Hi David -
Thanks for the response.
> On Jun 13, 2012, at 6:29 PM, Brent Hendrixson wrote:
>
> >
> > Hi all –
> >
> > My apologies if this is a redundant message. I am a newbie to R and
> > have had a terrible time trying to figure out how to set up an
> > analysis. I have installed and loaded the appropriate package
> > (phyloclim), but I'm not sure I have defined the arguments correctly.
> >
> > The usage for the command I’m trying to perform is:
> >
> > niche.equivalency.test(spec, n, maxent, mx = 2000)
>
> You might give the name of the package. (I'm not likely to have any
> experience with that package, but it might ring a bell so someone with
> the right background.)
The package is "phyloclim" (evolutionary biology).
>
> >
> > I am comfortable with the arguments "spec", "n", and "mx" but have
> > had problems with "maxent"
> >
> > maxent is a list containing the location of the MAXENT
> > application and its input files (see below)
> >
> >> From what I have gathered, the maxent argument is a list of four
> >> elements:
> >
> > app the path to the MAXENT application (MAXENT
> > is a JAVA program)
> >
> > samples the path to a SWD-formatted file with sample
> > points (e.g., samples.csv)
> >
> > background the path to a SWD-formatted file with background
> > points (e.g., background.csv)
> >
> > projections the path to a folder containing environmental GIS
> > layers to be used for projection of the MAXENT models
> >
> > Suppose all of these files are placed into the directory “C:
> > \Documents and Settings\hendrb\Desktop\R”. Can anyone determine if
> > I'm on the right track with the following syntax or am I way off?
> >
> >> app <- file.path("C:\\Documents and Settings\\hendrb\\Desktop\\R\
> >> \maxent.jar")
> >> samples <- file.path("C:\\Documents and Settings\\hendrb\\Desktop\\R
> >> \\allspecies_swd.csv")
> >> background <- file.path("C:\\Documents and Settings\\hendrb\\Desktop
> >> \\R\\background_swd.csv")
> >> projections <- file.path("C:\\Documents and Settings\\hendrb\
> >> \Desktop\\R")
> >> maxent <- list(app, samples, background, projections)
> >
> > When I try to execute the command niche.equivalency.test based on
> > the above information, I get the following statement:
> >
> >> niche.equivalency.test(spec, n = 10, maxent, mx = 2000)
> > Error in read.table(file = file, header = header, sep = sep, quote =
> > quote, :
> > 'file' must be a character string or connection
>
> Right. So what is the object named "spec"? The R interpreter is
> expecting a file name or a connection object.
The object "spec" is a vector of mode = character and length = 2 (it contains
the names of two different species that I'm comparing). I did define it
correctly (to my knowledge). It looks like:
spec <- c("aphonopelma_mojave", "aphonopelma_newmojave")
I'm just unsure if everything else for the "maxent" argument is defined
correctly and whether I have set up the list appropriately. If the syntax is
okay, then I just need to check the files. Unfortunately, the error message
does not indicate which file is throwing stuff off...
Thanks again!
> >
> > I'm incredibly confused by all of this and sincerely appreciate any
> > help you can provide.
> >
> > Regards,
> >
> > Brent
> >
>
>
> David Winsemius, MD
> West Hartford, CT
>
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