Package 'Orcs'

Omnidirectional R Code Snippets.

Description

Omnidirectional R Code Snippets

Details

The package provides a variety of functions which I regularly use during my everyday work.

Author(s)

Florian Detsch, Tim Appelhans, Baptiste Auguie, OpenStreetMap contributors

Maintainer: Florian Detsch [email protected]

---

Assign SSH Key to Local Git Repository

Description

Assign an SSH key to a local Git repository to bypass user/password prompts during 'git push. See Generating an SSH Key for further information on how to generate an SSH key and add it to your GitHub account.

Usage

assignSSH(user, repo)

Arguments

user	GitHub user name as character. If not specified, information on GitHub user and repository name is taken from the current working environment.
repo	GitHub repository name as character, see 'user'.

See Also

https://docs.github.com/articles/generating-an-ssh-key/.

Examples

## Not run: 
## for an arbitrary git repository
assignSSH()

## for this very git repository
assignSSH(user = "fdetsch", repo = "Orcs")

## End(Not run)

---

Build a Book without Underscores

Description

Since the use of underscores ('_') is not permitted when streaming bookdown documents via GitHub Pages, this wrapper function serves to remove any unwanted underscores from subfolders and link .html documents created by bookdown::render_book().

Usage

buildBook(output_dir = "book", ...)

Arguments

output_dir	Output directory as character.
...	Arguments passed to bookdown::render_book().

Note

While all remaining arguments passed to bookdown::render_book() remain untouched, and hence their specification is freely up to the user, the default value of 'output_dir' is explicitly set to "book" here. If this were not the case (i.e. if the default value were used), the output document would be created in "_book" which is not desirable for obvious reasons.

Author(s)

Florian Detsch

---

Bump Package 'Version:' and 'Date:' in DESCRIPTION File

Description

This function let's you bump the version number and creation date of your package's DESCRIPTION file. Additionally, it bumps the version numbers of a NEWS.md file and automatically generates a corresponding plain NEWS file (for R-help pages). Supported versioning system is MAJOR.MINOR.PATCH.

Usage

bumpVersion(
  element = "patch",
  pkg.repo = ".",
  news = file.path(pkg.repo, "NEWS.md"),
  plain_news = TRUE
)

Arguments

element	character, one of "major", "minor", "patch" (default) to be bumped.
pkg.repo	Path to package repository folder. Default is current working directory, i.e. ".".
news	The NEWS.md file of the repo (assumed to be in top level path). If this exists, the first line of that file will be rewritten to be "\<packagename\> \<major.minor.patch\>". Note that the current implementation assumes that the NEWS file is in .md format. A plain NEWS file (for R-help pages) will be generated automatically.
plain_news	whether to generate a plain NEWS file in the package root directory from the NEWS.md file supplied to argument 'news'.

Author(s)

Tim Appelhans

See Also

https://semver.org/

---

Compare Two Density Distributions Side by Side

Description

This function will produce a plot of two density functions displayed side by side.

Usage

compareDistributions(
  left,
  right,
  add.spread = TRUE,
  print.stats = TRUE,
  xlim = NULL,
  ylim = NULL,
  clrs = c("purple", "lightblue"),
  xlab = "density",
  ylab = "value",
  ...
)

Arguments

left	numeric vector.
right	numeric vector.
add.spread	logical, whether to plot the spread (q25 to q75 and the median).
print.stats	logical, whether to print summary statistics for each distribution.
xlim, ylim	numeric axis limits, see lattice::xyplot().
clrs	A character vector of length 2 specifying the colors for the filled density regions.
xlab, ylab	character axis labels, see graphics::plot().
...	Additional arguments passed to stats::density().

Value

A trellis object.

