Merge branch 'refs/heads/master' into CRAN

r-spatialecology · Nov 7, 2019 · 23b257a · 23b257a
2 parents 113c8ef + 86a657e
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: landscapemetrics
 Title: Landscape Metrics for Categorical Map Patterns
-Version: 1.2.2
+Version: 1.3
 Authors@R: c(person("Maximillian H.K.", "Hesselbarth",
              role = c("aut", "cre"),
              email = "[email protected]",

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# landscapemetrics 1.3
+* Bugfixes
+    * Remove NAs on patch level for shape index
+
 # landscapemetrics 1.2.2
 * Bugfixes
     * Bug in `lsm_p_circle()` when whole landscape contains only one patch

diff --git a/R/lsm_c_shape_cv.R b/R/lsm_c_shape_cv.R
@@ -139,7 +139,8 @@ lsm_c_shape_cv_calc <- function(landscape, directions, resolution = NULL){
                               resolution = resolution)
 
     # calculate cv
-    shape_cv <- stats::aggregate(x = shape[, 5], by = shape[, 2], FUN = raster::cv)
+    shape_cv <- stats::aggregate(x = shape[, 5], by = shape[, 2], FUN = raster::cv,
+                                 na.rm = TRUE)
 
     tibble::tibble(
         level = "class",

diff --git a/R/lsm_c_shape_mn.R b/R/lsm_c_shape_mn.R
@@ -139,7 +139,8 @@ lsm_c_shape_mn_calc <- function(landscape, directions, resolution = NULL){
                               resolution = resolution)
 
     # calculate mean
-    shape_mn <- stats::aggregate(x = shape[, 5], by = shape[, 2], FUN = mean)
+    shape_mn <- stats::aggregate(x = shape[, 5], by = shape[, 2], FUN = mean,
+                                 na.rm = TRUE)
 
     tibble::tibble(
         level = "class",

diff --git a/R/lsm_c_shape_sd.R b/R/lsm_c_shape_sd.R
@@ -139,7 +139,8 @@ lsm_c_shape_sd_calc <- function(landscape, directions, resolution = NULL){
                               resolution = resolution)
 
     # calculate sd
-    shape_sd <- stats::aggregate(x = shape[, 5], by = shape[, 2], FUN = stats::sd)
+    shape_sd <- stats::aggregate(x = shape[, 5], by = shape[, 2], FUN = stats::sd,
+                                 na.rm = TRUE)
 
     tibble::tibble(
         level = "class",

diff --git a/R/lsm_l_shape_cv.R b/R/lsm_l_shape_cv.R
@@ -1,6 +1,6 @@
 #' SHAPE_CV (landscape level)
 #'
-#' @description Covariance of variation shape index (Shape metric)
+#' @description Coefficient of variation shape index (Shape metric)
 #'
 #' @param landscape Raster* Layer, Stack, Brick or a list of rasterLayers.
 #' @param directions The number of directions in which patches should be
@@ -139,7 +139,8 @@ lsm_l_shape_cv_calc <- function(landscape, directions, resolution = NULL){
                               resolution = resolution)
 
     # calculate cv
-    shape_cv <- raster::cv(shape$value)
+    shape_cv <- raster::cv(shape$value,
+                           na.rm = TRUE)
 
     tibble::tibble(
         level = "landscape",

diff --git a/R/lsm_l_shape_mn.R b/R/lsm_l_shape_mn.R
@@ -139,7 +139,7 @@ lsm_l_shape_mn_calc <- function(landscape, directions, resolution = NULL){
                               resolution = resolution)
 
     # calculate mean
-    shape_mn <- mean(shape$value)
+    shape_mn <- mean(shape$value, na.rm = TRUE)
 
     tibble::tibble(
         level = "landscape",

diff --git a/R/lsm_l_shape_sd.R b/R/lsm_l_shape_sd.R
@@ -139,7 +139,7 @@ lsm_l_shape_sd_calc <- function(landscape, directions, resolution = NULL){
                               resolution = resolution)
 
     # calculate sd
-    shape_sd <- stats::sd(shape$value)
+    shape_sd <- stats::sd(shape$value, na.rm = TRUE)
 
     tibble::tibble(
         level = "landscape",

diff --git a/R/lsm_p_shape.R b/R/lsm_p_shape.R
@@ -135,7 +135,7 @@ lsm_p_shape.list <- function(landscape, directions = 8) {
 lsm_p_shape_calc <- function(landscape, directions, resolution = NULL){
 
