Merge pull request #186 from r-spatialecology/master

Update v1.4.5
r-spatialecology · Jul 8, 2020 · 1bdfa0d · 1bdfa0d
2 parents 8fe4b89 + c0bae69
commit 1bdfa0d
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diff --git a/.travis.yml b/.travis.yml
@@ -5,8 +5,8 @@
 # DO NOT CHANGE THE CODE BELOW
 before_install:
   - sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable --yes
-  - sudo apt-get update -qq
-  - sudo apt-get install --yes libudunits2-dev libproj-dev libgeos-dev libgdal-dev libgsl0-dev bwidget
+  - sudo apt-get --yes --force-yes update -qq
+  - sudo apt-get install --yes libudunits2-dev libproj-dev libgeos-dev libgdal-dev libgsl0-dev bwidget  
   - sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test
   - sudo apt-get -qq update
   - sudo apt-get -qq install gcc
@@ -34,7 +34,6 @@ after_script: R -q -e 'tic::after_script()'
 # Header
 language: r
 sudo: true
-dist: trusty
 cache: packages
 warnings_are_errors: false
 
@@ -47,8 +46,8 @@ env:
 notifications:
   email:
     recipients:
-      - maximilian.hesselbarth@uni-goettingen.de
-    on_success: always # default: change
+      - mhk.hesselbarth@gmail.com
+    on_success: change # default: change
     on_failure: always # default: always
 
 #services

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -23,6 +23,6 @@ Before making changes make sure to pull changes in from upstream by doing either
 * Push up to your account
 * Submit a pull request to home base at `r-spatialecology/landscapemetrics`
 
-### Questions? Get in touch: [[email protected]](mailto:[email protected]) or [maximilian.hesselbarth@uni-goettingen.de](mailto:maximilian.hesselbarth@uni-goettingen.de)
+### Questions? Get in touch: [[email protected]](mailto:[email protected]) or [mhk.hesselbarth@gmail.com](mailto:mhk.hesselbarth@gmail.com)
 
 ### Thanks for contributing!
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: landscapemetrics
 Title: Landscape Metrics for Categorical Map Patterns
-Version: 1.4.4
+Version: 1.4.5
 Authors@R: c(person("Maximillian H.K.", "Hesselbarth",
              role = c("aut", "cre"),
              email = "[email protected]",
@@ -77,6 +77,6 @@ ByteCompile: true
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.0
+RoxygenNote: 7.1.1.9000
 SystemRequirements: C++11
 VignetteBuilder: knitr
diff --git a/NAMESPACE b/NAMESPACE
@@ -32,8 +32,12 @@ S3method(get_boundaries,RasterBrick)
 S3method(get_boundaries,RasterLayer)
 S3method(get_boundaries,RasterStack)
 S3method(get_boundaries,list)
-S3method(get_boundaries,matrix)
 S3method(get_boundaries,stars)
+S3method(get_centroids,RasterBrick)
+S3method(get_centroids,RasterLayer)
+S3method(get_centroids,RasterStack)
+S3method(get_centroids,list)
+S3method(get_centroids,stars)
 S3method(get_circumscribingcircle,RasterBrick)
 S3method(get_circumscribingcircle,RasterLayer)
 S3method(get_circumscribingcircle,RasterStack)
@@ -43,7 +47,6 @@ S3method(get_nearestneighbour,RasterBrick)
 S3method(get_nearestneighbour,RasterLayer)
 S3method(get_nearestneighbour,RasterStack)
 S3method(get_nearestneighbour,list)
-S3method(get_nearestneighbour,matrix)
 S3method(get_nearestneighbour,stars)
 S3method(get_patches,RasterBrick)
 S3method(get_patches,RasterLayer)
@@ -783,6 +786,8 @@ export(data_info)
 export(extract_lsm)
 export(get_adjacencies)
 export(get_boundaries)
+export(get_boundaries_calc)
+export(get_centroids)
 export(get_circumscribingcircle)
 export(get_nearestneighbour)
 export(get_patches)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,14 @@
+# landscapemetrics 1.4.5
+* Bugfixes
+    * Fix of patch id in `get_circumscribingcircle()`
+* Improvements
+    * `lsm_p_gyrate` has an argument to force the cell centroid to be within patch
+    * `get_nearestneighbour()` can now return ID of neighbouring patch
+    * `get_boundaries()` allows now to specify edge depth
+    * `get_boundaries()` can return the patch id for edge cells
+* New gunctions
+    * `get_centroid()` returns the coordinates of each patch centroid
+
 # landscapemetrics 1.4.4
 * Improvements
     * Set labels = FALSE as default for all plotting functions (messy for larger raster)

diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -76,6 +76,10 @@ rcpp_get_entropy <- function(x, base = "log2") {
     .Call('_landscapemetrics_rcpp_get_entropy', PACKAGE = 'landscapemetrics', x, base)
 }
 
+find_min <- function(points, i, m) {
+    .Call('_landscapemetrics_find_min', PACKAGE = 'landscapemetrics', points, i, m)
+}
+
 #' @title First nearest neighbor distance
 #'
 #' @description Efficiently calculate the distance to the first nearest neighbor.

