncdf4::nc_open(). (this in-
cludes DAP urls).
• A netcdf object returned by ncdf4::nc_open().
vars one of:
• NULL: reads all variables.
• a character vector with the name of the variables to read.
• a function that takes a vector with all the variables and returns either a
character vector with the name of variables to read or a numeric/logical
vector that indicates a subset of variables.
out character indicating the type of output desired
subset a list of subsetting objects. See below.
key if TRUE, returns a data.table keyed by the dimensions of the data.
... in GlanceNetCDF(), ignored. Is there for convenience so that a call to ReadNetCDF()
can be also valid for GlanceNetCDF().

Value
The return format is specified by out. It can be a data table in which each column is a variable and
each row, an observation; an array with named dimensions; or a vector. Since it’s possible to return
multiple arrays or vectors (one for each variable), for consistency the return type is always a list.
ReadNetCDF 63

Either of these two options are much faster than the first since the most time consuming part is the
melting of the array returned by ncdf4::ncvar_get. out = "vector" is particularly useful for adding
new variables to an existing data frame with the same dimensions.
When not all variables specified in vars have the same number of dimensions, the shorter variables
will be recycled. E.g. if reading a 3D pressure field and a 2D surface temperature field, the latter
will be turned into a 3D field with the same values in each missing dimension.
GlanceNetCDF() returns a list of variables and dimensions included in the file with a nice printing
method.

Subsetting
In the most basic form, subset will be a named list whose names must match the dimensions
specified in the NetCDF file and each element must be a vector whose range defines a contiguous
subset of data. You don’t need to provide and exact range that matches the actual gridpoints of
the file; the closest gridpoint will be selected. Furthermore, you can use NA to refer to the existing
minimum or maximum.
So, if you want to get Southern Hemisphere data from the from a file that defines latitude as lat,
then you can use:

subset = list(lat = -90:0)

More complex subsetting operations are supported. If you want to read non-contiguous chunks of
data, you can specify each chunk into a list inside subset. For example this subset

subset = list(list(lat = -90:-70, lon = 0:60),

list(lat = 70:90, lon = 300:360))

will return two contiguous chunks: one on the South-West corner and one on the North-East corner.
Alternatively, if you want to get the four corners that are combination of those two conditions,

subset = list(lat = list(-90:-70, 70:90),

lon = list(0:60, 300:360))

Both operations can be mixed together. So for example this

subset = list(list(lat = -90:-70,

lon = 0:60),
time = list(c("2000-01-01", "2000-12-31"),
c("2010-01-01", "2010-12-31")))

returns one spatial chunk for each of two temporal chunks.

The general idea is that named elements define ’global’ subsets ranges that will be applied to every
other subset, while each unnamed element define one contiguous chunk. In the above example,
time defines two temporal ranges that every subset of data will have.
The above example, then, is equivalent to
64 ReadNetCDF

subset = list(list(lat = -90:-70,

lon = 0:60,
time = c("2000-01-01", "2000-12-31")),
list(lat = -90:-70,
lon = 0:60,
time = c("2010-01-01", "2010-12-31")))

but demands much less typing.

Examples
file <- system.file("extdata", "temperature.nc", package = "metR")
# Get a list of variables.
variables <- GlanceNetCDF(file)
print(variables)

# The object returned by GlanceNetCDF is a list with lots

# of information
str(variables)

# Read only the first one, with name "var".

field <- ReadNetCDF(file, vars = c(var = names(variables$vars[1])))
# Add a new variable.
# ¡Make sure it's on the same exact grid!
field[, var2 := ReadNetCDF(file, out = "vector")]

## Not run:
# Using a DAP url
url <- "http://iridl.ldeo.columbia.edu/SOURCES/.Models/.SubX/.GMAO/.GEOS_V2p1/.hindcast/.ua/dods"
field <- ReadNetCDF(url, subset = list(M = 1,
P = 10,
S = "1999-01-01"))

# In this case, opening the netcdf file takes a non-neglible

# amount of time. So if you want to iterate over many dimensions,
# then it's more efficient to open the file first and then read it.

ncfile <- ncdf4::nc_open(url)

field <- ReadNetCDF(ncfile, subset = list(M = 1,
P = 10,
S = "1999-01-01"))

# Using a function in `vars` to read all variables that

# start with "radar_".
ReadNetCDF(radar_file, vars = \(x) startsWith(x, "radar_"))

## End(Not run)
reverselog_trans 65

reverselog_trans Reverse log transform

Description

Reverse log transformation. Useful when plotting and one axis is in pressure levels.

Usage

reverselog_trans(base = 10)

Arguments

base Base of the logarithm

See Also

Other ggplot2 helpers: DivideTimeseries(), MakeBreaks(), WrapCircular(), geom_arrow(),

geom_contour2(), geom_contour_fill(), geom_label_contour(), geom_relief(), geom_streamline(),
guide_colourstrip(), map_labels, scale_divergent, scale_longitude, stat_na(), stat_subset()

Examples
# Adiabatic temperature profile
gamma <- 0.286
t <- data.frame(p = c(1000, 950, 850, 700, 500, 300, 200, 100))
t$t <- 300*(t$p/1000)^gamma

library(ggplot2)
ggplot(t, aes(p, t)) +
geom_line() +
coord_flip() +
scale_x_continuous(trans = "reverselog")

scale_divergent Divergent colour scales

Description

Wrapper around ggplot’s scale_colour_gradient2 with inverted defaults of high and low.
66 scale_divergent

Usage
scale_colour_divergent(
...,
low = scales::muted("blue"),
mid = "white",
high = scales::muted("red"),
midpoint = 0,
space = "Lab",
na.value = "grey50",
guide = "colourbar"
)

scale_color_divergent(
...,
low = scales::muted("blue"),
mid = "white",
high = scales::muted("red"),
midpoint = 0,
space = "Lab",
na.value = "grey50",
guide = "colourbar"
)

scale_fill_divergent(
...,
low = scales::muted("blue"),
mid = "white",
high = scales::muted("red"),
midpoint = 0,
space = "Lab",
na.value = "grey50",
guide = "colourbar"
)

Arguments
... Arguments passed on to continuous_scale
scale_name The name of the scale that should be used for error messages as-
sociated with this scale.
palette A palette function that when called with a numeric vector with values
between 0 and 1 returns the corresponding output values (e.g., scales::area_pal()).
name The name of the scale. Used as the axis or legend title. If waiver(), the
default, the name of the scale is taken from the first mapping used for that
aesthetic. If NULL, the legend title will be omitted.
breaks One of:
• NULL for no breaks
• waiver() for the default breaks computed by the transformation object
scale_divergent 67

