[R] Overlapping area script

[achughes]

Dear All


I would really appreciate some help with a script which a colleague wrote
for me (attached), but I am having problems running (and have not been able
to contact my colleague).
The script is designed to compare the area of suitable habitat in binary
projections of a large number of species current and future distributions,
and create an excel file detailing the total area suitable in the present
and future scenario, in addition to the area which overlaps.
These maps are made from Maxent outputs, which have been reclassified to
give binary projections for each species and will be used to assess how
climatic change may potentially effect the total area which is suitable for
each species. However despite considerable effort I cannot get the attached
script to run. It creates an excel with the first species current and future
areas of suitable extent detailed, but "NA" for overlap, then gives error
warnings (shown below), but changes I have tried have failed to make the
script run any further (though I have generated new error messages...)

Any help or advice would be very greatly appreciated, I can also send some
example files of current and future distributions if anyone thinks they
maybe able to help.
Thanks and best wishes

Alice C Hughes 


"+ png(paste(out.dir, spp,'_overlap.png', sep=''),
width=nrow(spp.asc),height=ncol(spp.asc), units='px', res=300, pointsize=5,
bg='white') #start the plot
+ par(mar=c(0,0,0,0)+0.1) #remove any plot margins
+ image(overlap, ann=FALSE,axes=FALSE,col=cols, zlim=c(0,3)) #plot the
richness
+ legend.gradient(legend.pnts,cols=cols,limits=c(0,3), title='overlap',
cex=2)
+ dev.off()
+ }
Error in nrow(spp.asc) : object 'bat.asc' not found
In addition: There were 12 warnings (use warnings() to see them)
> 
> write.csv(overlap.matrix, paste(out.dir, "all_species.csv",sep=''))

http://r.789695.n4.nabble.com/file/n4625913/area2.r area2.r 


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