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