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: annemariefische...@gmail.com
Sent: Thu, 09 Jul 2015 07:25:06 +0200
To: jrkrid...@inbox.com, annemarie...@hotmail.com, r-help@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@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...@hotmail.com
Sent: Wed, 8 Jul 2015 20:22:57 +
To: r-help@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=1)
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]]
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Re: [R] Maxent Jarfile
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: annemariefische...@gmail.com Cc: David Winsemius; John Kane; R. Mailing List Subject: Re: [R] Maxent Jarfile __ R-help@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.
Re: [R] Maxent Jarfile
This suggests that you either have the maxent.jar file in the wrong place or with the wrong name. I suspect when you get the first two lines of the script to work you will be okay. -Roy On Jul 9, 2015, at 10:10 AM, annemariefische...@gmail.com wrote: 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: annemariefische...@gmail.com Cc: David Winsemius; John Kane; R. Mailing List Subject: Re: [R] Maxent Jarfile ** 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.mendelss...@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. __ R-help@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.
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: annemariefische...@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, annemariefische...@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: annemariefische...@gmail.com
Sent: Thu, 09 Jul 2015 07:25:06 +0200
To: jrkrid...@inbox.com, annemarie...@hotmail.com, r-help@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@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...@hotmail.com
Sent: Wed, 8 Jul 2015 20:22:57 +
To: r-help@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=1)
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
Re: [R] Maxent Jarfile
Dear Annemie,
The mailing list accepts only a limited number of extensions. Your
attachment got stripped for the mail. It is probably easier to put the
files on-line and send us the link to the files.
Best regards,
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie Kwaliteitszorg / team Biometrics Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium
To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey
2015-07-09 7:25 GMT+02:00 annemariefische...@gmail.com:
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@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...@hotmail.com
Sent: Wed, 8 Jul 2015 20:22:57 +
To: r-help@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=1)
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@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@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@r-project.org mailing list
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@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...@hotmail.com
Sent: Wed, 8 Jul 2015 20:22:57 +
To: r-help@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=1)
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@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@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@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.
Re: [R] Maxent Jarfile
You would do better to contact the package owner for this, as it's a
problem specific to the package. In this case the problem looks to be
in dismo, so you should use packageDescription(dismo) to discover
that Robert Hijmans is the person to contact. I would suggest running
maxent() first to see if it works. If it does then the problem is
elsewhere, so use find(niche.equivalency.test) to find out what
package that function is in, and email the maintainer of that package
for help.
Oh, and also read the posting guide:
http://www.r-project.org/posting-guide.html :-)
Bob
(who is not going to wait 15 hours to send this)
On 8 July 2015 at 22:22, Annemarie Fischer annemarie...@hotmail.com wrote:
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=1)
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@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.
--
Bob O'Hara
Biodiversity and Climate Research Centre
Senckenberganlage 25
D-60325 Frankfurt am Main,
Germany
Tel: +49 69 798 40226
Mobile: +49 1515 888 5440
WWW: http://www.bik-f.de/root/index.php?page_id=219
Blog: http://occamstypewriter.org/boboh/
Journal of Negative Results - EEB: www.jnr-eeb.org
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R-help@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.
Re: [R] Maxent Jarfile
Thanks Annemarie,
Things came through okay. I'll defer to the experts on substantive advice.
John Kane
Kingston ON Canada
-Original Message-
From: annemariefische...@gmail.com
Sent: Thu, 09 Jul 2015 07:25:06 +0200
To: jrkrid...@inbox.com, annemarie...@hotmail.com, r-help@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@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...@hotmail.com
Sent: Wed, 8 Jul 2015 20:22:57 +
To: r-help@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=1)
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]]
__
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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.
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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.
Re: [R] Maxent Jarfile
Hi Roy, I managed to make the code work, the issue was with underscores in the files. Thanks for your help. From: Roy Mendelssohn - NOAA Federal [via R] Sent: Thursday 9 July 2015 20:36 To: annafischer86 Subject: Re: Maxent Jarfile -- View this message in context: http://r.789695.n4.nabble.com/Maxent-Jarfile-tp4709586p4709665.html Sent from the R help mailing list archive at Nabble.com. [[alternative HTML version deleted]] __ R-help@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.
Re: [R] Maxent Jarfile
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: annemariefische...@gmail.com
Sent: Thu, 09 Jul 2015 07:25:06 +0200
To: jrkrid...@inbox.com, annemarie...@hotmail.com, r-help@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@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...@hotmail.com
Sent: Wed, 8 Jul 2015 20:22:57 +
To: r-help@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=1)
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@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
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, annemariefische...@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: annemariefische...@gmail.com
Sent: Thu, 09 Jul 2015 07:25:06 +0200
To: jrkrid...@inbox.com, annemarie...@hotmail.com, r-help@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@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...@hotmail.com
Sent: Wed, 8 Jul 2015 20:22:57 +
To: r-help@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=1)
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@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do
[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=1)
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@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.
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...@hotmail.com
Sent: Wed, 8 Jul 2015 20:22:57 +
To: r-help@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=1)
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@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@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.
