[R] phyloclim help

[Brent Hendrixson]

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")

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...

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
>