• A numeric vector of positions

• A function that takes the limits as input and returns breaks as output
(e.g., a function returned by scales::extended_breaks()). Also ac-
cepts rlang lambda function notation.
minor_breaks One of:
• NULL for no minor breaks
• waiver() for the default breaks (one minor break between each major
break)
• A numeric vector of positions
• A function that given the limits returns a vector of minor breaks. Also
accepts rlang lambda function notation.
n.breaks An integer guiding the number of major breaks. The algorithm may
choose a slightly different number to ensure nice break labels. Will only
have an effect if breaks = waiver(). Use NULL to use the default number
of breaks given by the transformation.
labels One of:
• NULL for no labels
• waiver() for the default labels computed by the transformation object
• A character vector giving labels (must be same length as breaks)
• A function that takes the breaks as input and returns labels as output.
Also accepts rlang lambda function notation.
limits One of:
• NULL to use the default scale range
• A numeric vector of length two providing limits of the scale. Use NA to
refer to the existing minimum or maximum
• A function that accepts the existing (automatic) limits and returns new
limits. Also accepts rlang lambda function notation. Note that setting
limits on positional scales will remove data outside of the limits. If
the purpose is to zoom, use the limit argument in the coordinate system
(see coord_cartesian()).
rescaler A function used to scale the input values to the range [0, 1]. This is
always scales::rescale(), except for diverging and n colour gradients
(i.e., scale_colour_gradient2(), scale_colour_gradientn()). The
rescaler is ignored by position scales, which always use scales::rescale().
Also accepts rlang lambda function notation.
oob One of:
• Function that handles limits outside of the scale limits (out of bounds).
Also accepts rlang lambda function notation.
• The default (scales::censor()) replaces out of bounds values with
NA.
• scales::squish() for squishing out of bounds values into range.
• scales::squish_infinite() for squishing infinite values into range.
trans For continuous scales, the name of a transformation object or the object
itself. Built-in transformations include "asn", "atanh", "boxcox", "date",
68 scale_label_colour_continuous

"exp", "hms", "identity", "log", "log10", "log1p", "log2", "logit", "modu-

lus", "probability", "probit", "pseudo_log", "reciprocal", "reverse", "sqrt"
and "time".
A transformation object bundles together a transform, its inverse, and meth-
ods for generating breaks and labels. Transformation objects are defined in
the scales package, and are called <name>_trans (e.g., scales::boxcox_trans()).
You can create your own transformation with scales::trans_new().
expand For position scales, a vector of range expansion constants used to add
some padding around the data to ensure that they are placed some distance
away from the axes. Use the convenience function expansion() to gen-
erate the values for the expand argument. The defaults are to expand the
scale by 5% on each side for continuous variables, and by 0.6 units on each
side for discrete variables.
position For position scales, The position of the axis. left or right for y
axes, top or bottom for x axes.
super The super class to use for the constructed scale
low, high Colours for low and high ends of the gradient.
mid colour for mid point
midpoint The midpoint (in data value) of the diverging scale. Defaults to 0.
space colour space in which to calculate gradient. Must be "Lab" - other values are
deprecated.
na.value Colour to use for missing values
guide Type of legend. Use "colourbar" for continuous colour bar, or "legend" for
discrete colour legend.

See Also
Other ggplot2 helpers: DivideTimeseries(), MakeBreaks(), WrapCircular(), geom_arrow(),
geom_contour2(), geom_contour_fill(), geom_label_contour(), geom_relief(), geom_streamline(),
guide_colourstrip(), map_labels, reverselog_trans(), scale_longitude, stat_na(), stat_subset()

Examples
library(ggplot2)
ggplot(reshape2::melt(volcano), aes(Var1, Var2, z = value)) +
geom_contour(aes(color = ..level..)) +
scale_colour_divergent(midpoint = 130)

scale_label_colour_continuous
Scales for contour label aesthetics

Description
Scales for contour label aesthetics
scale_label_colour_continuous 69

Usage
scale_label_colour_continuous(
...,
aesthetics = c("label_colour"),
guide = ggplot2::guide_colorbar(available_aes = "label_colour")
)

scale_label_alpha_continuous(
...,
range = c(0.1, 1),
aesthetics = c("label_alpha")
)

scale_label_size_continuous(
name = waiver(),
breaks = waiver(),
labels = waiver(),
limits = NULL,
range = c(1, 6),
trans = "identity",
guide = "legend"
)

Arguments
... Arguments passed on to continuous_scale
minor_breaks One of:
• NULL for no minor breaks
• waiver() for the default breaks (one minor break between each major
break)
• A numeric vector of positions
• A function that given the limits returns a vector of minor breaks. Also
accepts rlang lambda function notation.
oob One of:
• Function that handles limits outside of the scale limits (out of bounds).
Also accepts rlang lambda function notation.
• The default (scales::censor()) replaces out of bounds values with
NA.
• scales::squish() for squishing out of bounds values into range.
• scales::squish_infinite() for squishing infinite values into range.
na.value Missing values will be replaced with this value.
expand For position scales, a vector of range expansion constants used to add
some padding around the data to ensure that they are placed some distance
away from the axes. Use the convenience function expansion() to gen-
erate the values for the expand argument. The defaults are to expand the
scale by 5% on each side for continuous variables, and by 0.6 units on each
side for discrete variables.
70 scale_label_colour_continuous

