[R] Maxent Jarfile

Thu Jul 9 18:47:56 CEST 2015

Have you been able to run the example that comes with dismo::maxent such as at the bottom of:

http://www.inside-r.org/packages/cran/dismo/docs/maxent

-Roy

> On Jul 9, 2015, at 9:38 AM, annemariefischer86 at gmail.com wrote:
> 
> 
> 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=0
> 
> ‎https://www.dropbox.com/s/jffg48y4dojzsb3/R%20Studio%20code.txt?dl=0
> 
> ‎https://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.
>>> 
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>> 
>> ____________________________________________________________
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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.
> 
> 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.
> 
> ______________________________________________
> 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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