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.)
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.
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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