position For position scales, The position of the axis. left or right for y
axes, top or bottom for x axes.
super The super class to use for the constructed scale
aesthetics Character string or vector of character strings listing the name(s) of the aes-
thetic(s) that this scale works with. This can be useful, for example, to apply
colour settings to the colour and fill aesthetics at the same time, via aesthetics =
c("colour", "fill").
guide Type of legend. Use "colourbar" for continuous colour bar, or "legend" for dis-
crete colour legend.
range Output range of alpha values. Must lie between 0 and 1.
name The name of the scale. Used as the axis or legend title. If waiver(), the default,
the name of the scale is taken from the first mapping used for that aesthetic. If
NULL, the legend title will be omitted.
breaks One of:
• NULL for no breaks
• waiver() for the default breaks computed by the transformation object
• A numeric vector of positions
• A function that takes the limits as input and returns breaks as output (e.g.,
a function returned by scales::extended_breaks()). Also accepts rlang
lambda function notation.
labels One of:
• NULL for no labels
• waiver() for the default labels computed by the transformation object
• A character vector giving labels (must be same length as breaks)
• A function that takes the breaks as input and returns labels as output. Also
accepts rlang lambda function notation.
limits One of:
• NULL to use the default scale range
• A numeric vector of length two providing limits of the scale. Use NA to
refer to the existing minimum or maximum
• A function that accepts the existing (automatic) limits and returns new
limits. Also accepts rlang lambda function notation. Note that setting
limits on positional scales will remove data outside of the limits. If the
purpose is to zoom, use the limit argument in the coordinate system (see
coord_cartesian()).
trans For continuous scales, the name of a transformation object or the object itself.
Built-in transformations include "asn", "atanh", "boxcox", "date", "exp", "hms",
"identity", "log", "log10", "log1p", "log2", "logit", "modulus", "probability",
"probit", "pseudo_log", "reciprocal", "reverse", "sqrt" and "time".
A transformation object bundles together a transform, its inverse, and methods
for generating breaks and labels. Transformation objects are defined in the scales
package, and are called <name>_trans (e.g., scales::boxcox_trans()). You
can create your own transformation with scales::trans_new().
scale_longitude 71

scale_longitude Helpful scales for maps

Description
These functions are simple wrappers around scale_x_continuous and scale_y_continuous with
helpful defaults for plotting longitude, latitude and pressure levels.

Usage
scale_x_longitude(
name = "",
ticks = 30,
breaks = seq(-180, 360, by = ticks),
expand = c(0, 0),
labels = LonLabel,
trans = "identity",
...
)

scale_y_longitude(
name = "",
ticks = 60,
breaks = seq(-180, 360, by = ticks),
expand = c(0, 0),
labels = LonLabel,
trans = "identity",
...
)

scale_x_latitude(
name = "",
ticks = 30,
breaks = seq(-90, 90, by = ticks),
expand = c(0, 0),
labels = LatLabel,
...
)

scale_y_latitude(
name = "",
ticks = 30,
breaks = seq(-90, 90, by = ticks),
expand = c(0, 0),
labels = LatLabel,
...
)
72 scale_longitude

scale_x_level(name = "", expand = c(0, 0), trans = "sa_height", ...)

scale_y_level(name = "", expand = c(0, 0), trans = "sa_height", ...)

Arguments
name The name of the scale. Used as the axis or legend title. If waiver(), the default,
the name of the scale is taken from the first mapping used for that aesthetic. If
NULL, the legend title will be omitted.
ticks spacing between breaks
breaks One of:
• NULL for no breaks
• waiver() for the default breaks computed by the transformation object
• A numeric vector of positions
• A function that takes the limits as input and returns breaks as output (e.g.,
a function returned by scales::extended_breaks()). Also accepts rlang
lambda function notation.
expand For position scales, a vector of range expansion constants used to add some
padding around the data to ensure that they are placed some distance away from
the axes. Use the convenience function expansion() to generate the values for
the expand argument. The defaults are to expand the scale by 5% on each side
for continuous variables, and by 0.6 units on each side for discrete variables.
labels One of:
• NULL for no labels
• waiver() for the default labels computed by the transformation object
• A character vector giving labels (must be same length as breaks)
• A function that takes the breaks as input and returns labels as output. Also
accepts rlang lambda function notation.
trans For continuous scales, the name of a transformation object or the object itself.
Built-in transformations include "asn", "atanh", "boxcox", "date", "exp", "hms",
"identity", "log", "log10", "log1p", "log2", "logit", "modulus", "probability",
"probit", "pseudo_log", "reciprocal", "reverse", "sqrt" and "time".
A transformation object bundles together a transform, its inverse, and methods
for generating breaks and labels. Transformation objects are defined in the scales
package, and are called <name>_trans (e.g., scales::boxcox_trans()). You
can create your own transformation with scales::trans_new().
... Other arguments passed on to scale_(x|y)_continuous()

See Also
Other ggplot2 helpers: DivideTimeseries(), MakeBreaks(), WrapCircular(), geom_arrow(),
geom_contour2(), geom_contour_fill(), geom_label_contour(), geom_relief(), geom_streamline(),
guide_colourstrip(), map_labels, reverselog_trans(), scale_divergent, stat_na(), stat_subset()
scale_mag 73

Examples
data(geopotential)
library(ggplot2)
ggplot(geopotential[date == date[1]], aes(lon, lat, z = gh)) +
geom_contour() +
scale_x_longitude() +
scale_y_latitude()

data(temperature)
ggplot(temperature[lon == lon[1] & lat == lat[1]], aes(air, lev)) +
geom_path() +
scale_y_level()

scale_mag Scale for vector magnitudes

Description
Allows to control the size of the arrows in geom_arrow. Highly experimental.

Usage
scale_mag(
name = ggplot2::waiver(),
labels = ggplot2::waiver(),
max_size = 1,
default_unit = "cm",
max = ggplot2::waiver(),
guide = guide_vector(),
...
)

scale_mag_continuous(
name = ggplot2::waiver(),
labels = ggplot2::waiver(),
max_size = 1,
default_unit = "cm",
max = ggplot2::waiver(),
guide = guide_vector(),
...
)

labels One of:

• NULL for no labels
• waiver() for the default labels computed by the transformation object
• A character vector giving labels (must be same length as breaks)
• A function that takes the breaks as input and returns labels as output. Also
accepts rlang lambda function notation.
max_size size of the arrow in centimetres
default_unit ignored
max magnitude of the reference arrow in data units. Will be the maximum value if
waiver()
guide type of legend
... Other arguments passed on to scale_(x|y)_continuous()

Examples
library(ggplot2)
g <- ggplot(seals, aes(long, lat)) +
geom_vector(aes(dx = delta_long, dy = delta_lat), skip = 2)

g + scale_mag("Seals velocity")

g + scale_mag("Seals velocity", max = 1)

g + scale_mag("Seals velocity", max_size = 2)

g + scale_mag("Seals velocity", default_unit = "mm")

season Assign seasons to months

Description
Assign seasons to months

Usage
season(x, lang = c("en", "es"))

seasonally(x)

is.full_season(x)

Arguments
x A vector of dates (alternative a numeric vector of months, for season())
lang Language to use.
Smooth2D 75

Value
season() returns a factor vector of the same length as x with the trimester of each month. seasonaly()
returns a date vector of the same length as x with the date "rounded" up to the centre month of each
season. is.full_season() returns a logical vector of the same length as x that is true only if the
3 months of each season for each year (December counts for the following year) are present in the
dataset.

