version 1.1.2

cran · Sep 7, 2016 · 8e0b1e7 · 8e0b1e7
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,23 +1,23 @@
 Package: landscapeR
-Title: Categorical Landscape Simulation Facilities
-Version: 1.1.1
-Date: 2016-08-31
+Title: Categorical Landscape Simulation Facility
+Version: 1.1.2
+Date: 2016-09-07
 Authors@R: c(person(given = "Dario", family = "Masante", role = c("aut", "cre"), email = "[email protected]"))
 Copyright: Natural Environment Research Council (NERC) and Centre for
         Ecology and Hydrology (CEH)
 URL: https://github.com/dariomasante/landscapeR
 BugReports: https://github.com/dariomasante/landscapeR/issues
 Imports: raster
 Suggests: knitr, rmarkdown
-Description: Package is aimed at simulating categorical maps on actual geographical realms, starting from either empty landscapes, or landscapes provided by the user (e.g. land use maps). landscapeR allows to tweak or create landscapes while retaining a high degree of control on its features, without the hassle of specifying each location attribute. In this it differs from other tools which generate null or neutral landscape in a theoretical space. The basic algorithm currently implemented uses a simple agent style/cellular automata growth model, with no rules (apart from areas of exclusion). Outputs are raster dataset exportable to any common GIS format.
+Description: Simulates categorical maps on actual geographical realms, starting from either empty landscapes or landscapes provided by the user (e.g. land use maps). Allows to tweak or create landscapes while retaining a high degree of control on its features, without the hassle of specifying each location attribute. In this it differs from other tools which generate null or neutral landscapes in a theoretical space. The basic algorithm currently implemented uses a simple agent style/cellular automata growth model, with no rules (apart from areas of exclusion). Outputs are raster dataset exportable to any common GIS format.
 License: GPL (>= 3)
 LazyLoad: yes
 LazyData: TRUE
 NeedsCompilation: no
 RoxygenNote: 5.0.1
 VignetteBuilder: knitr
-Packaged: 2016-08-31 11:57:20 UTC; dmasan
+Packaged: 2016-09-07 11:22:17 UTC; dmasan
 Author: Dario Masante [aut, cre]
 Maintainer: Dario Masante <[email protected]>
 Repository: CRAN
-Date/Publication: 2016-08-31 14:55:47
+Date/Publication: 2016-09-07 14:41:34
diff --git a/MD5 b/MD5
@@ -1,22 +1,22 @@
-303e5163cfde7076bef8e6a772b3aa89 *DESCRIPTION
+4b48ba9f5ec2f7179275812e51efb358 *DESCRIPTION
 61a106d579400fccc0ec8efc6d500d6d *NAMESPACE
-1e99ff8ad4de85ec84ab921035a463d9 *NEWS.md
+7cb151654e8ea7de65e62f09c6c7afec *NEWS.md
 b75f528daa3b271a7015d49cd186f3f6 *R/expandClass.R
 08127e0bda7cbdf93ab1755412b87cce *R/landscapeR-package.R
-4a1f72da6bd08a8ee32db7ab65efc1d6 *R/makeClass.R
+09bf83e8deb24866d53c660a2ca5c6c0 *R/makeClass.R
 d7728388222b867a1653574da7e0d3c2 *R/makeLine.R
-b43ef2ab9e8a680dcbfd8164ffb522e7 *R/makePatch.R
+a6cedcdefcbdb4832022d78fd3c5977f *R/makePatch.R
 6e7a0f6ed46c094b03637803ebfb5059 *R/rmSingle.R
 fe7ff7e0947c9daab2b4b00cf6d3e0c7 *R/zzz.R
 6424e2146149baa0cfc45a5600dcc513 *build/vignette.rds
 6fbe40d2a4c543685ea49b7d68d82b2c *inst/COPYRIGHTS
 464726e62c6ad0fe485a4b76f0a6567e *inst/doc/landscapeR.R
 01ab4ef1bc8374abb04acc2ed251db32 *inst/doc/landscapeR.Rmd
-db4c399909f3e18e8e22365257742ba4 *inst/doc/landscapeR.html
+69af454b18c51a43d4ce4d8c8458ba74 *inst/doc/landscapeR.html
 e0a0184bc8a14d18e6b2108e701825a4 *man/expandClass.Rd
 061baabcad8fd0f72cd37264dd888970 *man/landscapeR-package.Rd
 5339e574f87235fd0f82291592526f30 *man/makeClass.Rd
 ba89a8a6b8966f9c45ee861154fe59d5 *man/makeLine.Rd
-3e876f5cef42dd2568f6d278aa76e689 *man/makePatch.Rd
+67c94c78c8a133c470bce484ecb61c16 *man/makePatch.Rd
 71d7f5b8af09f17c4a3c2ff31673f644 *man/rmSingle.Rd
 01ab4ef1bc8374abb04acc2ed251db32 *vignettes/landscapeR.Rmd
diff --git a/NEWS.md b/NEWS.md
@@ -1,13 +1,23 @@
+landscapeR v1.1.2 (Patch release date: 2016-09-07)
+-----------------------------------------------
+CHANGES:
+
+* Bug fix in 'makeClass'
+* Clarified error messages
+
+
 landscapeR v1.1.1 (Patch release date: 2016-08-31)
 -----------------------------------------------
 CHANGES:
+
 * Fixed bug in 'rmSingle'
 * Replaced outdated version of documentation 
 
 
 landscapeR v1.1 (Release date: 2016-08-30)
 -----------------------------------------------
 CHANGES:
+
 * Removed dependency from package 'fastmatch'
 * Changed 'makePatch' and 'expandClass' function internals to gain significant speed improvements
 * Updated and improved error/warning messages and exception handling
@@ -18,6 +28,7 @@ CHANGES:
 * Fixed author list to CRAN standards
 