Author(s)

Tim Appelhans

Examples

compareDistributions(rnorm(1000, 2, 3), rnorm(1000, -5, 1))
compareDistributions(rnorm(1000, 2, 3), rnorm(1000, -5, 1), 
                     add.spread = FALSE)
compareDistributions(rnorm(1000, 2, 3), rnorm(1000, -5, 1), 
                     add.spread = TRUE, clrs = c("red", "brown"))
compareDistributions(rnorm(1000, 2, 5), rnorm(1000, -5, 4), 
                     print.stats = FALSE, add.spread = FALSE)
                     
## pass additional parameters to stats::density() 
compareDistributions(rnorm(1000, 2, 5), rnorm(1000, -5, 4), 
                     print.stats = FALSE, add.spread = FALSE, bw = 5)
compareDistributions(rnorm(1000, 2, 5), rnorm(1000, -5, 4), 
                     print.stats = FALSE, add.spread = FALSE, bw = 8,
                     kernel = "rectangular")
compareDistributions(rnorm(1000, 2, 5), rnorm(1000, -5, 4), 
                     print.stats = FALSE, add.spread = TRUE, bw = 8,
                     n = 3)
compareDistributions(rnorm(1000, 2, 5), rnorm(1000, -5, 4), 
                     print.stats = TRUE, add.spread = TRUE, bw = 0.1)
compareDistributions(rnorm(1000, 2, 5), rnorm(1000, -5, 4), 
                     print.stats = TRUE, add.spread = TRUE, bw = 0.5)

---

Convert Points to ⁠SpatialLines*⁠

Description

Create a ⁠SpatialLines*⁠ object from a Line object or set of point coordinates in one go, i.e. without being required to run through the single steps outlined in sp::SpatialLines().

Usage

## S4 method for signature 'matrix'
coords2Lines(coords, ID, data, match.ID = TRUE, ...)

## S4 method for signature 'Line'
coords2Lines(coords, ID, data, match.ID = TRUE, ...)

Arguments

coords	Line object or 2-column numeric matrix with x and y coordinates.
ID	character, see sp::Lines().
data	data.frame with data to add to the output ⁠SpatialLines*⁠ object (optional).
match.ID	logical, see sp::SpatialLinesDataFrame().
...	Further arguments passed on to sp::SpatialLines(), i.e. proj4string.

Value

If 'data' is missing, a SpatialLines object; else a SpatialLinesDataFrame object.

Examples

library(sp)

coords1 <- cbind(c(2, 4, 4, 1, 2), c(2, 3, 5, 4, 2))
sln1 <- coords2Lines(coords1, ID = "A")

coords2 <- cbind(c(5, 4, 2, 5), c(2, 3, 2, 2))
sln2 <- coords2Lines(coords2, ID = "B")

plot(sln1, col = "grey75")
plot(sln2, col = "grey25", add = TRUE)

---

Convert Points to ⁠SpatialPolygons*⁠

Description

Create a ⁠SpatialPolygons*⁠ object from a Polygon object or set of point coordinates in one go, i.e. without being required to run through the single steps outlined in sp::SpatialPolygons().

Usage

## S4 method for signature 'matrix'
coords2Polygons(coords, hole = NA, ID, data, match.ID = TRUE, ...)

## S4 method for signature 'Polygon'
coords2Polygons(coords, ID, data, match.ID = TRUE, ...)

Arguments

coords	Polygon object or 2-column numeric matrix with x and y coordinates.
hole	logical, see sp::Polygon().
ID	character, see sp::Polygons().
data	data.frame with data to add to the output ⁠SpatialPolygons*⁠ object (optional).
match.ID	logical, see sp::SpatialPolygonsDataFrame().
...	Further arguments passed on to sp::SpatialPolygons(), i.e. p0 and proj4string.

Value

If 'data' is missing, a SpatialPolygons object; else a SpatialPolygonsDataFrame object.

Examples

library(sp)

coords1 <- cbind(c(2, 4, 4, 1, 2), c(2, 3, 5, 4, 2))
spy1 <- coords2Polygons(coords1, ID = "A")

coords2 <- cbind(c(5, 4, 2, 5), c(2, 3, 2, 2))
spy2 <- coords2Polygons(coords2, ID = "B")

plot(spy1, col = "grey75")
plot(spy2, col = "grey25", add = TRUE)

---

Compute Selected Evaluation Metrics

Description

Compute selected evaluation metrics for binary (i.e. two-class) confusion matrices.

