[R] phyloclim help

[Brent Hendrixson]

David -

You have been a tremendous help.  This solved my problems.  It's working now!  

I switched to forward slashes and changed the directory to "C:/R".  I tweaked the memory available to maxent and VOILA!

Thank you!!! 

----------------------------------------
> CC: r-help at r-project.org
> From: dwinsemius at comcast.net
> To: behendrixson at hotmail.com
> Subject: Re: [R] phyloclim help
> Date: Fri, 15 Jun 2012 16:45:51 -0400
>
>
> 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
>