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)")}
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