Usage

evalMetrics(mat, type = c("accuracy", "precision", "recall"))

Arguments

mat	Binary confusion matrix (2-by-2; see Examples).
type	Target evaluation metric as character, defaults to "accuracy". Other available options are "precision" and "recall".

Value

A single numeric.

Author(s)

Florian Detsch

References

University of Michigan (2017) Applied Machine Learning in Python. Available online: https://www.coursera.org/learn/python-machine-learning/home/welcome.

Examples

in1 = matrix(c(96, 4, 8, 19), nc = 2L, byrow = TRUE)
rownames(in1) = c("Condition Positive", "Condition Negative")
colnames(in1) = c("Predicted Positive", "Predicted Negative")

evalMetrics(in1) # default: "accuracy"
evalMetrics(in1, "precision")
evalMetrics(in1, "recall")

in2 = matrix(c(26, 17, 7, 400), nc = 2, byrow = TRUE)
evalMetrics(in2, "precision")
evalMetrics(in2, "recall")

---

Convert Spatial Extent to Polygon

Description

Convert a spatial extent to polygons.

Usage

ext2spy(x, crs = "EPSG:4326", as_sf = TRUE)

Arguments

x	A SpatExtent object, or any object from which such an object can be extracted, e.g. SpatRaster.
crs	Coordinate reference system set via terra::crs().
as_sf	logical. If TRUE (default), the returned object is of class sf rather than ⁠Spatial*⁠.

Value

Depending on 'as_sf', either a c(sf, data.frame) or SpatVector object.

Author(s)

Florian Detsch

See Also

terra::ext().

Examples

ext = terra::ext(c(25, 70, -5, 30))
ext2spy(ext) # 'sf' (default)
ext2spy(ext, as_sf = FALSE) # 'Spatial*'

---

Take Measures in Case of Nonexisting Target Files

Description

If a target file already exists, it is simply being imported into R. However, if the specified target file does not exist, it is first created by a user-defined function and subsequently returned, thus rendering explicit calls to file.exists() unnecessary.

Usage

ifMissing(ofl, fun0 = terra::rast, fun1 = terra::writeRaster, arg1, ...)

Arguments

ofl	Target file name as character.
fun0	If 'ofl' exists, function to be applied to it. Defaults to terra::rast()).
fun1	If 'ofl' does not exist, function used to create it. Defaults to terra::writeRaster()).
arg1	Argument in 'fun1' (as character) that corresponds to 'ofl', e.g. 'filename' in terra::writeRaster() or 'file' in utils::write.table(). If missing (default), the target file name passed to 'fun1' needs to be explicitly included via '...'.
...	Additional arguments passed to 'fun0' and 'fun1'.

Value

If 'ofl' has already existed, the contents of 'ofl' derived from 'fun0'; else the output resultant from 'fun1'.

Author(s)

Florian Detsch

See Also

file.exists(), do.call().

Examples

# simply import existing file
logo <- system.file("ex/logo.tif", package = "terra")
s <- ifMissing(logo) 

# create nonexisting file and import it afterwards
logo2 <- file.path(tempdir(), "rlogo.tif")
s2 <- ifMissing(logo2, arg1 = "filename", x = s, datatype = "INT1U")

# this also works with text files and more sophisticated custom functions
fun = function(x, file = "", ...) {
  write.csv(x, file, ...)
  read.csv(file)
}

data(iris)
ofl <- file.path(tempdir(), "iris.csv")
iris2 <- ifMissing(ofl, fun1 = fun, x = iris, file = ofl, quote = FALSE, row.names = FALSE)

---

Combine Multiple Lattice Plots in a Faceted Grid (Panels)

Description

This function combines multiple lattice plot objects in a faceted grid. Note that the global plot settings (e.g. 'xlim', 'ylim', ...) are taken from the first object though the user can specify whether 'scales' should be identical or not. This is particularly useful when looping over large amounts of data using lapply() or the like (see Examples).

