+ version 1.0.1 - see news.md

.Rbuildignore

@@ -2,4 +2,6 @@
 ^\.Rproj\.user$
 ^.Rhistory$
 [~]
+appveyor.yml
+.travis.yml
 

.directory

@@ -0,0 +1,6 @@
+[Dolphin]
+Timestamp=2016,3,5,16,21,34
+Version=3
+
+[Settings]
+HiddenFilesShown=true

.travis.yml

@@ -0,0 +1,44 @@
+language: r
+sudo: required
+warnings_are_errors: true
+
+os:
+  - linux
+  - osx
+
+env:
+  global:
+    - NOT_CRAN=true
+    - _R_CHECK_FORCE_SUGGESTS_=False
+
+before_install: 
+  - echo "TRAVIS_OS_NAME = $TRAVIS_OS_NAME"
+  - echo "options(repos = c(CRAN='http://cran.rstudio.com'))" > ~/.Rprofile
+
+r_binary_packages:
+  - sp
+  - rgdal
+  - raster
+  - Rcpp
+  - plyr
+  - gdalUtils
+  - shape
+  - ape
+  - fastcluster
+  - PBSmapping
+  - RgoogleMaps
+  - testthat
+  - data.table
+  - doSNOW
+  - RColorBrewer
+  - scales
+  - vegan
+
+r_packages:
+  - covr
+  - rmarkdown
+  - testthat
+
+after_success:
+  - Rscript -e 'covr::codecov()'
+

DESCRIPTION

@@ -13,18 +13,18 @@ Description: This R package contains decision support tools for reserve
     Most of the functions that involve intensive data processing use code
     compiled in C++, provide options to run processing in parallel, or can make
     use of other software to reduce run time.
-License: GNU AFFERO GENERAL PUBLIC LICENSE (version 3)
+License: AGPL-3 
 URL: https://github.com/paleo13/marxan
 LazyData: true
 Collate:
     'dependencies.R'
     'RcppExports.R'
     'marxan-internal.R'
-    'misc.R'
-    'generics.R'
     'zonalSum.R'
+    'misc.R'
     'calcPuVsSpeciesData.R'
     'calcBoundaryData.R'
+    'generics.R'
     'MarxanData.R'
     'MarxanOpts.R'
     'MarxanResults.R'
@@ -47,15 +47,23 @@ Imports:
     fastcluster,
     PBSmapping,
     RgoogleMaps,
-    testthat,
     data.table,
     doSNOW,
-    knitr,
-    rmarkdown,
     RColorBrewer,
     scales,
+    snow,
     vegan
 LinkingTo: Rcpp
 VignetteBuilder: knitr
 Suggests:
+    rmarkdown,
     testthat,
+    knitr
+BinaryFiles: 'bin/MarOpt_v243_Linux32',
+    'bin/MarOpt_v243_Linux64',
+    'bin/MarOpt_v243_Mac32',
+    'bin/MarOpt_v243_Mac64',
+    'bin/Marxan.exe',
+    'bin/Marxan_x64.exe'
+SystemRequirements: C++11
+RoxygenNote: 5.0.1

NAMESPACE

@@ -1,4 +1,4 @@
-# Generated by roxygen2 (4.1.1): do not edit by hand
+# Generated by roxygen2: do not edit by hand
 
 S3method("costs<-",MarxanData)
 S3method("costs<-",MarxanSolved)
@@ -172,9 +172,12 @@ exportClasses(MarxanResults)
 exportClasses(MarxanSolved)
 exportClasses(MarxanUnsolved)
 exportMethods(SpatialPolygons2PolySet)
+exportMethods(cache)
 exportMethods(initialize)
+exportMethods(is.cached)
 exportMethods(is.comparable)
 exportMethods(plot)
+exportMethods(rasterize.gdal)
 exportMethods(show)
 exportMethods(spplot)
 exportMethods(zonalSum)

NEWS

@@ -1,3 +1,12 @@
+marxan 1.0.1
+--------
+* Fixed bug in boundary data calculations.
+* Fixed bug with n_preallocate in SpatialPolygons2Polyset
+* Pass CRAN manual checks - still failing some checks
+* Automated tests using Travis CI and AppVeyor.
+* Replace Makevars files with SystemRequirements in DESCRIPTION
+
+
 marxan 1.0.0
 --------
 * First major release.

