distancesMatrix: Calculate Distances Matrix

In hugomflavio/actel: Acoustic Telemetry Data Analysis

Calculate Distances Matrix

Description

Using a previously created transition layer (see transitionLayer), calculates the distances between spatial points. Adapted from Grant Adams's 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.

Usage

distancesMatrix(
  t.layer,
  starters = NULL,
  targets = NULL,
  coord.x = "x",
  coord.y = "y",
  id.col = NULL,
  actel = TRUE
)

Arguments

t.layer	A TransitionLayer object, generated by transitionLayer.
starters	A data frame with the points from which to start measuring the distance or the output of loadSpatial().
targets	A data frame with the points to which a way must be found.
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.

Details

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

Value

A matrix with the distances between each pair of points.

Examples

# 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)

hugomflavio/actel documentation built on Dec. 16, 2024, 1:16 p.m.