Usage

latticeCombineGrid(
  trellis.list,
  between = list(y = 0.3, x = 0.3),
  as.table = TRUE,
  ...
)

Arguments

trellis.list	A list containing lattice plot objects.
between	Space between panels.
as.table	If TRUE (default), drawing is top left to bottom right.
...	Additional arguments passed to latticeExtra::c.trellis().

Value

A single lattice plot object.

Author(s)

Tim Appelhans

See Also

latticeExtra::c.trellis().

Examples

library(lattice)

p1 = xyplot(1:10 ~ 1:10)
p2 = xyplot(10:1 ~ 1:10)

(
  p = latticeCombineGrid(
    list(p1, p2)
  )
)

if (requireNamespace("raster", quietly = TRUE)) {
  # load data
  # Use a probability map assuming high potential for city expansion is just 
  # resulting from proximity to current urban area:
  prd = raster::raster(system.file("extdata/probability.rst", package = "Orcs"))
  
  # observed city growth between 1990 and 2006
  obs = raster::raster(system.file("extdata/citygrowth.tif", package = "Orcs"))
  
  # masking current urban area since these pixels have no potential for change
  msk = raster::raster(system.file("extdata/citymask.tif", package = "Orcs"))
  
  # create data list
  dat <- list(prd, obs, msk)
  
  # create list of lattice plots
  plist <- lapply(dat, raster::spplot, scales = list(draw = TRUE))
  
  # # draw individually
  # plist[[1]]
  # plist[[2]]
  # plist[[3]]
    
  # combine to grid, using c(1, 3) layout
  p = latticeCombineGrid(plist, layout = c(1, 3))
  print(p)
}

---

Combine Multiple Lattice Plots Layerwise

Description

This function combines multiple lattice plot objects drawing each as a layer on top of the previous plots. Note that the global plot settings (e.g. 'xlim', 'ylim', ...) are taken from the first object. This is particularly useful when looping over large amounts of data using lapply() (see Examples).

Usage

latticeCombineLayer(trellis.list, ...)

Arguments

trellis.list	A list containing lattice plot objects.
...	Additional arguments passed to latticeExtra::as.layer().

Value

A single lattice plot object.

Author(s)

Tim Appelhans

See Also

latticeExtra::as.layer().

Examples

library(latticeExtra)
dat <- list(1:10,
            10:1,
            3:7,
            7:3)

plist <- lapply(seq(dat), function(i) {
 tmp <- xyplot(dat[[i]] ~ seq(dat[[i]]),
               type = "l", col = i)
})

p <- latticeCombineLayer(plist)

print(p)

---

Convert Between DOS and UNIX Line Endings

Description

This function converts between DOS and UNIX style line endings by invoking unix2dos (or dos2unix) upon a text file (see also system("unix2dos --help")). Note that 'unix2dos' must be installed on your local system, see Source.

Usage

lineEnding(infile, pattern = NULL, outfile = NULL, to = c("dos", "unix"), ...)

Arguments

infile	Input filename(s).
pattern	See list.files(). This will be ignored if 'infile' is specified.
outfile	Output filename. If not supplied, 'infile' will be overwritten.
to	Either "dos" or "unix".
...	Additional arguments passed to list.files(), only applicable if 'infile' is not specified.

Author(s)

Florian Detsch

Source

Dos2Unix/Unix2Dos Text file format converters.

See Also

list.files(), system().

Examples

## input file
infile <- paste(system.file(package = "Orcs"), "DESCRIPTION", sep = "/")

## convert to dos line endings and write to output file
ofl = file.path(tempdir(), "DESCRIPTION4wd")
lineEnding(infile, outfile = ofl, to = "dos")

---

Create data.frame from list

Description

Create a data.frame from a list directly, i.e. without being required to explicitly call rbind() first.

Usage

list2df(x, bind = c("rows", "cols"), ...)

Arguments

x	A list object.
bind	Binding direction. Available options are "rows" (default) and "cols" for rbind() and cbind(), respectively.
...	Additional arguments passed to data.frame().

Value

A data.frame object.