diff --git a/R/calculate_lsm.R b/R/calculate_lsm.R
@@ -5,18 +5,20 @@
 #' @param landscape Raster* Layer, Stack, Brick or a list of rasterLayers.
 #' @param level Level of metrics. Either 'patch', 'class' or 'landscape' (or vector with combination).
 #' @param metric Abbreviation of metrics (e.g. 'area').
-#' @param name Full name of metrics (e.g. 'core area')
+#' @param name Full name of metrics (e.g. 'core area').
 #' @param type Type according to FRAGSTATS grouping (e.g. 'aggregation metrics').
 #' @param what Selected level of metrics: either "patch", "class" or "landscape".
 #' It is also possible to specify functions as a vector of strings, e.g. `what = c("lsm_c_ca", "lsm_l_ta")`.
 #' @param directions The number of directions in which patches should be
 #' connected: 4 (rook's case) or 8 (queen's case).
-#' @param count_boundary Include landscape boundary in edge length
+#' @param count_boundary Include landscape boundary in edge length.
 #' @param consider_boundary Logical if cells that only neighbour the landscape
-#' boundary should be considered as core
+#' boundary should be considered as core.
 #' @param edge_depth Distance (in cells) a cell has the be away from the patch
-#' edge to be considered as core cell
-#' @param classes_max Potential maximum number of present classes
+#' edge to be considered as core cell.
+#' @param cell_center If true, the coordinates of the centroid are forced to be
+#' a cell center within the patch.
+#' @param classes_max Potential maximum number of present classes.
 #' @param neighbourhood The number of directions in which cell adjacencies are considered as neighbours:
 #' 4 (rook's case) or 8 (queen's case). The default is 4.
 #' @param ordered The type of pairs considered. Either ordered (TRUE) or unordered (FALSE).
@@ -69,6 +71,7 @@ calculate_lsm <- function(landscape,
                           count_boundary,
                           consider_boundary,
                           edge_depth,
+                          cell_center,
                           classes_max,
                           neighbourhood,
                           ordered,
@@ -89,6 +92,7 @@ calculate_lsm.RasterLayer <- function(landscape,
                                       count_boundary = FALSE,
                                       consider_boundary = FALSE,
                                       edge_depth = 1,
+                                      cell_center = FALSE,
                                       classes_max = NULL,
                                       neighbourhood = 4,
                                       ordered = TRUE,
@@ -108,6 +112,7 @@ calculate_lsm.RasterLayer <- function(landscape,
                      count_boundary = count_boundary,
                      consider_boundary = consider_boundary,
                      edge_depth = edge_depth,
+                     cell_center = cell_center,
                      classes_max = classes_max,
                      neighbourhood = neighbourhood,
                      ordered = ordered,
@@ -138,6 +143,7 @@ calculate_lsm.RasterStack <- function(landscape,
                                       count_boundary = FALSE,
                                       consider_boundary = FALSE,
                                       edge_depth = 1,
+                                      cell_center = FALSE,
                                       classes_max = NULL,
                                       neighbourhood = 4,
                                       ordered = TRUE,
@@ -165,6 +171,7 @@ calculate_lsm.RasterStack <- function(landscape,
                                count_boundary = count_boundary,
                                consider_boundary = consider_boundary,
                                edge_depth = edge_depth,
+                               cell_center = cell_center,
                                classes_max = classes_max,
                                neighbourhood = neighbourhood,
                                ordered = ordered,
@@ -198,6 +205,7 @@ calculate_lsm.RasterBrick <- function(landscape,
                                       count_boundary = FALSE,
                                       consider_boundary = FALSE,
                                       edge_depth = 1,
+                                      cell_center = FALSE,
                                       classes_max = NULL,
                                       neighbourhood = 4,
                                       ordered = TRUE,
@@ -225,6 +233,7 @@ calculate_lsm.RasterBrick <- function(landscape,
                                count_boundary = count_boundary,
                                consider_boundary = consider_boundary,
                                edge_depth = edge_depth,
+                               cell_center = cell_center,
                                classes_max = classes_max,
                                neighbourhood = neighbourhood,
                                ordered = ordered,
@@ -258,6 +267,7 @@ calculate_lsm.stars <- function(landscape,
                                 count_boundary = FALSE,
                                 consider_boundary = FALSE,
                                 edge_depth = 1,
+                                cell_center = FALSE,
                                 classes_max = NULL,
                                 neighbourhood = 4,
                                 ordered = TRUE,
@@ -285,6 +295,7 @@ calculate_lsm.stars <- function(landscape,
                                count_boundary = count_boundary,
                                consider_boundary = consider_boundary,
                                edge_depth = edge_depth,
+                               cell_center = cell_center,
                                classes_max = classes_max,
                                neighbourhood = neighbourhood,
                                ordered = ordered,
@@ -319,6 +330,7 @@ calculate_lsm.list <- function(landscape,
                                count_boundary = FALSE,
                                consider_boundary = FALSE,
                                edge_depth = 1,
+                               cell_center = FALSE,
                                classes_max = NULL,
                                neighbourhood = 4,
                                ordered = TRUE,
@@ -344,6 +356,7 @@ calculate_lsm.list <- function(landscape,
                                count_boundary = count_boundary,
                                consider_boundary = consider_boundary,
                                edge_depth = edge_depth,
+                               cell_center = cell_center,
                                classes_max = classes_max,
                                neighbourhood = neighbourhood,
                                ordered = ordered,
@@ -375,6 +388,7 @@ calculate_lsm_internal <- function(landscape,
                                    count_boundary,
                                    consider_boundary,
                                    edge_depth,
+                                   cell_center,
                                    classes_max,
                                    neighbourhood,
                                    ordered,