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. > > ____________________________________________________________ > 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.
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
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. >> >> ____________________________________________________________ >> 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.