Adhara Pardo (adharapv@gmail.com)
An R package for analysing spatial ecological data. This package is meant to provide a collection of self-written functions for spatial data processing.
The package can be installed by typing:
# the devtools package is needed to be able to load the package # install.packages("devtools") library(devtools) install_github("adarapv/gistools") library(gistools)
What follows is some simple examples of how this package can be used to handle spatial data and calculate a variety of landscape metrics. All the examples below make use of the Corine Land Cover dataset (Bossard et al., 2000).
library(raster);library(rgeos) library(SDMTools)
The function buffercreate()
create buffers of given size around a set of sites and calculates a series of landscape metrics as implemented in fragstats (McGarigal & Marks, 1995).
Example using the Corine Land Cover data (Bossard et al., 2000) for the province of Caceres (Spain):
#' Create buffers and extract a series of landscape metrics #' Input is a raster and a matrix of with site coordinates #' @inrast = input raster #' @inpoint = column containing species names #' @bufsize = buffer radius size #' @rastcell= cell size of the raster # Plot Corine Land Cover for the province of Caceres plot(corine,legend=FALSE,box=FALSE,axes=FALSE,main="Corine Land Cover 100x100m resolution") # Display 20 random sites points(sites[,1],sites[,2],col="black",pch="+",cex=1.5)
# Calculate landscape metrics for a sample of 20 sites (buffer size 5km) buffresults<-buffercreate(inrast=corine,inpoint=sites,bufsize=5000,rastcell=100) ... Calculating buffer for site 1 ... ... Calculating buffer for site 2 ... ... Calculating buffer for site 3 ... ... Calculating buffer for site 4 ... ... Calculating buffer for site 5 ... ... Calculating buffer for site 6 ... # Examine results for first 8 columns head(buffresults)[1:8] x y class n.patches total.area prop.landscape patch.density total.edge 1 2860658 2001861 18 1 10000 0.0001296849 1.296849e-08 400 2 2860658 2001861 22 9 39000000 0.5057709765 1.167164e-07 85000 3 2860658 2001861 23 1 2250000 0.0291790948 1.296849e-08 18200 4 2860658 2001861 26 9 6450000 0.0836467384 1.167164e-07 50800 5 2860658 2001861 28 3 28510000 0.3697315523 3.890546e-08 88000 6 2860658 2001861 29 1 280000 0.0036311762 1.296849e-08 4800
References
Bossard, M., Feranec, J., & Otahel, J. (2000). CORINE land cover technical guide: Addendum 2000.
McGarigal, K., & Marks, B. J. (1995). FRAGSTATS: spatial pattern analysis program for quantifying landscape structure.
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