Examples

lst <- list(letters[1:3], letters[4:6], letters[7:9])

do.call("rbind", lst) # results in matrix
list2df(lst)          # results in data.frame created using rbind()
list2df(lst, bind = "cols") # same for cbind()

---

Install and Load a Package from GitHub

Description

This function comprises multiple steps required to install and load a package directly from GitHub.

Usage

loadFromGit(repo = "fdetsch/Orcs", ...)

Arguments

repo	Repository address as character, defaults to "fdetsch/Orcs".
...	Additional arguments passed to remotes::install_github().

Author(s)

Florian Detsch

Examples

## Not run: 
## install 'Orcs' from GitHub
loadFromGit("fdetsch/Orcs")

## End(Not run)

---

Load Multiple Packages

Description

Load and attach multiple packages at once.

Usage

loadPkgs(pkgs, ...)

Arguments

pkgs	Packages to load as character.
...	Additional arguments passed to library(), except for 'character.only' which is set to TRUE.

Note

Package start-up messages are automatically disabled.

Author(s)

Florian Detsch

Examples

loadPkgs(c("terra", "lattice"))

---

Calculate Mean Difference Between Two Datasets

Description

Calculate the mean difference between two datasets as suggested by Wang et al. (2012).

Usage

## S4 method for signature 'SpatRaster'
meanDifference(x, y)

## S4 method for signature 'numeric'
meanDifference(x, y)

Arguments

x, y	Pairwise objects of class SpatRaster, RasterLayer or numeric.

Value

The mean difference between the two inputs as numeric.

Source

Wang et al. (2012) Impact of sensor degradation on the MODIS NDVI time series. Remote Sensing of Environment 119, 55-61, doi:10.1016/j.rse.2011.12.001.

Detsch et al. (2016) A Comparative Study of Cross-Product NDVI Dynamics in the Kilimanjaro Region - A Matter of Sensor, Degradation Calibration, and Significance. Remote Sensing 8(2), 159, doi:10.3390/rs8020159.

Examples

x <- 1:10
y <- 2:11
meanDifference(x, y)

---

Merge Objects Stored in a List

Description

Complementing existing merge methods, e.g. terra::merge() for ⁠Spat*⁠ objects, which typically work with one or two inputs only, this function accepts a list of objects that are to be merged together.

Usage

## S4 method for signature 'list,missing'
merge(x, by = 1L, all = TRUE, ...)

Arguments

x	A list of objects of the same type (e.g. ⁠Spat*⁠ or data.frame).
by, all	See merge.data.frame(). Ignored if data stored in 'x' is not of class data.frame.
...	Additional arguments passed to the underlying merge method (e.g. arguments compatible with terra::merge() and terra::writeRaster() for ⁠Spat*⁠ input). Ignored if data stored in 'x' is of class data.frame.

Value

A merged object (e.g. a new ⁠Spat*⁠ object with a larger spatial extent).

Author(s)

Florian Detsch

See Also

do.call(), Reduce().

Examples

## `SpatRaster` input
dms = list.files(system.file("extdata", package = "Orcs")
                 , pattern = "ASTGTM2.*dem.tif$", full.names = TRUE)
dms = lapply(dms, terra::rast)

dem = merge(dms[3:4])
terra::plot(dem)

## data.frame input
mrg = merge(list(iris, iris, iris)
            , by = c("Species", "Sepal.Length", "Petal.Width"))
head(mrg)

---

Convert Multiple R Markdown Files to Ordinary Markdown

Description

This function is a convenient wrapper around knitr::knit() as it automatically converts multiple R Markdown files (.Rmd) located in a specified folder (and, optionally, matching a particular pattern) to standard Markdown (.md).

Usage

multiKnit(path_in = ".", path_out = path_in, pattern = "*.Rmd$", ...)

Arguments

path_in	Input file path as character, defaults to the current working directory.
path_out	Output file path as character, defaults to 'path_in'.
pattern	Passed to list.files(), defaults to "*.Rmd$".
...	Additional arguments passed to knitr::knit().

Value

Output filenames as character.