R/MarxanData.R

@@ -213,18 +213,19 @@ setMethod(
 #' @param puvspecies_spo "data.frame" with data in \code{puvspecies} ordered by 'species' column. Defaults to \code{NULL}, and will generate data from \code{puvspecies}.
 #' @param skipchecks "logical" Skip data integrity checks? May improve speed for big data sets. Defaults to \code{FALSE}.
 #' @param .cache "environment" used to cache calculations. Defaults to a new environment.
+#' @param ... not used.
 #' @note Generally, users are not encouraged to change arguments to \code{.cache}.
 #' @return MarxanData object
 #' @seealso \code{\link[PBSmapping]{PolySet}}, \code{\link{read.MarxanData}}, \code{\link{write.MarxanData}}, \code{\link{format.MarxanData}}, \code{\link{MarxanData-class}}.
 #' @export
 #' @examples
-#' data(planningunits, species)
+#' data(taspu, tasinvis)
 #' x<-MarxanData(
-#' 	planningunits@@data,
+#' 	taspu@@data,
 #' 	data.frame(id=1L, target=12, spf=23, name='species1', stringsAsFactors=FALSE),
-#'  calcPuVsSpeciesData(planningunits, species[[1]]),
-#'  calcBoundaryData(planningunits),
-#'  SpatialPolygons2PolySet(planningunits)
+#'  calcPuVsSpeciesData(taspu, tasinvis[[1]]),
+#'  calcBoundaryData(taspu),
+#'  SpatialPolygons2PolySet(taspu)
 #' )
 MarxanData<-function(pu, species, puvspecies, boundary, polygons=NULL, puvspecies_spo=NULL, skipchecks=FALSE, .cache=new.env(), ...) {
 	# convert factors to characters
@@ -332,6 +333,10 @@ write.MarxanData<-function(x, dir=getwd(), ...) {
 #' @param polygons "SpatialPolygons" with planning unit data.
 #' @param rasters "RasterLayer", "RasterStack", "RasterBrick" with species distribution data.
 #' @param targets "numeric" vector for targets for each species (eg. 12), or "character" vector with percent-based targets (eg. '12\%'). Defaults to '20\%' for each species.
+#' @param spf "numeric" species penalty factors.
+#' @param sepdistance "numeric" species minimum separation distance.
+#' @param sepnum "numeric" species seperated feature occurences.
+#' @param targetocc "numeric" species occurence targets.
 #' @param pu "data.frame" planning unit data; with "integer" 'id', "numeric" 'cost', "integer" 'status' columns. Default behaviour is to generate a table with all costs and statuses set to 1 and 0 (respectively).
 #' @param species "data.frame" with species data; with "integer" 'id', "numeric" 'target', "numeric" 'spf', and "character" 'name' columns. Default behaviour is to base targets on \code{target} argument, set 'spf' to 1, and set 'names' use names of layers in \code{rasters} argument.
 #' @param puvspecies "data.frame" pu vs. species data; with "species", "pu", and "amount" columns. Defaults to \code{NULL}, and will be calculated using \code{calcPuVsSpeciesData}.
@@ -342,9 +347,9 @@ write.MarxanData<-function(x, dir=getwd(), ...) {
 #' @seealso \code{\link{MarxanData-class}}, \code{\link{MarxanData}}, \code{\link{read.MarxanData}}, \code{\link{write.MarxanData}}.
 #' @export format.MarxanData
 #' @examples
-#' data(planningunits, species)
-#' x<-MarxanData(planningunits, rasters=species, targets="10\%")
-#' y<-MarxanData(planningunits, rasters=species)
+#' data(taspu, tasinvis)
+#' x<-MarxanData(taspu, rasters=tasinvis, targets="10%")
+#' y<-MarxanData(taspu, rasters=tasinvis)
 #' stopifnot(identical(x,y))
 format.MarxanData<-function(polygons, rasters, targets="20%", spf=rep(1, nlayers(rasters)), sepdistance=rep(0, nlayers(rasters)), sepnum=rep(0L,nlayers(rasters)), targetocc=rep(0L,nlayers(rasters)), pu=NULL, species=NULL, puvspecies=NULL, puvspecies_spo=NULL, boundary=NULL, ..., verbose=FALSE) {
 	# init
@@ -640,7 +645,8 @@ setMethod(
 )
 
