Running examples in ‘phyloclim-Ex.R’ failed
The error most likely occurred in:

> ### Name: hypothesis.testing
> ### Title: Niche Equivalency and Background Similarity Test
> ### Aliases: niche.equivalency.test niche.identity.test identity.test
> ###   bg.similarity.test print.ntest plot.ntest
> 
> ### ** Examples
> 
> # 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
> # --------------------------------------
> species <- c("enneaphylla", "laciniata")
> data(sites)
> samples <- sites[grep(paste(species, collapse = "|"), sites$spec), ]
> 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 <- 9
> 
> # 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)")
+ }
Error in options(scipen = opsci) : invalid 'scipen'
Calls: niche.equivalency.test ... .local -> writeValues -> writeValues -> .local -> options
Execution halted
Found the following files/directories:
  ‘R.phyloclim.temp’

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  GiNA-package.Rd: EBImage
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following files/directories:
  ‘Pictures_analyzed’ ‘cutoff_vals’ ‘cutoff_vals1’ ‘gina_cran.JPG’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  GiNA-package.Rd: EBImage
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following files/directories:
  ‘Pictures_analyzed’ ‘cutoff_vals’ ‘cutoff_vals1’ ‘gina_cran.JPG’
Found the following files/directories:
  ‘Pictures_analyzed’ ‘cutoff_vals’ ‘cutoff_vals1’ ‘gina_cran.JPG’
Found the following files/directories:
  ‘Pictures_analyzed’ ‘cutoff_vals’ ‘cutoff_vals1’ ‘gina_cran.JPG’
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  GiNA-package.Rd: EBImage
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following files/directories:
  ‘Pictures_analyzed’ ‘cutoff_vals’ ‘cutoff_vals1’ ‘gina_cran.JPG’
Found the following files/directories:
  ‘Pictures_analyzed’ ‘cutoff_vals’ ‘cutoff_vals1’ ‘gina_cran.JPG’