Examples
season(1, lang = "en")
season(as.Date("2017-01-01"))

seasonally(as.Date(c("2017-12-01", "2018-01-01", "2018-02-01")))

is.full_season(as.Date(c("2017-12-01", "2018-01-01", "2018-02-01", "2018-03-01")))

Smooth2D Smooths a 2D field

Description
Smooth a 2D field using a user-supplied method.

Usage
Smooth2D(x, y, value, method = smooth_svd(0.01))

smooth_dct(kx = 0.5, ky = kx)

smooth_svd(variance_lost = 0.01)

Arguments
x, y Vector of x and y coordinates
value Vector of values
method The method to use smooth. Must be a function that takes a matrix and returns
the smoothed matrix. Build-in methods are smooth_svd() and smooth_dct().
kx, ky Proportion of components to keep in the x and y direction respectively. Lower
values increase the smoothness.
variance_lost Maximum percentage of variance lost after smoothing.

Details
smooth_svd() computes the SVD of the field and reconstructs it keeping only the leading values
that ensures a maximum variance lost. smooth_dct() computes the Discrete Cosine Transform of
the field and sets a proportion of the components to zero.
76 spherical

Value

A vector of the same length as value.

Examples
library(ggplot2)
# Creates a noisy version of the volcano dataset and applies the smooth
volcano <- reshape2::melt(datasets::volcano, value.name = "original")
volcano$noisy <- with(volcano, original + 1.5*rnorm(length(original)))

volcano$smooth_svd <- with(volcano, Smooth2D(Var2, Var1, noisy, method = smooth_svd(0.005)))

volcano$smooth_dct <- with(volcano, Smooth2D(Var2, Var1, noisy, method = smooth_dct(kx = 0.4)))

volcano <- reshape2::melt(volcano, id.vars = c("Var1", "Var2"))

ggplot(volcano, aes(Var1, Var2)) +

geom_contour(aes(z = value, color = ..level..)) +
scale_color_viridis_c() +
coord_equal() +
facet_wrap(~variable, ncol = 2)

spherical Transform between spherical coordinates and physical coordinates

Description

Transform a longitude or latitude interval into the equivalent in meters depending on latitude.

Usage

dlon(dx, lat, a = 6731000)

dlat(dy, a = 6731000)

dx(dlon, lat, a = 6731000)

dy(dlat, a = 6731000)

Arguments

dx, dy interval in meters

lat latitude, in degrees
a radius of the Earth
dlon, dlat interval in degrees
standard_atmosphere 77

Examples

library(data.table)
data(geopotential)
geopotential <- geopotential[date == date[1]]

# Geostrophic wind
geopotential[, c("u", "v") := GeostrophicWind(gh, lon, lat)] # in meters/second
geopotential[, c("dlon", "dlat") := .(dlon(u, lat), dlat(v))] # in degrees/second
geopotential[, c("u2", "v2") := .(dx(dlon, lat), dy(dlat))] # again in degrees/second

standard_atmosphere Standard atmosphere

Description
Utilities to use the International Standard Atmosphere. It uses the International Standard Atmo-
sphere up to the tropopause (11 km by definition) and then extends up to the 500 km using the
ARDC Model Atmosphere.

Usage
sa_pressure(height)

sa_height(pressure)

sa_temperature(height)

sa_height_trans(pressure_in = "hPa", height_in = "km")

sa_pressure_trans(height_in = "km", pressure_in = "hPa")

sa_height_breaks(n = 6, pressure_in = "hPa", height_in = "km", ...)

sa_height_axis(
name = ggplot2::waiver(),
breaks = sa_height_breaks(pressure_in = pressure_in, height_in = height_in),
labels = ggplot2::waiver(),
guide = ggplot2::waiver(),
pressure_in = "hPa",
height_in = "km"
)

sa_pressure_axis(
name = ggplot2::waiver(),
breaks = scales::log_breaks(n = 6),
78 standard_atmosphere

labels = scales::number_format(drop0trailing = TRUE, big.mark = "", trim = FALSE),

guide = ggplot2::waiver(),
height_in = "km",
pressure_in = "hPa"
)

Arguments
height height in meter
pressure pressure in pascals
height_in, pressure_in
units of height and pressure, respectively. Possible values are "km", "m" for
height and "hPa" and "Pa" for pressure. Alternatively, it can be a numeric con-
stant that multiplied to convert the unit to meters and Pascals respectively. (E.g.
if height is in feet, use height_in = 0.3048.)
n desiderd number of breaks.
... extra arguments passed to scales::breaks_extended.
name, breaks, labels, guide
arguments passed to ggplot2::sec_axis()

Details
sa_pressure(), sa_height(), sa_temperature() return, respectively, pressure (in pascals), height
(in meters) and temperature (in Kelvin).
sa_height_trans() and sa_pressure_trans() are two transformation functions to be used as
the trans argument in ggplot2 scales (e.g. scale_y_continuous(trans = "sa_height").
sa_height_axis() and sa_pressure_axis() return a secondary axis that transforms to height or
pressure respectively to be used as ggplot2 secondary axis (e.g. scale_y_continuous(sec.axis
= sa_height_axis())).
For convenience, and unlike the "primitive" functions, both the transformation functions and the
axis functions input and output in hectopascals and kilometres by default.

References
Standard atmosphere—Glossary of Meteorology. (n.d.). Retrieved 22 February 2021, from https:
//glossary.ametsoc.org/wiki/Standard_atmosphere

Examples
height <- seq(0, 100*1000, by = 1*200)

# Temperature profile that defines the standard atmosphere (in degrees Celsius)
plot(sa_temperature(height) - 273.15, height, type = "l")

# Pressure profile
plot(sa_pressure(height), height, type = "l")

# Use with ggplot2

stat_na 79

library(ggplot2)
data <- data.frame(height = height/1000, # height in kilometers
pressure = sa_pressure(height)/100) # pressures in hectopascals

# With the sa_*_axis functions, you can label the approximate height
# when using isobaric coordinates#'
ggplot(data, aes(height, pressure)) +
geom_path() +
scale_y_continuous(sec.axis = sa_height_axis("height"))

# Or the approximate pressure when using physical height

ggplot(data, aes(pressure, height)) +
geom_path() +
scale_y_continuous(sec.axis = sa_pressure_axis("level"))

# When working with isobaric coordinates,using a linear scale exagerates

# the thickness of the lower levels
ggplot(temperature[lat == 0], aes(lon, lev)) +
geom_contour_fill(aes(z = air)) +
scale_y_reverse()

# Using the standard atmospehre height transormation, the result

# is an approximate linear scale in height
ggplot(temperature[lat == 0], aes(lon, lev)) +
geom_contour_fill(aes(z = air)) +
scale_y_continuous(trans = "sa_height", expand = c(0, 0))

# The result is very similar to using a reverse log transform, which is the
# current behaviour of scale_y_level(). This transformation slightly
# overextends the higher levels.
ggplot(temperature[lat == 0], aes(lon, lev)) +
geom_contour_fill(aes(z = air)) +
scale_y_level()

stat_na Filter only NA values.

