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
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