Merge pull request #221 from r-spatialecology/main

v1.5.2
r-spatialecology · Feb 4, 2021 · 3b32508 · 3b32508
2 parents ac0a002 + d438017
commit 3b32508
Show file tree

Hide file tree

Showing 18 changed files with 139 additions and 115 deletions.
diff --git a/.github/workflows/Deploy-pkgdown.yaml b/.github/workflows/Deploy-pkgdown.yaml
@@ -2,7 +2,7 @@ on:
   push:
     branches:
       - CRAN
-      - master
+      - main
 
 name: Deploy-pkgdown
 
@@ -13,11 +13,14 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
-
       - uses: r-lib/actions/setup-r@v1
-
       - uses: r-lib/actions/setup-pandoc@v1
 
+      - name: Setup R
+        uses: r-lib/actions/setup-r@master
+        with:
+          crayon.enabled: 'FALSE'
+
       - name: Query dependencies
         run: |
           install.packages('remotes')

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -4,16 +4,17 @@ on:
   push:
     branches:
       - CRAN
-      - master
+      - main
   pull_request:
     branches:
       - CRAN
-      - master
+      - main
 
 name: R-CMD-check
 
 jobs:
   R-CMD-check:
+    if: "!contains(github.event.commits[0].message, '[skip-ci]')"
     runs-on: ${{ matrix.config.os }}
 
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})

diff --git a/.github/workflows/Render-README.yaml b/.github/workflows/Render-README.yaml
@@ -15,15 +15,23 @@ jobs:
       - uses: actions/checkout@v2
       - uses: r-lib/actions/setup-r@v1
       - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@master
+        with:
+          crayon.enabled: 'FALSE'
+
       - name: Install rmarkdown, remotes, and the local package
         run: |
           install.packages("remotes")
           remotes::install_local(".")
           remotes::install_cran("rmarkdown")
           remotes::install_cran("landscapetools")
         shell: Rscript {0}
+
       - name: Render README
         run: Rscript -e 'rmarkdown::render("README.Rmd")'
+
       - name: Commit results
         run: |
           git config --local user.email "[email protected]"

diff --git a/.github/workflows/Test-coverage.yaml b/.github/workflows/Test-coverage.yaml
@@ -2,16 +2,17 @@ on:
   push:
     branches:
       - CRAN
-      - master
+      - main
   pull_request:
     branches:
       - CRAN
-      - master
+      - main
 
 name: Test-coverage
 
 jobs:
   test-coverage:
+    if: "!contains(github.event.commits[0].message, '[skip-ci]')"
     runs-on: macOS-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -21,7 +21,7 @@ Before making any changes, make sure to pull changes in from upstream by either
 4. Make your changes (bonus points for making changes on a new branch)
 5. If you alter package functionality at all (e.g., the code itself, not just documentation) please do write some tests to cover the new functionality.
 6. Push changes to your account
-7. Submit a pull request to the master branch at `r-spatialecology/landscapemetrics`
+7. Submit a pull request to the main branch at `r-spatialecology/landscapemetrics`
 
 ### Questions? Get in touch: [[email protected]](mailto:[email protected]) or [[email protected]](mailto:[email protected])
 

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: landscapemetrics
 Title: Landscape Metrics for Categorical Map Patterns
-Version: 1.5.1
+Version: 1.5.2
 Authors@R: c(person("Maximillian H.K.", "Hesselbarth",
              role = c("aut", "cre"),
              email = "[email protected]",

diff --git a/NEWS.md b/NEWS.md
@@ -1,8 +1,14 @@
+# landscapemetrics 1.5.2
+* Bugfixes
+    * Bug in `lsm_l_ai` if class with only one cell exists
+* Various
+    * Renamed master to main branch
+
 # landscapemetrics 1.5.1
 * Improvements
     * Use GitHub actions
 * Bugfixes
- * Bug in `lsm_c_lsi`, `lsm_c_nlsi`, `lsm_l_lsi` not using cell surfaces
+    * Bug in `lsm_c_lsi`, `lsm_c_nlsi`, `lsm_l_lsi` not using cell surfaces
 
 # landscapemetrics 1.5.0
 * Improvements
@@ -23,7 +29,7 @@
     * `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
+* New functions
     * `get_centroid()` returns the coordinates of each patch centroid
 
 # landscapemetrics 1.4.4

diff --git a/R/lsm_c_ai.R b/R/lsm_c_ai.R
@@ -103,7 +103,7 @@ lsm_c_ai_calc <- function(landscape) {
     # calculate aggregation index
     ai <- (like_adjacencies / max_adj) * 100
 