Description
Useful for indicating or masking missing data. This stat subsets data where one variable is NA.

Usage
stat_na(
mapping = NULL,
data = NULL,
geom = "point",
position = "identity",
...,
80 stat_na

show.legend = NA,
inherit.aes = TRUE
)

Aesthetics
stat_na understands the following aesthetics (required aesthetics are in bold)

• x
• y
• na
• width
• height

See Also
stat_subset for a more general way of filtering data.
Other ggplot2 helpers: DivideTimeseries(), MakeBreaks(), WrapCircular(), geom_arrow(),
geom_contour2(), geom_contour_fill(), geom_label_contour(), geom_relief(), geom_streamline(),
stat_subset 81

guide_colourstrip(), map_labels, reverselog_trans(), scale_divergent, scale_longitude,

stat_subset()

Examples
library(ggplot2)
library(data.table)
surface <- reshape2::melt(volcano)
surface <- within(surface, value[Var1 %between% c(20, 30) & Var2 %between% c(20, 30)] <- NA)
surface[sample(1:nrow(surface), 100, replace = FALSE), 3] <- NA

ggplot(surface, aes(Var1, Var2, z = value)) +

geom_contour_fill(na.fill = TRUE) +
stat_na(aes(na = value), geom = "tile")

stat_subset Subset values

Description
Removes values where subset evaluates to FALSE. Useful for showing only statistical significant
values, or an interesting subset of the data without manually subsetting the data.

Usage
stat_subset(
mapping = NULL,
data = NULL,
geom = "point",
position = "identity",
...,
show.legend = NA,
inherit.aes = TRUE
)

A function will be called with a single argument, the plot data. The return
value must be a data.frame, and will be used as the layer data. A function
can be created from a formula (e.g. ~ head(.x, 10)).
geom The geometric object to use display the data
position Position adjustment, either as a string, or the result of a call to a position adjust-
ment function.
... Other arguments passed on to layer(). These are often aesthetics, used to set
an aesthetic to a fixed value, like colour = "red" or size = 3. They may also
be parameters to the paired geom/stat.
show.legend logical. Should this layer be included in the legends? NA, the default, includes if
any aesthetics are mapped. FALSE never includes, and TRUE always includes. It
can also be a named logical vector to finely select the aesthetics to display.
inherit.aes If FALSE, overrides the default aesthetics, rather than combining with them.
This is most useful for helper functions that define both data and aesthetics and
shouldn’t inherit behaviour from the default plot specification, e.g. borders().

Aesthetics
stat_subset understands the following aesthetics (required aesthetics are in bold)

• x
• y
• subset
• width
• height

See Also
stat_na for a more specialized stat for filtering NA values.
Other ggplot2 helpers: DivideTimeseries(), MakeBreaks(), WrapCircular(), geom_arrow(),
geom_contour2(), geom_contour_fill(), geom_label_contour(), geom_relief(), geom_streamline(),
guide_colourstrip(), map_labels, reverselog_trans(), scale_divergent, scale_longitude,
stat_na()

Examples

library(ggplot2)
ggplot(reshape2::melt(volcano), aes(Var1, Var2)) +
geom_contour(aes(z = value)) +
stat_subset(aes(subset = value >= 150 & value <= 160),
shape = 3, color = "red")
surface 83

surface Surface height

Description
Surface height of central Argentina on a lambert grid.

Usage
surface

Format
A data.table with 53224 rows and 5 variables.
lon longitude in degrees
lat latitude in degrees
height height in meters
x x coordinates of projection
y y coordinates of projection

temperature Air temperature

Description
A global air temperature field for 2017-07-09.

Usage
temperature

Format
A data.table with 10512 rows and 3 variables:
lon longitude in degrees from 0 to 360
lat latitude in degrees
lev pressure level in hPa)
air air temperature in Kelvin

Source
https://psl.noaa.gov/data/gridded/data.ncep.reanalysis.derived.pressure.html
84 thermodynamics

thermodynamics Thermodynamics

Description

Functions related to common atmospheric thermodynamic relationships.

Usage

IdealGas(p, t, rho, R = 287.058)

Adiabat(p, t, theta, p0 = 1e+05, kappa = 2/7)

VirtualTemperature(p, t, e, tv, epsilon = 0.622)

MixingRatio(p, e, w, epsilon = 0.622)

ClausiusClapeyron(t, es)

DewPoint(p, ws, td, epsilon = 0.622)

Arguments

p pressure
t temperature
rho density
R gas constant for air
theta potential temperature
p0 reference pressure
kappa ratio of dry air constant and specific heat capacity at constant pressure
e vapour partial pressure
tv virtual temperature
epsilon ratio of dry air constant and vapour constant
w mixing ratio
es saturation vapour partial pressure
ws saturation mixing ratio
td dewpoint
thermodynamics 85

Details
IdealGas computes pressure, temperature or density of air according to the ideal gas law P = ρRT .
Adiabat computes pressure, temperature or potential temperature according to the adiabatic rela-
tionship θ = T (P 0/P )κ .
VirtualTemperature computes pressure, temperature, vapour partial pressure or virtual tempera-
ture according to the virtual temperature definition T (1 − e/P (1 − ))−1 .
MixingRatio computes pressure, vapour partial temperature, or mixing ratio according to w =
e/(P − e).
ClausiusClapeyron computes saturation pressure or temperature according to the August-Roche-
Magnus formula es = aexpbT /(T + c) with temperature in Kelvin and saturation pressure in Pa.
DewPoint computes pressure, saturation mixing ration or dew point from the relationship ws =
es(T d)/(p − es(T d)). Note that the computation of dew point is approximated.
Is important to take note of the units in which each variable is provided. With the default values,
pressure should be passed in Pascals, temperature and potential temperature in Kelvins, and density
in kg/m3 . ClausiusClayperon and DewPoint require and return values in those units.
The defaults value of the R and kappa parameters are correct for dry air, for the case of moist air,
use the virtual temperature instead of the actual temperature.