Author(s)

Florian Detsch

---

Insert Offset Text Annotation into trellis Plot

Description

This is a wrapper function around Orcs:::calcOffsetGridText and grid based text drawing functions (currently including grid::grid.text() and grid.stext()) that automatically adds offset text annotations to a trellis plot.

Usage

offsetGridText(
  x,
  y = NULL,
  labels,
  xlim = NULL,
  ylim = NULL,
  pos = NULL,
  stext = FALSE,
  offset = 0.02,
  ...
)

Arguments

x	A numeric vector containing x coordinates, or a 2-column matrix containing x and y coordinates.
y	A numeric vector containing y coordinates, or NULL if 'x' is a two-column matrix.
labels	The text to be written as character.
xlim, ylim	X and Y-axis limits (c(min, max)) of the current plot. If not supplied, limits are automatically calculated from supplied x and y coordinates.
pos	Text position specifier(s) as integer used by graphics::text(). If not supplied, optimal text positions will be determined with respect to neighboring locations using plotrix::thigmophobe().
stext	logical, defaults to FALSE. If TRUE, shadow text will be drawn around 'labels'.
offset	A numeric offset in normalized parent coordinates ("npc", see grid::unit()).
...	Additional arguments passed to the respective grid text drawing function (depends on 'stext').

Author(s)

Florian Detsch

Examples

KiLi = terra::rast(system.file("extdata/KiLi.tif", package = "Orcs"))

# kilimanjaro peaks
peaks = data.frame(Peak = c("Kibo", "Mawenzi", "Shira")
                   , Lon = c(37.359031, 37.455061, 37.210408)
                   , Lat = c(-3.065053, -3.095436, -3.038222))

peaks = sf::st_as_sf(peaks, crs = 4326, coords = c("Lon", "Lat"))

# visualization
xlim_kili <- c(37.15, 37.55)
ylim_kili <- c(-3.25, -2.9)

if (requireNamespace("raster", quietly = TRUE)) {
   p = raster::spplot(KiLi[[1]], col.regions = "transparent", colorkey = FALSE, 
              xlim = xlim_kili, ylim = ylim_kili,
              scales = list(draw = TRUE, y = list(rot = 90)), 
              sp.layout = rgb2spLayout(KiLi, quantiles = c(0, 1), alpha = .8)) + 
     latticeExtra::layer(sp.points(as(peaks, "Spatial"), cex = 1.5, pch = 20, col = "black"))
   
   print(p)
   
   grid::downViewport(lattice::trellis.vpname(name = "figure"))
   offsetGridText(x = sf::st_coordinates(peaks), labels = peaks$Peak,  
                  xlim = xlim_kili, ylim = ylim_kili, stext = TRUE, offset = .02,
                  gp = grid::gpar(fontsize = 16))
}

---

Dimensions of a data.frame

Description

Similar to base-R nrow(), ncol() and dim(), this set of functions let's you retrieve the number of rows and columns of a data.frame.

Usage

nrowC(x)

ncolC(x)

dimC(x)

Arguments

x	A data.frame.

Value

dimC() returns an integer vector of length 2 (number of rows and columns); nrowC() (or ncolC()) returns the number of rows (or columns) as a single integer.

Functions

• nrowC():

• ncolC():

• dimC():

Author(s)

Florian Detsch

Examples

dat <- data.frame(a = 1:4, b = 2:5, c = 3:6)

nrowC(dat)

---

Parallelized 7-Zip Compression

Description

By calling the Unix terminal or Windows command prompt, this function performs parallelized 7-zip compression of selected files based on the built-in parallel package.

Usage

par7zip(outfile, nodes = 1L, ...)

Arguments

outfile	Target file for compression as character. A file extension compatible with 7-zip needs to be included, see supported formats. If missing, this defaults to the found input file names with a ⁠.7z⁠ extension attached.
nodes	Number of cores to use for parallelization as integer, defaults to 1L.
...	Additional arguments passed to list.files().

Value

Output filename(s) as character.

Author(s)

Florian Detsch

See Also

list.files(), system()

---

Return File Name without Extension

Description

As opposed to basename(), this function returns the pure basename of one or multiple file names, i.e. without extension.