     # convert to matrix
-    if (class(landscape) != "matrix"){
+    if (class(landscape) != "matrix") {
         resolution <- raster::res(landscape)
         landscape <- raster::as.matrix(landscape)
     }
@@ -157,16 +157,20 @@ lsm_p_shape_calc <- function(landscape, directions, resolution = NULL){
 
     area_patch$m <- area_patch$value - area_patch$n ^ 2
 
+    # m should be 0 but is not due to some integer/double numerical issues
+    area_patch$m[area_patch$m < 0] <- 0
+
     area_patch$minp <- ifelse(test = area_patch$m == 0, yes = area_patch$n * 4,
                               no = ifelse(test = area_patch$n ^ 2 < area_patch$value & area_patch$value <= area_patch$n * (1 + area_patch$n),
                                           yes = 4 * area_patch$n + 2,
                                           no = ifelse(test = area_patch$value > area_patch$n * (1 + area_patch$n),
                                                       yes = 4 * area_patch$n + 4,
                                                       no = NA)))
-    # Throw warning that ifelse didn't work
-    if(anyNA(area_patch$minp)) {
-        warning("Calculation of shape index produced NA", call. = FALSE)
-    }
+    # this should not be possible anymore
+    # # Throw warning that ifelse didn't work
+    # if (anyNA(area_patch$minp)) {
+    #     warning("Calculation of shape index produced NA", call. = FALSE)
+    # }
 
     tibble::tibble(
         level = "patch",

diff --git a/README.Rmd b/README.Rmd
@@ -33,6 +33,16 @@ status](https://codecov.io/gh/r-spatialecology/landscapemetrics/branch/master/gr
 
 **landscapemetrics** supports `raster` spatial objects and takes `RasterLayer`, `RasterStacks`, `RasterBricks` or lists of `RasterLayer` as input arguments. Every function can be used in a piped workflow, as it always takes the data as the first argument and returns a tibble. 
 
+### Citation
+
+To cite `landscapemetrics` or acknowledge its use, please cite the
+following Software note, substituting the version of the application
+that you used for ‘version 0’: Hesselbarth, M.H.K., Sciaini, M., With,
+K.A., Wiegand, K., Nowosad, J. 2019. landscapemetrics: an open-source R
+tool to calculate landscape metrics. - Ecography 42:1648-1657 (ver. 0). 
+
+For more information see [Publication record](https://r-spatialecology.github.io/landscapemetrics/articles/articles/publication_record.html) vignette. The get a BibTex entry, please use `citation("landscapemetrics")`.
+
 ## Installation
 
 There are several ways to install **landscapemetrics**:
@@ -123,10 +133,6 @@ One of the major motivations behind **landscapemetrics** is the idea to provide
 
 Maintainers and contributors must follow this repository’s [CODE OF CONDUCT](CODE_OF_CONDUCT.md).
 
-### Citation
-
-To cite `landscapemetrics` or acknowledge its use, please cite the following Software note, substituting the version of the application that you used for ‘version 0’: Hesselbarth, M.H.K., Sciaini, M., With, K.A., Wiegand, K., Nowosad, J. 2019. landscapemetrics: an open-source R tool to calculate landscape metrics. - Ecography 42:1-10 (ver. 0). For more information see [Publication record](https://r-spatialecology.github.io/landscapemetrics/articles/articles/publication_record.html) vignette.
-
 ### References
 
 - McGarigal, K., Cushman, S.A., and Ene E. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for Categorical and Continuous Maps. Computer software program produced by the authors at the University of Massachusetts, Amherst. Available at the following website: <http://www.umass.edu/landeco/research/fragstats/fragstats.html>

diff --git a/README.md b/README.md
@@ -35,6 +35,19 @@ Stepinski 2019).
 as input arguments. Every function can be used in a piped workflow, as
 it always takes the data as the first argument and returns a tibble.
 