Value
Each function returns the value of the missing state variable.

References
http://www.atmo.arizona.edu/students/courselinks/fall11/atmo551a/ATMO_451a_551a_files/WaterVapor.pdf

See Also
Other meteorology functions: Derivate(), EOF(), GeostrophicWind(), WaveFlux(), waves

Examples
IdealGas(1013*100, 20 + 273.15)
IdealGas(1013*100, rho = 1.15) - 273.15

(theta <- Adiabat(70000, 20 + 273.15))

Adiabat(70000, theta = theta) - 273.15

# Relative humidity from T and Td

t <- 25 + 273.15
td <- 20 + 273.15
p <- 1000000
(rh <- ClausiusClapeyron(td)/ClausiusClapeyron(t))

# Mixing ratio
ws <- MixingRatio(p, ClausiusClapeyron(t))
w <- ws*rh
DewPoint(p, w) - 273.15 # Recover Td
86 WaveFlux

Trajectory Compute trajectories

Description
Computes trajectories of particles in a time-varying velocity field.

Usage
Trajectory(formula, x0, y0, cyclical = FALSE, data = NULL, res = 2)

Arguments
formula a formula indicating dependent and independent variables in the form of dx +
dy ~ x + y + t.
x0, y0 starting coordinates of the particles.
cyclical logical vector of boundary condition for x and y.
data optional data.frame containing the variables.
res resolution parameter (higher numbers increases the resolution)

WaveFlux Calculate wave-activity flux

Description
Calculate wave-activity flux

Usage
WaveFlux(gh, u, v, lon, lat, lev, g = 9.81, a = 6371000)

Arguments
gh geopotential height
u mean zonal velocity
v mean meridional velocity
lon longitude (in degrees)
lat latitude (in degrees)
lev pressure level (in hPa)
g acceleration of gravity
a Earth’s radius
waves 87

Details

Calculates Plum-like wave activity fluxes

Value

A list with elements: longitude, latitude, and the two horizontal components of the wave activity
flux.

References

Takaya, K. and H. Nakamura, 2001: A Formulation of a Phase-Independent Wave-Activity Flux

for Stationary and Migratory Quasigeostrophic Eddies on a Zonally Varying Basic Flow. J. Atmos.
Sci., 58, 608–627, doi:10.1175/15200469(2001)058<0608:AFOAPI>2.0.CO;2
Adapted from https://github.com/marisolosman/Reunion_Clima/blob/master/WAF/Calculo_
WAF.ipynb

See Also

Other meteorology functions: Derivate(), EOF(), GeostrophicWind(), thermodynamics, waves

waves Fourier transform

Description

Perform a fourier transform of the data and return the

Usage

FitWave(y, k = 1)

BuildWave(
x,
amplitude,
phase,
k,
wave = list(amplitude = amplitude, phase = phase, k = k),
sum = TRUE
)

FilterWave(y, k, action = sign(k[k != 0][1]))

WaveEnvelope(y)
88 waves

Arguments
y numeric vector to transform
k numeric vector of wave numbers
x numeric vector of locations (in radians)
amplitude numeric vector of amplitudes
phase numeric vector of phases
wave optional list output from FitWave
sum whether to perform the sum or not (see Details)
action integer to disambiguate action for k = 0 (see Details)

Details
FitWave uses fft to make a fourier transform of the data and then returns a list of parameters for
each wave number kept. The amplitude (A), phase (φ) and wave number (k) satisfy:
X
y= Acos((x − φ)k)

The phase is calculated so that it lies between 0 and 2π/k so it represents the location (in radians)
of the first maximum of each wave number. For the case of k = 0 (the mean), phase is arbitrarily set
to 0.
BuildWave is FitWave’s inverse. It reconstructs the original data for selected wavenumbers. If sum
is TRUE (the default) it performs the above mentioned sum and returns a single vector. If is FALSE,
then it returns a list of k vectors consisting of the reconstructed signal of each wavenumber.
FilterWave filters or removes wavenumbers specified in k. If k is positive, then the result is the
reconstructed signal of y only for wavenumbers specified in k, if it’s negative, is the signal of y
minus the wavenumbers specified in k. The argument action must be be manually set to -1 or +1
if k=0.
WaveEnvelope computes the wave envelope of y following Zimin (2003). To compute the envelope
of only a restricted band, first filter it with FilterWave.

Value
FitWaves returns a a named list with components
k wavenumbers
amplitude amplitude of each wavenumber
phase phase of each wavenumber in radians
r2 explained variance of each wavenumber
BuildWave returns a vector of the same length of x with the reconstructed vector if sum is TRUE or,
instead, a list with components
k wavenumbers
x the vector of locations
y the reconstructed signal of each wavenumber
FilterWave returns a vector of the same length as y ‘
waves 89

References
Zimin, A.V., I. Szunyogh, D.J. Patil, B.R. Hunt, and E. Ott, 2003: Extracting Envelopes of Rossby
Wave Packets. Mon. Wea. Rev., 131, 1011–1017, doi:10.1175/15200493(2003)131<1011:EEORWP>2.0.CO;2

See Also
Other meteorology functions: Derivate(), EOF(), GeostrophicWind(), WaveFlux(), thermodynamics

Examples
data(geopotential)
library(data.table)
# January mean of geopotential height
jan <- geopotential[month(date) == 1, .(gh = mean(gh)), by = .(lon, lat)]

# Stationary waves for each latitude

jan.waves <- jan[, FitWave(gh, 1:4), by = .(lat)]
library(ggplot2)
ggplot(jan.waves, aes(lat, amplitude, color = factor(k))) +
geom_line()

# Build field of wavenumber 1

jan[, gh.1 := BuildWave(lon*pi/180, wave = FitWave(gh, 1)), by = .(lat)]
ggplot(jan, aes(lon, lat)) +
geom_contour(aes(z = gh.1, color = ..level..)) +
coord_polar()

# Build fields of wavenumber 1 and 2

waves <- jan[, BuildWave(lon*pi/180, wave = FitWave(gh, 1:2), sum = FALSE), by = .(lat)]
waves[, lon := x*180/pi]
ggplot(waves, aes(lon, lat)) +
geom_contour(aes(z = y, color = ..level..)) +
facet_wrap(~k) +
coord_polar()