Usage

pureBasename(path, slash = FALSE)

Arguments

path	File name(s) as character.
slash	A logical determining whether to add a leading slash ("/") to the returned file name.

Value

File name(s) without extension as character.

Author(s)

Florian Detsch

See Also

tools::file_path_sans_ext().

Examples

ifl = tempfile(fileext = ".tif")
pureBasename(ifl)
pureBasename(ifl, slash = TRUE)

---

Get p-Value from 'lm' Object

Description

Retrieve the p-value associated with a univariate linear regression.

Usage

pvalue(mod)

Arguments

mod	An object of class lm.

Value

A numeric p-value.

Source

retrieving p-values in lm on R-help mailing list.

See Also

stats::lm().

Examples

## taken from ?lm
ctl <- c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14)
trt <- c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69)
group <- gl(2, 10, 20, labels = c("Ctl","Trt"))
weight <- c(ctl, trt)
lm.D9 <- lm(weight ~ group)

pvalue(lm.D9)

---

Convert an RGB ⁠Raster*⁠ to Use with spplot()

Description

This function takes a red-green-blue SpatRaster or ⁠Raster*⁠ object and produces a list with color information that can be passed on as 'sp.layout' to sp::spplot().

Usage

rgb2spLayout(x, quantiles = c(0.02, 0.98), alpha = 1)

Arguments

x	A 3-layered ⁠SpatRaster*⁠ or ⁠Raster*⁠ object.
quantiles	Upper and lower quantiles used for color stretching.
alpha	Level of transparency.

Author(s)

Tim Appelhans, Florian Detsch

See Also

terra::plotRGB().

Examples

b = terra::rast(system.file("ex/logo.tif", package="terra"))

## using plotRGB
terra::plotRGB(b)

## convert raster to list
lout = rgb2spLayout(b)
lout_alph = rgb2spLayout(b, alpha = 0.5)

## create random spatial points for plotting
df = data.frame(
  dat = rnorm(100, 2, 1)
  , x = rnorm(100, 50, 20)
  , y = rnorm(100, 50, 25)
)

df = sf::st_as_sf(df, coords = c("x", "y"))

## plot spatial points with rgb background
if (require(sp, quietly = TRUE)) {
  spplot(as(df, "Spatial"), sp.layout = lout)
  spplot(as(df, "Spatial"), sp.layout = lout_alph)
}

---

Remove Duplicated Columns from data.frame

Description

Automatically detect and remove columns from a data.frame based on duplicated headers.

Usage

rmDuplCols(x, keep_first = TRUE, ...)

Arguments

x	Input data.frame.
keep_first	A logical determining whether the first column of an otherwise duplicated header should be kept, defaults to TRUE.
...	Currently not in use.

Value

Revised data.frame.

Author(s)

Florian Detsch

See Also

duplicated().

Examples

## sample data
set.seed(123)
dat <- data.frame(matrix(rnorm(28), nc = 7))
names(dat) <- c("Col1", "Col1", "Col1", "Col2", "Col3", "Col3", "Col4")

dat
rmDuplCols(dat)
rmDuplCols(dat, keep_first = FALSE)

---

Set Working Directory Dependent on Current OS

Description

Similar to setwd(), this function sets the working directory to a user-defined path. Rather than supplying a single 'dir' argument, however, both an OS-sensitive path to the desired hard disk partition and, optionally, an extension of this file path are required.

Usage

setwdOS(lin = "/media/permanent/", win = "C:/", ext = NULL)

Arguments

lin, win	Absolute file paths to the Linux and Windows partition as character.
ext	Optional file path extension as character that will be added to 'lin' or 'win' after automatic OS determination.

Author(s)

Florian Detsch

See Also

switch().

Examples

## Not run: 
# desired partition
setwdOS()

# including file path extension
setwdOS(ext = "kilimanjaro/nubiscope")

## End(Not run)

---

Draw Shadow Text

Description

Create and draw shadow text by wrapping a textual expression into a colored framing.

