[R] Maxent Jarfile

[John Kane]

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

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.
> 
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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.

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