distancefile: Get a table or matrix with the distances between pairs of...
In OscarGOGO/Makurhini: Makurhini: Analyzing landscape connectivity

distancefile

R Documentation

Get a table or matrix with the distances between pairs of nodes.

Description

Get a table or matrix with the distances (Euclidean or cost distances) between pairs of nodes. It can be used as a connector file.

Usage

distancefile(
  nodes,
  id,
  type = "centroid",
  distance_unit = NULL,
  keep = NULL,
  resistance = NULL,
  resist.units = FALSE,
  CostFun = NULL,
  ngh = NULL,
  mask = NULL,
  threshold = NULL,
  geometry_out = NULL,
  bounding_circles = NULL,
  parallel = FALSE,
  ActiveParallel = FALSE,
  least_cost.java = FALSE,
  cores.java = 1,
  ram.java = NULL,
  pairwise = TRUE,
  write = NULL
)

Arguments

`nodes`	object of class `sf, SpatialPolygons, RasterLaryer or SpatRaster` (terra package). It must be in a projected coordinate system. If nodes is a `raster` layer then raster values (Integer) will be taken as "id".
`id`	`character`. If nodes is a shapefile then you must specify the column name with the node ID in the shapefile data table.
`type`	`character`. Choose one of the distance options: - `"centroid"` (faster option, default), where Euclidean distance is calculated from feature centroid - `"edge"`, where Euclidean distance is calculated from feature edges. - `"least-cost"` that takes into account obstacles and local friction of the landscape (see, gdistance package). - `"commute-time"` that is analogous to the resistance distance of circuitscape. The commute-time distance is based on the random walk theory and calculated using the electrical circuit theory (See, gdistance package). If the type is equal to `"least-cost"` or `"commute-time"`, then you have to use the "resistance" argument.
`distance_unit`	`character`. If `"least-cost"` or `"commute-time"` is selected or `resist.units = TRUE` then you can set a distance unit ("m", "km", "inch", "foot", "yard", "mile"). Default equal to meters "m" (see, unit_convert).
`keep`	`numeric`. In case you have selected the `"edge"` distance, use this option to simplify the geometry and reduce the number of vertices. The value can range from 0 to 1 and is the proportion of points to retain (default equal to `NULL`). The higher the value, the higher the speed but less precision.
`resistance`	`raster`. Raster object with resistance values. If `least_cost.java = TRUE`, then resistance must bee an integer raster (i.e., integer values).
`resist.units`	`logical`. If `resist.units = TRUE` and `type = "least-cost"` then cost units are converted to metric units by multiplying the cost by the raster resolution.
`CostFun`	`function`. A function to compute the cost to move between cells. Available only if you you have selected the `"least-cost"` or `"commute-time"` distance. The default is the mean (isotropic cost distance): `function(x) 1/mean(x)`. If resistance is a conductance raster then you can use: `function(x) mean(x)`
`ngh`	`numeric`. Neighbor graph (directions) for distance calculations: 4 (von Neu-mann neighbourhood), 8 (Moore neighborhood) or 16. Available only if you have selected the `"least-cost"` or `"commute-time"` distance.
`mask`	object of class `sf, sfc, sfg. SpatialPolygons`. For higher processing speed of `"least-cost"` or `"commute-time"` distances. Use this option to clip the resistance at the extent of the mask.
`threshold`	`numeric`. Distance threshold, pairs of nodes with a distance value above this threshold will be discarded.
`geometry_out`	`numeric`. You can use this argument if you have selected the `"least-cost"` or `"commute-time"` distance. If some spatial geometries are out of the resistance extent, then a buffer zone the large enough to cover these spatial geometries and with this numeric value will be added to the resistance, so that it is possible to calculate a cost distance value for the pairs of nodes that involve these geometries and avoid an error. If NULL, then the Euclidean distance between centroids (`type = "centroid"`) will be calculated to find these distances.
`bounding_circles`	`numeric`. If a value is entered, this will create bounding circles around pairs of core areas (recommended for speed, large resistance rasters or pixel resolution < 150 m). Buffer distances are entered in map units.
`parallel`	`logical` or `numerical`. Recommended for a large number of nodes or very large RasterLayer.
`ActiveParallel`	`logical`. It should be `TRUE` if there is already an open parallelization plan.
`least_cost.java`	`logical`. If `TRUE` then the programming language and computing platform 'java' will be used to estimate the least-cost distance using a resistance raster and the following formula: `function(x) 1/mean(x)`. It is necessary to have java installed. This option use the package `graph4lg` to reduce computation times.
`cores.java`	`numeric`. Computer cores used to run the .jar file (see, `graph4lg` ), default = `1`.
`ram.java`	`numeric`. RAM gigabytes to run the .jar file (see, `graph4lg` ), default = `NULL`.
`pairwise`	`logical`. If `TRUE` a pairwise table of class `data.frame` is returned (From, To, distance) otherwise it will be a `matrix`.
`write`	`character`. Output path, with name and extension ".txt".