+### Citation
+
+To cite `landscapemetrics` or acknowledge its use, please cite the
+following Software note, substituting the version of the application
+that you used for ‘version 0’: Hesselbarth, M.H.K., Sciaini, M., With,
+K.A., Wiegand, K., Nowosad, J. 2019. landscapemetrics: an open-source R
+tool to calculate landscape metrics. - Ecography 42:1648-1657 (ver. 0).
+
+For more information see [Publication
+record](https://r-spatialecology.github.io/landscapemetrics/articles/articles/publication_record.html)
+vignette. The get a BibTex entry, please use
+`citation("landscapemetrics")`.
+
 ## Installation
 
 There are several ways to install **landscapemetrics**:
@@ -124,7 +137,7 @@ lsm_p_enn(landscape)
 #>  8     1 patch     1     8 enn     2   
 #>  9     1 patch     1     9 enn     4.12
 #> 10     1 patch     2    10 enn     4.47
-#> # ... with 17 more rows
+#> # … with 17 more rows
 
 # calculate the total area and total class edge length
 lsm_l_ta(landscape)
@@ -161,13 +174,13 @@ calculate_lsm(landscape, level = "patch")
 #>  8     1 patch     1     8 area   0.0001
 #>  9     1 patch     1     9 area   0.0003
 #> 10     1 patch     2    10 area   0.0035
-#> # ... with 314 more rows
+#> # … with 314 more rows
 ```
 
 ### Utility functions
 
 **landscapemetrics** further provides several visualization functions,
-e.g. show all labeld patches or the core area of all patches. All
+e.g. show all labeled patches or the core area of all patches. All
 visualization functions start with the prefix `show_`
 (e.g. `show_cores()`).
 
@@ -193,17 +206,6 @@ warmly welcome to do so\! For more information see
 Maintainers and contributors must follow this repository’s [CODE OF
 CONDUCT](CODE_OF_CONDUCT.md).
 
-### Citation
-
-To cite `landscapemetrics` or acknowledge its use, please cite the
-following Software note, substituting the version of the application
-that you used for ‘version 0’: Hesselbarth, M.H.K., Sciaini, M., With,
-K.A., Wiegand, K., Nowosad, J. 2019. landscapemetrics: an open-source R
-tool to calculate landscape metrics. - Ecography 42:1-10 (ver. 0). For
-more information see [Publication
-record](https://r-spatialecology.github.io/landscapemetrics/articles/articles/publication_record.html)
-vignette.
-
 ### References
 
   - McGarigal, K., Cushman, S.A., and Ene E. 2012. FRAGSTATS v4: Spatial

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,3 +1,6 @@
+## Update Version: 1.3
+Minor bugfixes
+
 ## Update Version: 1.2.2
 Small bugfixes and improvments of existing functions
 

diff --git a/inst/CITATION b/inst/CITATION
@@ -11,5 +11,5 @@ citEntry(
     journal = {"Ecography"},
 	volume = {"42"},
 	year = {"2019"},
-	pages = {"1-10"},
-  textVersion  = "Hesselbarth, M.H.K., Sciaini, M., With, K.A., Wiegand, K., Nowosad, J. 2019. landscapemetrics: an open-source R tool to calculate landscape metrics. - Ecography 42:1-10 (ver. 0).")
+	pages = {"1648-1657"},
+  textVersion  = "Hesselbarth, M.H.K., Sciaini, M., With, K.A., Wiegand, K., Nowosad, J. 2019. landscapemetrics: an open-source R tool to calculate landscape metrics. - Ecography 42:1648-1657(ver. 0).")
diff --git a/man/figures/README-unnamed-chunk-1-1.png b/man/figures/README-unnamed-chunk-1-1.png
diff --git a/man/lsm_l_shape_cv.Rd b/man/lsm_l_shape_cv.Rd
diff --git a/vignettes/articles/publication_record.Rmd b/vignettes/articles/publication_record.Rmd
@@ -8,7 +8,7 @@ output:
 
 We try to maintain a list of publications that have used the `landscapemetrics` package. If you have used `landscapemetrics` in your own work, we would love to hear from you. Please [file an issue on GitHub](https://github.com/r-spatialecology/landscapemetrics/issues/new/) so we can add your work to this list.
 
-To cite `landscapemetrics` or acknowledge its use, please cite the following Software note, substituting the version of the application that you used for ‘version 0’: Hesselbarth, M.H.K., Sciaini, M., With, K.A., Wiegand, K., Nowosad, J. 2019. landscapemetrics: an open-source R tool to calculate landscape metrics. - Ecography 42:1-10 (ver. 0).
+To cite `landscapemetrics` or acknowledge its use, please cite the following Software note, substituting the version of the application that you used for ‘version 0’: Hesselbarth, M.H.K., Sciaini, M., With, K.A., Wiegand, K., Nowosad, J. 2019. landscapemetrics: an open-source R tool to calculate landscape metrics. - Ecography 42:1648-1657 (ver. 0).
 
 ## A list of publications