 
-#' @describeIn is.cached
+#' @rdname is.cached
+#' @export
 setMethod(
 	f="is.cached", 
 	signature(x="MarxanData", name="character"), 
@@ -649,7 +655,8 @@ setMethod(
 	}
 )
 
-#' @describeIn cache
+#' @rdname cache
+#' @export
 setMethod(
 	f="cache", 
 	signature(x="MarxanData", name="character", y="ANY"), 
@@ -658,7 +665,8 @@ setMethod(
 	}
 )
 
-#' @describeIn cache
+#' @rdname cache
+#' @export
 setMethod(
 	f="cache", 
 	signature(x="MarxanData", name="character", y="missing"), 
@@ -668,7 +676,7 @@ setMethod(
 )
 
 #' @rdname is.comparable
-#' export
+#' @export
 setMethod(
 	f="is.comparable",
 	signature(x="MarxanData", y="MarxanData"),
@@ -732,14 +740,14 @@ targets.MarxanData<-function(x) {
 	return(x)
 }
 
+#' @rdname maxtargets
 #' @export
-#' @describeIn maxtargets
 maxtargets.MarxanData<-function(x) {
 	return(x@species$maxtargets)
 }
 
+#' @rdname maxtargets
 #' @export
-#' @describeIn maxtargets
 `maxtargets<-.MarxanData`<-function(x, value) {
 	stopifnot(is.numeric(value) & !any(is.na(value)))
 	x@species$maxtargets<-value

R/MarxanOpts.R

@@ -22,7 +22,7 @@ NULL
 #' @slot VERBOSITY "integer" Amount of output displayed on the program screen. Defaults to 1L.
 #' @slot NCORES "integer" Number of cores to use for processing. Defaults to 1L.
 
-#' @note This class was not called "MarxanPars" due to the inevitable conflicts with \code{\link[base]{par}}.
+#' @note This class was not called "MarxanPars" due to the inevitable conflicts with \code{\link[graphics]{par}}.
 #' @export
 setClass("MarxanOpts",
 	representation(
@@ -118,12 +118,12 @@ setClass("MarxanOpts",
 #' @seealso \code{\link{MarxanOpts-class}},  \code{\link{read.MarxanOpts}}, \code{\link{write.MarxanOpts}}.
 #' @export
 #' @examples
-#' x<-MarxanOpts(NCORES=4, NUMREPS=2, NUMITNS=5)
+#' x<-MarxanOpts(NCORES=4L, NUMREPS=2L, NUMITNS=5L)
 MarxanOpts<-function(..., ignore.extra=FALSE) {
 	x<-new('MarxanOpts')
 	args<-as.list(substitute(list(...)))[c(-1L)]
 	extra<-which(!names(args) %in% names(getSlots("MarxanOpts")))
-	if (length(extra)>0) {		
+	if (length(extra)>0) {
 		if (ignore.extra) {
 			args<-args[-extra]
 		} else {

R/MarxanResults.R

@@ -15,7 +15,7 @@ NULL
 #' @slot best "integer" with index of best solution.
 #' @slot log "character" with Marxan log  file (otuput_log.dat). 
 #' @export
-#' @seealso \code{\link{MarxanResults}}, \code{\link{read.MarxanResults}}, \code{\link{write.MarxanResults}}.
+#' @seealso \code{\link{MarxanResults}}, \code{\link{read.MarxanResults}}.
 setClass("MarxanResults",
 	representation(
 		summary="data.frame",
@@ -384,7 +384,7 @@ dotchart.MarxanResults<-function(x, var="score", nbest=1, n=50) {
 	)
 }
 
