You would do better to contact the package owner for this, as it's a problem specific to the package. In this case the problem looks to be in dismo, so you should use packageDescription("dismo") to discover that Robert Hijmans is the person to contact. I would suggest running maxent() first to see if it works. If it does then the problem is elsewhere, so use find("niche.equivalency.test") to find out what package that function is in, and email the maintainer of that package for help.
Oh, and also read the posting guide: <http://www.r-project.org/posting-guide.html> :-) Bob (who is not going to wait 15 hours to send this) On 8 July 2015 at 22:22, Annemarie Fischer <annemarie...@hotmail.com> wrote: > 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@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. -- Bob O'Hara Biodiversity and Climate Research Centre Senckenberganlage 25 D-60325 Frankfurt am Main, Germany Tel: +49 69 798 40226 Mobile: +49 1515 888 5440 WWW: http://www.bik-f.de/root/index.php?page_id=219 Blog: http://occamstypewriter.org/boboh/ Journal of Negative Results - EEB: www.jnr-eeb.org ______________________________________________ R-help@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.