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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