[R] phyloclim help

[Brent Hendrixson]

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
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