[R] Maxent Jarfile

annemariefischer86 at gmail.com annemariefischer86 at gmail.com
Thu Jul 9 18:38:01 CEST 2015


Hi John,

I have attempted to add links to the files to the thread directly, but my message was not ‎authorized. I'm not sure why. 

‎https://www.dropbox.com/s/gqk908gw9ze9553/error.txt?dl=0https://www.dropbox.com/s/jffg48y4dojzsb3/R%20Studio%20code.txt?dl=0https://www.dropbox.com/s/npyppmm9lv4wy8b/Rhinolophus_species.csv?dl=0

I sincerely hope there are experts out there, as I still am having no luck and as yet no response from the package maintainer.

  Original Message  
From: David Winsemius
Sent: Thursday 9 July 2015 18:15
To: John Kane
Cc: R. Mailing List
Subject: Re: [R] Maxent Jarfile


On Jul 9, 2015, at 6:02 AM, John Kane wrote:

> Thanks Annemarie,
> Things came through okay. I'll defer to the experts on substantive advice.
> 

John;

It only came through to you by way of a copy sent directly to you. It did not come to you from the rhelp-server. If there are any experts out there, then they did not get a copy.

The advice to contact the package maintainer seemed the best avenue to proceed along.

David.


> John Kane
> Kingston ON Canada
> 
> 
>> -----Original Message-----
>> From: annemariefischer86 at gmail.com
>> Sent: Thu, 09 Jul 2015 07:25:06 +0200
>> To: jrkrideau at inbox.com, annemarie_dh at hotmail.com, r-help at r-project.org
>> Subject: Re: [R] Maxent Jarfile
>> 
>> ‎Hi John,
>> 
>> Sorry about that. Please find attached the code, error and input file.
>> 
>> Thanks,
>> Annemarie
>> 
>> 
>> Original Message
>> From: John Kane
>> Sent: Thursday 9 July 2015 00:26
>> To: Annemarie Fischer; r-help at r-project.org
>> Subject: Re: [R] Maxent Jarfile
>> 
>> Hi Annemarie,
>> You have sent the email in HTML and it is very close to unreadable. Could
>> you please resubmit the message in plain text. R-help does not accept
>> HTML and, as happened here, the text gets seriously mangled.
>> 
>> 
>> 
>> John Kane
>> Kingston ON Canada
>> 
>> 
>>> -----Original Message-----
>>> From: annemarie_dh at hotmail.com
>>> Sent: Wed, 8 Jul 2015 20:22:57 +0000
>>> To: r-help at r-project.org
>>> Subject: [R] Maxent Jarfile
>>> 
>>> Hi,
>>> I have been trying to solve the below problem for 2 days with no
>>> success.
>>> Hopefully you can help as i can find no assistance online.
>>> I am attempting to run the niche.equivalency.test and the
>>> bg.similarity.test using RStudio and Maxent. I keep getting the error:
>>> Error: Unable to access jarfile C:/ProgramError in file(fname, "r") :
>>> cannot open the connectionIn addition: Warning messages:1: running
>>> command 'java -jar C:/Program
>>> Files/R/R-3.1.3/library/dismo/java/maxent.jar -e
>>> R.phyloclim.temp/background.csv -s R.phyloclim.temp/samples.csv -j
>>> R.phyloclim.temp/proj/ -o R.phyloclim.temp/out/ -r removeduplicates
>>> nopictures autorun' had status 1 2: In file(fname, "r") : cannot open
>>> file 'R.phyloclim.temp/out/Rhinolophus blasii_proj.asc': No such file or
>>> directory
>>> I suspect the issue is that the file directory doesnt have "", but i
>>> have
>>> no idea how to add these in, as in RStudio values, the "" does appear.
>>> My code is:
>>> # load required
>> packageslibrary(raster)library(mgcv)library(dismo)library(rgdal)library(ellipse)library(sp)library(proj4)library(rgeos)
>>> library(rJava)library(maptools)library(rasterVis)library(phyloclim)
>>> # path to MAXENT# --------------maxent.exe <-
>>> paste(system.file(package="dismo"),
>>> "/java/maxent.jar", sep = "")
>>> # a data frame of coordinates where two species # have been detected
>>> ('presence points') and# a raster stack of environmental covariables#
>>> --------------------------------------
>>> ###Change to correct species usedfile <-
>>> paste(system.file(package="dismo"), "/ex/Rhinolophus_species.csv",
>>> sep="")# this is the file we will use:file
>>> #save(file, file="Molossidae_rarefied_points.rda")
>>> #data()#data(package = .packages(all.available = TRUE))
>>> #myData <- read.csv("file", header=TRUE, nrows=10000)
>>> Rhinolophus_species <- read.table(file, header=TRUE, sep=',')
>>> species <- c("Rhinolophus blasii", "Rhinolophus
>>> clivosus")#data(sites)samples <- Rhinolophus_species[grep(paste(species,
>>> collapse = "|"), Rhinolophus_species$Spp), ]data.path <-
>>> system.file("extdata", package = "phyloclim")preds <- list.files(path =
>>> data.path, pattern = "[.]asc")preds <- paste(data.path, preds, sep =
>>> "/")preds <- stack(lapply(X = preds, FUN = raster))
>>> # testing against 9 permutations of the data#
>>> -------------------------------------------reps <- 1000
>>> # run hypothesis tests# --------------------if
>>> (file.exists(maxent.exe)){
>>> net <- niche.equivalency.test(samples, preds, reps, maxent.exe) net;
>>> plot(net) bst <- bg.similarity.test(samples, preds, reps, app =
>>> maxent.exe) bst; plot(bst)} else { message("get a copy of MAXENT (see
>>> Details)")}
>>> [[alternative HTML version deleted]]
>>> 
>>> ______________________________________________
>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
>>> http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>> 
>> ____________________________________________________________
>> FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop!
>> 
>> ______________________________________________
>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
> 
> ____________________________________________________________
> Can't remember your password? Do you need a strong and secure password?
> Use Password manager! It stores your passwords & protects your account.
> 
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

David Winsemius
Alameda, CA, USA

______________________________________________
R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.



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