distmat: Calculate a pairwise landscape distance matrix (Euclidian or...

In Andrew-Shirk/sGD: Spatially explicit estimation of genetic diversity indices and Wright's neighborhood size (NS)

Description

Calculate a pairwise landscape distance matrix (Euclidian or cost-distance).

Usage

distmat(sp_points, method, file_name = NULL, landscape = NULL)

Arguments

sp_points	An object of class SpatialPoints (see sp package for details).
method	Specify the type of distance matrix to be produced, using "ed" for Euclidean distance and "cd" for cost-weighted (i.e. effective) distance. Accurate distance calculations require a projected coordinate system (e.g. UTM), so do not use geographical coordinates (e.g. longlat). If you calculate cost-weighted distances, make sure the points projection is the same as the landscape raster.
file_name	(optional) A character string that will be appended to the beginning of the output filename. If no name is specified, no file will be written to the working directory.
landscape	An object of class RasterLayer (see raster package for details)

Value

An NxN (N= sample size: i.e. nrow(xy)) matrix of pairwise Euclidean and/or effective landscape distances written to .csv comma delimited files with edmat or cdmat appended to the end of the filename.

Examples

library(sGD)
library(raster)
library(sp)

# read in locations and landscape data 
xy_file <- system.file("extdata","sGD_demo_xy.csv",package="sGD")
landscape_ascii <- system.file("extdata","sGD_demo_IBR_landscape.asc",package="sGD") 

# convert locations to SpatialPoints (sp package)
proj <- "+proj=utm +zone=10 +datum=NAD83"   
sp_points <- SpatialPoints(read.csv(xy_file)[,c(2,3)],proj4string=CRS(proj)) 

# convert landscape_ascii to raster object (raster package)
landscape <- raster(landscape_ascii,crs=CRS(proj))

# specify output file_name
file_name <- "sGD_demo" 

# run ed and cd matrix calculations
ed <- distmat(sp_points,method="ed",file_name = file_name)
cd <- distmat(sp_points,method="cd",file_name = file_name,landscape=landscape)

Andrew-Shirk/sGD documentation built on May 26, 2019, 6:38 a.m.