[R] Maxent Jarfile

[annemariefischer86 at gmail.com]

‎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
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> 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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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.