distancesMatrix | R Documentation |
Using a previously created transition layer (see transitionLayer
), calculates the distances
between spatial points. Adapted from Grant Adams' script "distance to closest mpa". if the argument 'actel'
is set to TRUE (default), an actel-compatible matrix is generated, and the user will be asked if they would
like to save the matrix as 'distances.csv' in the current directory.
distancesMatrix(
t.layer,
starters = NULL,
targets = starters,
coord.x = "x",
coord.y = "y",
id.col = NULL,
actel = TRUE
)
t.layer |
A TransitionLayer object, generated by |
starters |
A data frame with the points from which to start measuring the distance. Ignored if actel = TRUE (default), as the 'spatial.csv' is loaded as starters. |
targets |
A data frame with the points to which a way must be found. Ignored if actel = TRUE (default), as the 'spatial.csv' is loaded as targets. |
coord.x, coord.y |
The names of the columns containing the x and y coordinates in the starters and targets. Must be identical in the starters and targets. |
id.col |
The name of the column containing the IDs of the points to be used as starters and targets. Must be identical in both files. Ignored if actel = TRUE (default), as the stations' standard names are used. |
actel |
Logical: Should the distance matrix be optimized for actel? Defaults to TRUE. |
It is highly recommended to read the manual page regarding distances matrices before running this function. You can find it here: https://hugomflavio.github.io/actel-website/manual-distances.html
A matrix with the distances between each pair of points.
# check if R can run the distance functions
aux <- c(
length(suppressWarnings(packageDescription("raster"))),
length(suppressWarnings(packageDescription("gdistance"))),
length(suppressWarnings(packageDescription("sp"))),
length(suppressWarnings(packageDescription("terra"))))
missing.packages <- sapply(aux, function(x) x == 1)
if (any(missing.packages)) {
message("Sorry, this function requires packages '",
paste(c("raster", "gdistance", "sp", "terra")[missing.packages], collapse = "', '"),
"' to operate. Please install ", ifelse(sum(missing.packages) > 1, "them", "it"),
" before proceeding.")
} else {
# move to a temporary directory
old.wd <- getwd()
setwd(tempdir())
# Fetch location of actel's example files
aux <- system.file(package = "actel")[1]
# create a temporary spatial.csv file
file.copy(paste0(aux, "/example_spatial.csv"), "spatial.csv")
# import the shape file and use the spatial.csv
# to check the extents.
x <- shapeToRaster(shape = paste0(aux, "/example_shapefile.shp"),
coord.x = "x", coord.y = "y", size = 20)
raster::plot(x)
# Build the transition layer
t.layer <- transitionLayer(x)
# compile the distances matrix. Columns x and y in the spatial dataframe
# contain the coordinates of the stations and release sites.
distancesMatrix(t.layer, coord.x = 'x', coord.y = 'y')
# return to original directory
setwd(old.wd)
rm(old.wd)
}
rm(aux, missing.packages)
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