 NEW:
+
 * Added vignette
 * Added function 'rmSingle' to remove single tones and reduce salt-pepper effect
 * Added function  'makeLine' to create linear features (directional and convoluted). Beta version.
@@ -28,4 +39,5 @@ NEW:
 landscapeR v1.0.0 (Release date: 2016-05-22)
 -----------------------------------------------
 NEW FEATURES:
+
 * First release on CRAN
diff --git a/R/makeClass.R b/R/makeClass.R
@@ -35,28 +35,39 @@ makeClass <- function(context, npatch, size, pts = NULL, bgr=0, edge=FALSE, rast
     edge=FALSE
     warning('Edge output reset to FALSE. edge=TRUE only when raster output is not required (i.e. rast=FALSE)')
   }
-  if(is.null(pts)){
-    pts <- sample.int(length(context), npatch)
-  }
-  pts <- .toCellIndex(context, pts)
-  invalidPts <- which(pts > length(context) | pts < 1 | pts %% 1 != 0 | is.na(pts))
-  if(length(invalidPts) > 0){
-    stop('Seed point ', pts[invalidPts], ' not valid.')
-  }
-  if(length(pts) != npatch){ stop('Number of patches not matching number of seed points provided') }
-
   mtx <- t(raster::as.matrix(context))
   if(length(size)==1){
     size <- rep(size, npatch)
   }
+  bgrCells <- which(is.element(mtx, bgr))
+  if(length(bgrCells) == 0){
+    stop('No background cells available with value ', bgr, '. Try checking argument "bgr".')
+  }
   if(length(bgr > 1)){
-    bgrCells <- which(is.element(mtx, bgr))
     bgr <- bgr[1]
     mtx[bgrCells] <- bgr
   }
+  if(is.null(pts)){
+    pts <- sample(bgrCells, npatch)
+  }
+  pts <- .toCellIndex(context, pts)
+  ## invalidPts <- which(pts > length(mtx) | pts < 1 | pts %% 1 != 0 | is.na(pts))
+  ## if(length(invalidPts) > 0){
+  if(length(pts) != npatch){ stop('Number of patches not matching number of seed points provided.') }
+  invalidPts <- !is.element(pts, bgrCells)
+  if(any(invalidPts)){
+    if(all(invalidPts)){
+      stop('All seed points invalid.')
+    } else {
+      warning('Invalid seed points: ', paste(pts[invalidPts], collapse='; '), '\n Invalid points were ignored.')
+      pts <- pts[!invalidPts]
+      size <- size[!invalidPts]
+      npatch <- length(pts)
+    }
+  }
   lst <- list()
   for(np in 1:npatch){
-    l <- makePatch(context=mtx, spt=pts[np], size=size[np], bgr=bgr, edge=edge, val=val)
+    l <- makePatch(context=mtx, spt=pts[np], size=size[np], bgr=bgr, edge=edge, val=val, rast = FALSE)
     if(edge==TRUE){
       eg <- l[[2]]
       l <- l[[1]]

diff --git a/R/makePatch.R b/R/makePatch.R
@@ -1,5 +1,6 @@
-#" Create a single patch. Note that function \code{makeClass} should be used preferably (see details).
+#" Create a single patch
 #'
+#' @description Function will create a single patch. \strong{NOTE}: \code{makeClass} should be used preferably when creating a single patch, as better error and exception handling is provided.
 #' @param context Raster object or matrix, an empty landscape raster or a mask indicating where the patch cannot be generated (see bgr below).
 #' @param size integer. Size of the patch to be generated, as number of raster cells.
 #' @param spt integer or matrix. The seed point location around which the patch is generated (a random point is given by default). It can be an integer, as index of the cell in the raster, or a two columns matrix indicating x and y coordinates (an integer vector of length 2 is accepted too).
@@ -11,7 +12,6 @@
 #' list of two vectors is returned: one for the inner raster cells and the second for cells at the edge of the patch.
 #' @details The patch is created starting from the seed point and iteratively sampling randomly neighbouring cells at the edge of the patch.
 #' There is a tolerance of +/- 3 cells from the patch size declared in \code{size} argument.
-#' Note that \code{makeClass} should be used preferably when creating a single patch, as better error and exception handling is provided for there.
 #' Also, argument \code{bgr} accepts a single value only, unlike \code{makeClass} that accept multiple.
 #' @examples
 #' library(raster)