[R] phyloclim help

[Brent Hendrixson]

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