-#' @describeIn is.cached
+#' @rdname is.cached
 setMethod(
 	f="is.cached", 
 	signature(x="MarxanResults", name="character"), 
@@ -393,7 +393,7 @@ setMethod(
 	}
 )
 
-#' @describeIn cache
+#' @rdname cache
 setMethod(
 	f="cache", 
 	signature(x="MarxanResults", name="character", y="ANY"), 
@@ -402,7 +402,7 @@ setMethod(
 	}
 )
 
-#' @describeIn cache
+#' @rdname cache
 setMethod(
 	f="cache", 
 	signature(x="MarxanResults", name="character", y="missing"), 

R/MarxanSolved.R

@@ -71,7 +71,7 @@ print.MarxanSolved<-function(x) {
 	print.MarxanResults(x@results, FALSE)
 }
 
-# ' @export
+#' @export
 setMethod(
 	'show',
 	'MarxanSolved',
@@ -496,13 +496,13 @@ targets.MarxanSolved<-function(x) {
 }
 
 #' @export
-#' @describeIn maxtargets
+#' @rdname maxtargets
 maxtargets.MarxanSolved<-function(x) {
 	return(maxtargets.MarxanData(x@data))
 }
 
 #' @export
-#' @describeIn maxtargets
+#' @rdname maxtargets
 `maxtargets<-.MarxanSolved`<-function(x,value) {
 	stopifnot(is.numeric(value) & !any(is.na(value)))
 	x@data@species$maxtargets<-value

R/MarxanUnsolved.R

@@ -225,13 +225,13 @@ targets.MarxanUnsolved<-function(x) {
 }
 
 #' @export
-#' @describeIn maxtargets
+#' @rdname maxtargets
 maxtargets.MarxanUnsolved<-function(x) {
 	return(maxtargets.MarxanData(x@data))
 }
 
 #' @export
-#' @describeIn maxtargets
+#' @rdname maxtargets
 `maxtargets<-.MarxanUnsolved`<-function(x,value) {
 	stopifnot(is.numeric(value) & !any(is.na(value)))
 	x@data@species$maxtargets<-value

R/Polygons2PolySet.R

@@ -7,33 +7,33 @@ NULL
 #' 
 #' @param x "SpatialPolygons" or "SpatialPolygonsDataFrame" object.
 #' @param n_preallocate "integer" How much memory should be preallocated for processing? Ideally, this number should equal the number of vertices in the "SpatialPolygons" object. If dtaa processing is taking too long consider increasing this value.
-#' @usage SpatialPolygons2PolySet(x, n=10000L)
+#' @usage SpatialPolygons2PolySet(x, n_preallocate=10000L)
 #' @return "PolySet" object.
 #' @note Be aware that this function is designed to be as fast as possible, but as a result it depends on C++ code and if used inappropriately this function will crash R.
 #' @seealso For a slower, more stable equivalent see \code{\link[maptools]{SpatialPolygons2PolySet}}.
 #' @export
 #' @examples 
-#' data(planningunits)
-#' x <- SpatialPolygons2PolySet(planningunits)
+#' data(taspu)
+#' x <- SpatialPolygons2PolySet(taspu)
 setGeneric("SpatialPolygons2PolySet", function(x, ...) standardGeneric("SpatialPolygons2PolySet"))
 
-#' describeIn SpatialPolygons2PolySet
+#' @rdname SpatialPolygons2PolySet
 #' @export
 setMethod(
 	"SpatialPolygons2PolySet",
 	signature(x="SpatialPolygonsDataFrame"),
 	function(x, n_preallocate = 10000L) {
-		return(rcpp_Polygons2PolySet(x@polygons))
+		return(rcpp_Polygons2PolySet(x@polygons, n_preallocate))
 	}
 )
 
-#' describeIn SpatialPolygons2PolySet
+#' @rdname SpatialPolygons2PolySet
 #' @export
 setMethod(
 	"SpatialPolygons2PolySet",
 	signature(x="SpatialPolygons"),
 	function(x, n_preallocate = 10000L) {
-		return(rcpp_Polygons2PolySet(x@polygons))
+		return(rcpp_Polygons2PolySet(x@polygons, n_preallocate))
 	}
 )