On Jun 13, 2012, at 11:00 PM, Brent Hendrixson wrote:
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")
The error message made clear that someplace along the line there was a
missing argument to the read.table function.
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...
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.
--
David
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
David Winsemius, MD
West Hartford, CT
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