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)
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
I'm incredibly confused by all of this and sincerely appreciate any help you
can provide.
Regards,
Brent
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