Usage

stextGrob(
  label,
  x = grid::unit(0.5, "npc"),
  y = grid::unit(0.5, "npc"),
  col = "white",
  fill = "black",
  r = 0.1,
  gp = grid::gpar(),
  vp = NULL,
  name = NULL,
  ...
)

Arguments

label	A character or expression vector, see grid::textGrob().
x, y	Horizontal and vertical text position as grid::unit() objects passed to grid::grid.text().
col, fill	Framing and fill color passed to grid::gpar().
r	Blur radius of colored framing as numeric.
name, gp, vp	Graphical parameters passed to grid::gTree().
...	Additional arguments passed to [grid::grid.text()].

Value

A text grob created by grid::gTree().

Author(s)

Baptiste Auguie, Florian Detsch

Examples

library(grid)
grid.newpage()
grid.rect(gp = gpar(fill = "grey"))
grid.stext("test")

---

Substrings of a Character Vector (C++ Style)

Description

Extract substrings from a character vector in C++.

Usage

substrC(x, pos, len)

Arguments

x	A character vector.
pos	The start point of the substring as integer. Position indications start from 1L, which is the default in R.
len	The length of the substring as integer.

Value

A character vector of the same length as 'x'.

See Also

https://cplusplus.com/reference/string/string/substr/, substr().

Examples

substrC("Hello, world!", pos = 1, len = 5)

---

Remove Whitespace from Images

Description

This is a wrapper function around convert -trim to automatically remove any whitespace from locally saved images. Note that 'ImageMagick' must be installed on your local system, see Source.

Usage

trimImages(path = ".", pattern = c(".png$", ".tiff$"))

Arguments

path	File path leading to image files as character, defaults to the current working directory.
pattern	A regular expression as character accepted by list.files(), defaults to c(".png$", ".tiff$").

Value

A character vector containing the names of the processed images.

Author(s)

Florian Detsch

Source

Ooms J (2018) The magick package: Advanced Image-Processing in R. Available online: https://cran.r-project.org/package=magick/vignettes/intro.html.

See Also

system()

Examples

## Not run: 
## trim image of bart simpson
download.file("http://pngimg.com/uploads/simpsons/simpsons_PNG93.png?i=1"
              , destfile = (ofl <- file.path(tempdir(), "bart.png", fsep = "\\"))
              , mode = "wb")

par(mfrow = c(1, 2))

img = brick(ofl)
plotRGB(img)

jnk = trimImages(tempdir(), "bart.png")
trm = brick(jnk)
plotRGB(trm)

dev.off()

## End(Not run)

---

Unlist the Outcome of strsplit()

Description

Per default, strsplit() returns a list, with each entry holding the vector of splits of the initial string(s). This function is a simple wrapper that casts unlist() upon the returned list to produce a concatenated character vector consisting of the single split elements.

Usage

unlistStrsplit(x, split, ...)

Arguments

x	A character vector with elements to be split.
split	A character vector used for splitting, see strsplit().
...	Additional arguments passed to strsplit().

Author(s)

Florian Detsch

Examples

## 1st example
x <- "This is a test."
unlistStrsplit(x, " ")

## 2nd example; note that 'split' defaults to 'whitespace'
x2 <- "This is a 2nd test."
unlistStrsplit(c(x, x2))

---

Factor with Unsorted Levels

Description

Casting factor() upon a (character) vector usually results in alphabetically ordered factor levels. Although this seems reasonable in most cases, the automated ordering of factor levels is seldomly desirable in the context of visualization, e.g. when working with tiled lattice or ggplot2 figures. This function returns a factor with levels ordered according to their first appearance in the supplied vector.

Usage

unsortedFactor(x, ...)

Arguments

x	A character vector with elements to converted to factor.
...	Additional arguments passed to factor().

Author(s)

Florian Detsch

Examples

mnth <- month.abb

## factor levels are being sorted
fc_mnth <- factor(mnth)
levels(fc_mnth)

## factor levels remain unsorted
fc_mnth2 <- unsortedFactor(mnth)
levels(fc_mnth2)

---