# Field with waves 0 to 2 filtered

jan[, gh.no12 := gh - BuildWave(lon*pi/180, wave = FitWave(gh, 0:2)), by = .(lat)]
ggplot(jan, aes(lon, lat)) +
geom_contour(aes(z = gh.no12, color = ..level..)) +
coord_polar()

# Much faster
jan[, gh.no12 := FilterWave(gh, -2:0), by = .(lat)]
ggplot(jan, aes(lon, lat)) +
geom_contour(aes(z = gh.no12, color = ..level..)) +
coord_polar()

# Using positive numbers returns the field

jan[, gh.only12 := FilterWave(gh, 2:1), by = .(lat)]
ggplot(jan, aes(lon, lat)) +
geom_contour(aes(z = gh.only12, color = ..level..)) +
coord_polar()
90 WrapCircular

# Compute the envelope of the geopotential

jan[, envelope := WaveEnvelope(gh.no12), by = .(lat)]
ggplot(jan[lat == -60], aes(lon, gh.no12)) +
geom_line() +
geom_line(aes(y = envelope), color = "red")

WrapCircular Wrap periodic data to any range

Description
Periodic data can be defined only in one period and be extended to any arbitrary range.

Usage
WrapCircular(x, circular = "lon", wrap = c(0, 360))

Arguments
x a data.frame
circular the name of the circular dimension
wrap the wrap for the data to be extended to

Value
A data.frame.

See Also
geom_contour2
Other ggplot2 helpers: DivideTimeseries(), MakeBreaks(), geom_arrow(), geom_contour2(),
geom_contour_fill(), geom_label_contour(), geom_relief(), geom_streamline(), guide_colourstrip(),
map_labels, reverselog_trans(), scale_divergent, scale_longitude, stat_na(), stat_subset()

Examples
library(ggplot2)
library(data.table)
data(geopotential)
g <- ggplot(geopotential[date == date[1]], aes(lon, lat)) +
geom_contour(aes(z = gh)) +
coord_polar() +
ylim(c(-90, -10))

# This plot has problems in lon = 0

g
WrapCircular 91

# But using WrapCircular solves it.

g %+% WrapCircular(geopotential[date == date[1]], "lon", c(0, 360))

# Aditionally data can be just repeatet to the right and

# left
ggplot(WrapCircular(geopotential[date == date[1]], wrap = c(-180, 360 + 180)),
aes(lon, lat)) +
geom_contour(aes(z = gh))

# The same behaviour is now implemented directly in geom_contour2

# and geom_contour_fill
ggplot(geopotential[date == date[1]], aes(lon, lat)) +
geom_contour2(aes(z = gh), xwrap = c(-180, 360 + 180))
Index

∗ datasets JumpBy, 54
as.discretised_scale, 4 logic, 55
geom_arrow, 20 Mag, 56
geom_contour2, 24 Percentile, 61
geom_contour_fill, 28 %~% (logic), 55
geom_contour_tanaka, 30 %in%, 55
geom_label_contour, 33
geom_relief, 36 Adiabat (thermodynamics), 84
geom_streamline, 39 aes(), 21, 25, 29, 31, 34, 37, 40, 80, 81
geopotential, 43 aes_(), 21, 25, 29, 31, 34, 37, 40, 80, 81
stat_na, 79 AnchorBreaks (MakeBreaks), 57
stat_subset, 81 Angle (Mag), 56
surface, 83 Anomaly, 3, 55–57, 61
temperature, 83 as.discretised_scale, 4
∗ ggplot2 helpers as.path, 9, 53
DivideTimeseries, 14 AssignSeason (season), 74
geom_arrow, 20 autoplot, 17
geom_contour2, 24
base::svd, 16
geom_contour_fill, 28
borders(), 22, 26, 29, 32, 35, 38, 41, 80, 82
geom_label_contour, 33
BuildWave (waves), 87
geom_relief, 36
geom_streamline, 39 ClausiusClapeyron (thermodynamics), 84
MakeBreaks, 57 continuous_scale, 5, 66, 69
map_labels, 58 ConvertLongitude, 10
reverselog_trans, 65 coord_cartesian(), 6, 7, 67, 70
scale_divergent, 65 coriolis, 11
scale_longitude, 71 cross (is.cross), 53
stat_na, 79 cut.eof, 11, 17
stat_subset, 81
WrapCircular, 90 data.table, 60
∗ meteorology functions data.table::dcast, 51
Derivate, 12 denormalise, 12
EOF, 15 denormalize (denormalise), 12
GeostrophicWind, 44 Derivate, 12, 17, 45, 60, 85, 87, 89
thermodynamics, 84 Detrend (FitLm), 19
WaveFlux, 86 DewPoint (thermodynamics), 84
waves, 87 discretised_scale
∗ utilities (as.discretised_scale), 4
Anomaly, 3 Divergence (Derivate), 12