-    # if NaN (mathematical reason) set to NA
+    # max_adj can be zero if only one cell is present; set to NA
     ai[is.nan(ai)] <- NA
 
     return(tibble::tibble(level = "class",

diff --git a/R/lsm_l_ai.R b/R/lsm_l_ai.R
@@ -14,7 +14,7 @@
 #' AI is an 'Aggregation metric'. It equals the number of like adjacencies divided
 #' by the theoretical maximum possible number of like adjacencies for that class summed over each
 #' class for the entire landscape.
-#' The metric is based on he adjacency matrix and the the single-count method.
+#' The metric is based on he adjacency matrix and the single-count method.
 #'
 #' \subsection{Units}{Percent}
 #' \subsection{Range}{0 <= AI <= 100}
@@ -82,7 +82,7 @@ lsm_l_ai_calc <- function(landscape, resolution = NULL) {
                               resolution = resolution)
 
     # final AI index
-    result <- sum(ai$value * (pland$value / 100))
+    result <- sum(ai$value * (pland$value / 100), na.rm = TRUE)
 
     return(tibble::tibble(level = "landscape",
                           class = as.integer(NA),

diff --git a/README.Rmd b/README.Rmd
@@ -2,13 +2,15 @@
 output:
   github_document:
     html_preview: false
+editor_options: 
+  chunk_output_type: console
 ---
 
 ```{r setup, include = FALSE}
 knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>",
-  fig.path = "man/figures/REAsDME-",
+  fig.path = "man/figures/README-",
   out.width = "100%"
 )
 ```
@@ -18,7 +20,7 @@ knitr::opts_chunk$set(
 | Continuous Integration | Development | CRAN | License |
 |-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------|
 | ![R-CMD-check](https://github.com/r-spatialecology/landscapemetrics/workflows/R-CMD-check/badge.svg) | [![lifecycle](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable) | [![CRAN status](https://www.r-pkg.org/badges/version/landscapemetrics)](https://cran.r-project.org/package=landscapemetrics) | [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) |
-| [![Coverage](https://codecov.io/gh/r-spatialecology/landscapemetrics/branch/master/graph/badge.svg)](https://codecov.io/github/r-spatialecology/landscapemetrics?branch=master) | [![Project Status](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) | [![CRAN downloads](http://cranlogs.r-pkg.org/badges/grand-total/landscapemetrics)](http://cran.rstudio.com/web/packages/landscapemetrics/index.html) | [![DOI](https://img.shields.io/badge/DOI-10.1111/ecog.04617-blue.svg)](https://doi.org/10.1111/ecog.04617) |
+| [![Coverage](https://codecov.io/gh/r-spatialecology/landscapemetrics/branch/main/graph/badge.svg)](https://codecov.io/github/r-spatialecology/landscapemetrics?branch=main) | [![Project Status](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) | [![CRAN downloads](http://cranlogs.r-pkg.org/badges/grand-total/landscapemetrics)](http://cran.rstudio.com/web/packages/landscapemetrics/index.html) | [![DOI](https://img.shields.io/badge/DOI-10.1111/ecog.04617-blue.svg)](https://doi.org/10.1111/ecog.04617) |
 
 # landscapemetrics <img src="man/figures/logo.png" align="right" width="150" />
 
@@ -45,13 +47,13 @@ For more information see [Publication record](https://r-spatialecology.github.io
 
 There are several ways to install **landscapemetrics**:
 
-```r
+```{r, eval = FALSE, echo = TRUE}
 # Get the stable version from CRAN
 install.packages("landscapemetrics")
 
 # Alternatively, you can install the development version from Github
-# install.packages("devtools")
-devtools::install_github("r-spatialecology/landscapemetrics")
+# install.packages("remotes")
+remotes::install_github("r-spatialecology/landscapemetrics")
 ```
 
 #### Announcement
@@ -92,7 +94,7 @@ All functions return an identical structured tibble:
 
 Every function follows the same implementation design, so the usage is quite straightforward:
 
-```{r, message=FALSE, warning=FALSE}
+```{r, message = FALSE, warning = FALSE}
 library(landscapemetrics)
 library(landscapetools)
 
@@ -109,7 +111,7 @@ lsm_c_te(landscape)
 
 There is also a wrapper around every metric in the package to quickly calculate a bunch of metrics:
 
-```{r, message=FALSE}
+```{r, message = FALSE}
 # calculate all metrics on patch level
 calculate_lsm(landscape, level = "patch")
 ```

