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.
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. >>> >>> ____________________________________________________________ >>> 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. > > ______________________________________________ > 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.********************** "The contents of this message do not reflect any position of the U.S. Government or NOAA." ********************** Roy Mendelssohn Supervisory Operations Research Analyst NOAA/NMFS Environmental Research Division Southwest Fisheries Science Center ***Note new address and phone*** 110 Shaffer Road Santa Cruz, CA 95060 Phone: (831)-420-3666 Fax: (831) 420-3980 e-mail: Roy.Mendelssohn at noaa.gov www: http://www.pfeg.noaa.gov/ "Old age and treachery will overcome youth and skill." "From those who have been given much, much will be expected" "the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
?Hi Roy, This example gives me the following error on trying to run the first line: Error: unexpected '&' in "jar <- paste(system.file(package="dismo"), "/java/maxent.jar", sep=&" I am currently attempting to run using the code given in the below thread: http://r.789695.n4.nabble.com/phyloclim-help-td4633283.html ? Original Message ? From: Roy Mendelssohn - NOAA Federal Sent: Thursday 9 July 2015 18:48 To: annemariefischer86 at gmail.com Cc: David Winsemius; John Kane; R. Mailing List Subject: Re: [R] Maxent Jarfile
?Hi Roy, Using the code in the other path also did not work, as I am not sure what to use for the projections or background. ? Original Message ? From: Roy Mendelssohn - NOAA Federal Sent: Thursday 9 July 2015 18:48 To: annemariefischer86 at gmail.com Cc: David Winsemius; John Kane; R. Mailing List Subject: Re: [R] Maxent Jarfile 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. >>> >>> ____________________________________________________________ >>> 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. > > ______________________________________________ > 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.********************** "The contents of this message do not reflect any position of the U.S. Government or NOAA." ********************** Roy Mendelssohn Supervisory Operations Research Analyst NOAA/NMFS Environmental Research Division Southwest Fisheries Science Center ***Note new address and phone*** 110 Shaffer Road Santa Cruz, CA 95060 Phone: (831)-420-3666 Fax: (831) 420-3980 e-mail: Roy.Mendelssohn at noaa.gov www: http://www.pfeg.noaa.gov/ "Old age and treachery will overcome youth and skill." "From those who have been given much, much will be expected" "the arc of the moral universe is long, but it bends toward justice" -MLK Jr.