92
INDEX 93

DivideTimeseries, 14, 23, 27, 30, 36, 38, 42, GeomTextContour (geom_label_contour), 33
58, 59, 65, 68, 72, 80, 82, 90 geopotential, 43
dlat (spherical), 76 GeostrophicWind, 14, 17, 44, 85, 87, 89
dlon (spherical), 76 GetSMNData, 45
dx (spherical), 76 GetTopography, 47
dy (spherical), 76 ggplot(), 21, 25, 29, 31, 34, 37, 40, 80, 81
ggplot2, 60
element_text(), 49 ggplot2::binned_scale(), 4
EOF, 14, 15, 45, 60, 85, 87, 89 ggplot2::geom_contour, 24, 28
EOF(), 12 ggplot2::geom_raster, 38
EPflux, 18 ggplot2::geom_segment, 20
expansion(), 6, 68, 69, 72 ggplot2::geom_tile, 38
ggplot2::sec_axis(), 78
f (coriolis), 11 ggplot2::stat_contour, 33, 35, 57
fft, 88 GlanceNetCDF (ReadNetCDF), 62
FilterWave (waves), 87 GlanceNetCDF(), 62
FitLm, 19 grid::arrow, 22, 41
FitWave (waves), 87 grid::unit(), 49
Formula::Formula, 16, 51 guide_colourstrip, 15, 23, 27, 30, 36, 38,
fortify(), 21, 25, 29, 31, 34, 37, 41, 80, 81 42, 58, 59, 65, 68, 72, 81, 82, 90
guide_vector, 48
geom_arrow, 15, 20, 27, 30, 36, 38, 42, 58, 59,
65, 68, 72, 73, 80, 82, 90 IdealGas (thermodynamics), 84
geom_contour, 28 Impute2D, 26, 29, 50
geom_contour2, 15, 23, 24, 30, 36, 38, 42, 58, ImputeEOF, 50
59, 65, 68, 72, 80, 82, 90 Interpolate, 9, 52
geom_contour_fill, 15, 23, 27, 28, 36, 38, irlba::irlba, 16
42, 57–59, 65, 68, 72, 80, 82, 90 is.cross, 53
geom_contour_fill(), 8, 50 is.full_season (season), 74
geom_contour_tanaka, 30
geom_label_contour, 15, 23, 27, 30, 33, 38, JumpBy, 3, 54, 56, 57, 61
42, 58, 59, 65, 68, 72, 80, 82, 90
geom_relief, 15, 23, 27, 30, 36, 36, 42, 58, label_placer_flattest(), 26, 34
59, 65, 68, 72, 80, 82, 90 labs(), 49
geom_shadow (geom_relief), 36 lambda, 5–8, 67, 69, 70, 72, 74
geom_streamline, 15, 23, 27, 30, 36, 38, 39, Laplacian (Derivate), 12
58, 59, 65, 68, 72, 80, 82, 90 LatLabel (map_labels), 58
geom_text_contour (geom_label_contour), layer(), 22, 25, 29, 31, 34, 38, 41, 80, 82
33 logic, 3, 55, 55, 57, 61
geom_vector (geom_arrow), 20 LonLabel (map_labels), 58
GeomArrow (geom_arrow), 20
GeomContour2 (geom_contour2), 24 Mag, 3, 55, 56, 56, 61
GeomContourTanaka MakeBreaks, 15, 23, 27, 30, 36, 38, 42, 57, 59,
(geom_contour_tanaka), 30 65, 68, 72, 80, 82, 90
GeomLabelContour (geom_label_contour), map, 59
33 map_labels, 15, 23, 27, 30, 36, 38, 42, 58, 58,
GeomRelief (geom_relief), 36 65, 68, 72, 81, 82, 90
GeomShadow (geom_relief), 36 MaskLand, 59
GeomStreamline (geom_streamline), 39 mean, 3, 50
94 INDEX

metR, 60 scale_label_colour_continuous, 68
metR-package (metR), 60 scale_label_size_continuous
MixingRatio (thermodynamics), 84 (scale_label_colour_continuous),
68
ncdf4::nc_open(), 62 scale_latitude (scale_longitude), 71
ncdf4::ncvar_get, 63 scale_longitude, 15, 23, 27, 30, 36, 38, 42,
ncvar_get, 62 58, 59, 65, 68, 71, 81, 82, 90
scale_mag, 73
Percentile, 3, 55–57, 61 scale_mag_continuous (scale_mag), 73
predict, 17 scale_x_continuous, 71
scale_x_latitude (scale_longitude), 71
ReadNetCDF, 62 scale_x_level (scale_longitude), 71
ReadNetCDF(), 62 scale_x_longitude (scale_longitude), 71
RepeatCircular (WrapCircular), 90 scale_y_continuous, 71
ResidLm (FitLm), 19
scale_y_latitude (scale_longitude), 71
reverselog_trans, 15, 23, 27, 30, 36, 38, 42,
scale_y_level, 60
58, 59, 65, 68, 72, 81, 82, 90
scale_y_level (scale_longitude), 71
scale_y_longitude (scale_longitude), 71
sa_height (standard_atmosphere), 77
ScaleDiscretised
sa_height_axis (standard_atmosphere), 77
(as.discretised_scale), 4
sa_height_breaks (standard_atmosphere),
77 scales::area_pal(), 5, 7, 66
sa_height_trans (standard_atmosphere), scales::boxcox_trans(), 6, 7, 68, 70, 72
77 scales::breaks_extended, 78
sa_pressure (standard_atmosphere), 77 scales::censor(), 6, 8, 67, 69
sa_pressure_axis (standard_atmosphere), scales::extended_breaks(), 5, 7, 67, 70,
77 72
sa_pressure_trans scales::rescale(), 6, 8, 67
(standard_atmosphere), 77 scales::squish(), 6, 8, 67, 69
sa_temperature (standard_atmosphere), 77 scales::squish_infinite(), 6, 8, 67, 69
scale_color_divergent scales::trans_new(), 6, 7, 68, 70, 72
(scale_divergent), 65 screeplot, 17
scale_colour_divergent season, 74
(scale_divergent), 65 seasonally (season), 74
scale_colour_gradient2, 65 Similar (logic), 55
scale_colour_gradient2(), 6, 8, 67 Smooth2D, 75
scale_colour_gradientn(), 6, 8, 67 smooth_dct (Smooth2D), 75
scale_divergent, 15, 23, 27, 30, 36, 38, 42, smooth_svd (Smooth2D), 75
58, 59, 65, 65, 72, 81, 82, 90 spherical, 42, 76
scale_fill_discretised standard_atmosphere, 77
(as.discretised_scale), 4 stat_contour2 (geom_contour2), 24
scale_fill_discretised(), 30 stat_contour_fill, 60
scale_fill_divergent (scale_divergent), stat_contour_fill (geom_contour_fill),
65 28
scale_fill_divergent_discretised stat_na, 15, 23, 27, 30, 36, 38, 42, 58, 59, 65,
(as.discretised_scale), 4 68, 72, 79, 82, 90
scale_label_alpha_continuous stat_streamline (geom_streamline), 39
(scale_label_colour_continuous), stat_subset, 15, 23, 27, 30, 36, 38, 42, 58,
68 59, 65, 68, 72, 80, 81, 81, 90
INDEX 95

StatArrow (geom_arrow), 20
StatContour2 (geom_contour2), 24
StatContourFill (geom_contour_fill), 28
StatNa (stat_na), 79
stats::.lm.fit, 19
StatStreamline (geom_streamline), 39
StatSubset (stat_subset), 81
StatTextContour (geom_label_contour), 33
summary, 17
surface, 83

temperature, 83
theme(), 49
thermodynamics, 14, 17, 45, 84, 87, 89
Trajectory, 86
transformation object, 5, 7, 66, 70, 72

varimax, 16
VirtualTemperature (thermodynamics), 84
Vorticity (Derivate), 12

waiver(), 49
WaveEnvelope (waves), 87
WaveFlux, 14, 17, 45, 85, 86, 89
waves, 14, 17, 45, 85, 87, 87
WrapCircular, 15, 23, 27, 30, 36, 38, 42, 58,
59, 65, 68, 72, 80, 82, 90

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