[R] Maxent Jarfile
annemariefischer86 at gmail.com
annemariefischer86 at gmail.com
Thu Jul 9 20:00:00 CEST 2015
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.
>>>
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>>
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>> ______________________________________________
>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
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>> 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/
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