R code snippets of useful, slightly generic scripts used in the VertNet Biodiversity Informatics Training Workshop

BatchClipRasterSnippet.R

#################################################
###VertNet Biodiversity Informatics Training Workshop
###June 2013
#
#     Example of clipping rasters with a ForLoop
#
# MSK, 20130625
#################################################
getwd()
setwd()

install.packages(c('dismo','raster','sp','maptools')); #if you have not already installed these packages

library(dismo)
library(raster)
library(sp)
library(maptools)
library(rgdal)


bc <- getData('worldclim', var = 'bio', res = 10)
#Or:
# set the working directory to the path that contains your .bil files
setwd()

# create a list of .bil files that exist in the wd
files <- list.files(pattern='\\.bil$')

# combine all list elements into a stack
s <- stack(files)

#read in a shape poly
# are your shapefiles in another directory than your grids? you can setwd() again or put in the full path
#How would you see other arguments for readShapePoly()?
Africa<-readShapePoly(file.choose())
plot(Africa, add=T)


# crop to your study extent
s.crop <- crop(s, Africa)
# plot(s.crop[[1]])

# looping through list
bioNum<-c(1:19)

for (i in 1:length(files)){
    writeRaster(s.crop, filename="bio.asc", bylayer=TRUE, overwrite=TRUE)
}


#Simple generic example, with lots of room for customization