Edits to conform to CRAN

Author: bobmuscarella

DESCRIPTION

@@ -1,11 +1,11 @@
 Package: ENMeval
 Type: Package
-Title: Automated runs and evaluations of ecological niche models
+Title: Automated Runs and Evaluations of Ecological Niche Models
 Version: 0.2.0
-Date: 2014-10-5
+Date: 2015-10-5
 Author: Robert Muscarella, Peter J. Galante, Mariano Soley-Guardia, Robert A. Boria, Jamie M. Kass, Maria Uriarte and Robert P. Anderson
 Maintainer: Robert Muscarella <[email protected]>
 Description: Automatically partitions data into evaluation bins, executes ecological niche models across a range of settings, and calculates a variety of evaluation statistics.  Current version only implements ENMs with Maxent (Phillips et al. 2006).
 License: GPL
 Depends: dismo, methods, rJava (>= 0.5-0), parallel, raster, R (>= 2.10)
-Imports: doParallel, foreach
+Imports: doParallel, foreach, utils, graphics, stats, grDevices

NAMESPACE

@@ -1,4 +1,8 @@
 import("dismo", "methods", "rJava", "raster", "parallel", "doParallel", "foreach")
+importFrom("grDevices", "rainbow")
+importFrom("graphics", "abline", "arrows", "axis", "box", "par","plot")
+importFrom("stats", "var")
+importFrom("utils", "setTxtProgressBar", "txtProgressBar")
 exportPattern("^[[:alpha:]]+")
 exportClasses(
     "ENMevaluation" 

man/ENMeval-package.Rd

@@ -34,7 +34,7 @@ Robert Muscarella, Peter J. Galante, Mariano Soley-Guardia, Robert A. Boria, Jam
 Maintainer: Robert Muscarella <bob.muscarella@gmail.com>
 }
 \references{ 
-Hijmans, R. J., Phillips, S., Leathwick, J. and Elith, J. 2011. dismo package for R. Available online at: \url{http://cran.r-project.org/web/packages/dismo/index.html}.
+Hijmans, R. J., Phillips, S., Leathwick, J. and Elith, J. 2011. dismo package for R. Available online at: \url{https://cran.r-project.org/package=dismo}.
 
 Muscarella, R., Galante, P. J., Soley-Guardia, M., Boria, R. A., Kass, J. M., Uriarte, M., and Anderson, R. P. 2014. ENMeval: An R package for conducting spatially independent evaluations and estimating optimal model complexity for Maxent ecological niche models. \emph{Methods in Ecology and Evolution}, \bold{5}: 1198-1205.
 

man/ENMevaluate.Rd

@@ -107,7 +107,7 @@ An object of class \code{ENMevaluation} with named slots:
 
 Elith, J., Phillips, S. J., Hastie, T., Dudik, M., Chee, Y. E., and Yates, C. J. (2011) A statistical explanation of MaxEnt for ecologists. \emph{Diversity and Distributions}, \bold{17}: 43-57.
 
-Hijmans, R. J., Phillips, S., Leathwick, J. and Elith, J. (2011) dismo package for R. Available online at: \url{http://cran.r-project.org/web/packages/dismo/index.html}.
+Hijmans, R. J., Phillips, S., Leathwick, J. and Elith, J. (2011) dismo package for R. Available online at: \url{https://cran.r-project.org/package=dismo}.
 
 Lobo, J. M., Jimenez-Valverde, A., and Real, R. (2008) AUC: A misleading measure of the performance of predictive distribution models. \emph{Global Ecology and Biogeography}, \bold{17}: 145-151.
 

man/calc.niche.overlap.Rd

@@ -19,7 +19,7 @@ Compute pairwise "niche overlap" in geographic space for Maxent predictions. The
 \value{ A matrix with the lower triangle giving values of pairwise "niche overlap" in geographic space.  Row and column names are given by the \code{\link{make.args}} argument when run by the \code{\link{ENMevaluate}} function. }
 
 \references{
-Hijmans, R. J., Phillips, S., Leathwick, J. and Elith, J. (2011) dismo package for R. Available online at: \url{http://cran.r-project.org/web/packages/dismo/index.html}.
+Hijmans, R. J., Phillips, S., Leathwick, J. and Elith, J. (2011) dismo package for R. Available online at: \url{https://cran.r-project.org/package=dismo}.
 	
 Schoener, T. W. (1968) The \emph{Anolis} lizards of Bimini: resource partitioning in a complex fauna. \emph{Ecology}, \bold{49}: 704-726.
 	

man/get.evaluation.bins.Rd

@@ -63,7 +63,7 @@ The \code{checkerboard1} and \code{checkerboard2} methods are designed to partit
 }
 
 \references{ 
-Hijmans, R. J., Phillips, S., Leathwick, J. and Elith, J. 2011. dismo package for R. Available online at: \url{http://cran.r-project.org/web/packages/dismo/index.html}.
+Hijmans, R. J., Phillips, S., Leathwick, J. and Elith, J. 2011. dismo package for R. Available online at: \url{https://cran.r-project.org/package=dismo}.
 
 Pearson, R. G., Raxworthy, C. J., Nakamura, M. and Peterson, A. T. 2007. Predicting species distributions from small numbers of occurrence records: a test case using cryptic geckos in Madagascar. \emph{Journal of Biogeography}, \bold{34}: 102-117.