[R] Overlapping area script

[Uwe Ligges]

That script is simple broken, the object bat.asc is used but not defined 
anywhere. Since the code is also not really optimal, you may want to ask 
an expert who knows how to write such script and how to test if their 
code work in the end.

Best,
Uwe Ligges



On 14.05.2012 14:12, achughes wrote:
>
> Dear Uwe
> I did previously attach the script, but I include it again here in addition to current and future projections (which come from different directories).Help would very much be appreciated!
> Alice
>
> Date: Mon, 14 May 2012 04:52:04 -0700
> From: ml-node+s789695n4629915h14 at n4.nabble.com
> To: dr_achughes at hotmail.co.uk
> Subject: Re: Overlapping area script
>
>
>
> 	
>
> On 11.05.2012 11:06, achughes wrote:
>
>> 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).
>
>
> I think you have to contact your colleague or you have to provide the
>
> full script including the objects trhat are used within that script.
>
> The error message told you that the  object 'bat.asc' was not found.
>
> My suggestion would be to contact a local expert if your colleague is
>
> unavailable.
>
>
> Best,
>
> Uwe Ligges
>
>
>
>> 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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>>
>
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