[R] phyloclim help

[David Winsemius]

On Jun 15, 2012, at 3:43 PM, Brent Hendrixson wrote:

>
> Hi David -
>
>> Looking at the package documentation I see this:
>>
>> maxent: A list containing the location of the MAXENT application and
>> its input files (see
>> details).
>>
>> Maybe I was wrong about 'spec' and the malformed argument is  
>> 'maxent'.
>> If I had been constructing it I would have created a _named_ list:
>>
>> maxent <- list( app =app,
>> samples =samples,
>> background, # cannot tell if a csv file meets the
>> requiremtn
>> # "The path to a SWD-formatted file with
>> background points."
>> projections =projections) # that value .../R looks
>> pretty suspicious, too.
>>
>
> Your advice definitely helped - THANK YOU!  However, I'm now getting  
> another error that seems to be tied to the maxent java program  
> itself.  Here's the syntax I have used for the  
> niche.equivalency.test (recall that it consists of 4 elements: spec,  
> n, maxent, mx=2000)
>
> spec <- c("aphonopelma_mojave", "aphonopelma_newmojave")
>
> app <- file.path("C:\\Documents and Settings\\hendrb\\Desktop\\R\ 
> \maxent.jar")
>
> samples <- file.path("C:\\Documents and Settings\\hendrb\\Desktop\\R\ 
> \samples.csv")
>
> background <- file.path("C:\\Documents and Settings\\hendrb\\Desktop\ 
> \R\\background.csv")
>
> projections <- file.path("C:\\Documents and Settings\\hendrb\\Desktop 
> \\R")
>
> maxent <- list(app=app, samples=samples, background=background,  
> projections=projections)
>
> After I defined each of those, I tried to execute the command as  
> follows:
>
> niche.equivalency.test(spec, n=100, maxent, mx=2000)
>
> And here was the message I received:
>
> Unable to access jarfile C:\Documents

That hanging "Documents" being listed as the file target makes me  
think that the file specification is creating errors due to spaces in  
Windows directories. In Windows it is often the case that backslashes  
need to be doubled or replaced with forward slashes.I see that you  
already know that, but would have tried the forward slash gambit as  
well. (I am not sure why you are passing hte results of file.path(...)  
when you already have a complete file name. I would also try just  
giving it a file specification with just a character argument.)


> Error in file(file, "r") : cannot open the connection
> In addition: Warning messages:
> 1: running command 'java -mx2000m -jar C:\Documents and Settings 
> \hendrb\Desktop\R\maxent.jar -e R.phyloclim.temp/background.csv -s  
> R.phyloclim.temp/samples.csv -j C:\Documents and Settings\hendrb 
> \Desktop\R -o R.phyloclim.temp/out -r removeduplicates nopictures  
> outputformat=raw autorun' had status 1
> 2: In file(file, "r") :
>   cannot open file 'aphonopelma_mojave_C:\Documents and Settings 
> \hendrb\Desktop\R.asc': Invalid argument
>
> Like I mentioned, it seems that this particular error is unrelated  
> to R code but I'm unsure why the jarfile (maxent.jar) cannot be  
> accessed.
>
> Any thoughts?
>
> The above command did produce a new file that serves as the input  
> for the jarfile.
>
> Thanks again for your help!
>
> Brent
> 		 	   		

David Winsemius, MD
West Hartford, CT