diff --git a/README.md b/README.md
@@ -1,10 +1,10 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-| Continuous Integration                                                                                                                                                          | Development                                                                                                                | CRAN                                                                                                                                                 | License                                                                                                         |
-| ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------- |
-| ![R-CMD-check](https://github.com/r-spatialecology/landscapemetrics/workflows/R-CMD-check/badge.svg)                                                                            | [![lifecycle](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable) | [![CRAN status](https://www.r-pkg.org/badges/version/landscapemetrics)](https://cran.r-project.org/package=landscapemetrics)                         | [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) |
-| [![Coverage](https://codecov.io/gh/r-spatialecology/landscapemetrics/branch/master/graph/badge.svg)](https://codecov.io/github/r-spatialecology/landscapemetrics?branch=master) | [![Project Status](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)                 | [![CRAN downloads](http://cranlogs.r-pkg.org/badges/grand-total/landscapemetrics)](http://cran.rstudio.com/web/packages/landscapemetrics/index.html) | [![DOI](https://img.shields.io/badge/DOI-10.1111/ecog.04617-blue.svg)](https://doi.org/10.1111/ecog.04617)      |
+| Continuous Integration                                                                                                                                                      | Development                                                                                                                | CRAN                                                                                                                                                 | License                                                                                                         |
+| --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------- |
+| ![R-CMD-check](https://github.com/r-spatialecology/landscapemetrics/workflows/R-CMD-check/badge.svg)                                                                        | [![lifecycle](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable) | [![CRAN status](https://www.r-pkg.org/badges/version/landscapemetrics)](https://cran.r-project.org/package=landscapemetrics)                         | [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) |
+| [![Coverage](https://codecov.io/gh/r-spatialecology/landscapemetrics/branch/main/graph/badge.svg)](https://codecov.io/github/r-spatialecology/landscapemetrics?branch=main) | [![Project Status](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)                 | [![CRAN downloads](http://cranlogs.r-pkg.org/badges/grand-total/landscapemetrics)](http://cran.rstudio.com/web/packages/landscapemetrics/index.html) | [![DOI](https://img.shields.io/badge/DOI-10.1111/ecog.04617-blue.svg)](https://doi.org/10.1111/ecog.04617)      |
 
 # landscapemetrics <img src="man/figures/logo.png" align="right" width="150" />
 
@@ -52,8 +52,8 @@ There are several ways to install **landscapemetrics**:
 install.packages("landscapemetrics")
 
 # Alternatively, you can install the development version from Github
-# install.packages("devtools")
-devtools::install_github("r-spatialecology/landscapemetrics")
+# install.packages("remotes")
+remotes::install_github("r-spatialecology/landscapemetrics")
 ```
 
 #### Announcement
@@ -113,40 +113,40 @@ library(landscapetools)
 show_landscape(landscape)
 ```
 
-<img src="man/figures/REAsDME-unnamed-chunk-1-1.png" width="100%" />
+<img src="man/figures/README-unnamed-chunk-2-1.png" width="100%" />
 
 ``` r
 
 # calculate for example the Euclidean nearest-neighbor distance on patch level
 lsm_p_enn(landscape)
-#> [90m# A tibble: 27 x 6[39m
+#> # A tibble: 27 x 6
 #>    layer level class    id metric value
-#>    [3m[90m<int>[39m[23m [3m[90m<chr>[39m[23m [3m[90m<int>[39m[23m [3m[90m<int>[39m[23m [3m[90m<chr>[39m[23m  [3m[90m<dbl>[39m[23m
-#> [90m 1[39m     1 patch     1     1 enn     7   
-#> [90m 2[39m     1 patch     1     2 enn     4   
-#> [90m 3[39m     1 patch     1     3 enn     2.83
-#> [90m 4[39m     1 patch     1     4 enn     2   
-#> [90m 5[39m     1 patch     1     5 enn     2   
-#> [90m 6[39m     1 patch     1     6 enn     2.83
-#> [90m 7[39m     1 patch     1     7 enn     4.12
-#> [90m 8[39m     1 patch     1     8 enn     4.12
-#> [90m 9[39m     1 patch     1     9 enn     4.24
-#> [90m10[39m     1 patch     2    10 enn     4.47
-#> [90m# … with 17 more rows[39m
+#>    <int> <chr> <int> <int> <chr>  <dbl>
+#>  1     1 patch     1     1 enn     7   
+#>  2     1 patch     1     2 enn     4   
+#>  3     1 patch     1     3 enn     2.83
+#>  4     1 patch     1     4 enn     2   
+#>  5     1 patch     1     5 enn     2   
+#>  6     1 patch     1     6 enn     2.83
+#>  7     1 patch     1     7 enn     4.12
+#>  8     1 patch     1     8 enn     4.12
+#>  9     1 patch     1     9 enn     4.24
+#> 10     1 patch     2    10 enn     4.47
+#> # … with 17 more rows
 
 # calculate the total area and total class edge length
 lsm_l_ta(landscape)
-#> [90m# A tibble: 1 x 6[39m
+#> # A tibble: 1 x 6
 #>   layer level     class    id metric value
-#>   [3m[90m<int>[39m[23m [3m[90m<chr>[39m[23m     [3m[90m<int>[39m[23m [3m[90m<int>[39m[23m [3m[90m<chr>[39m[23m  [3m[90m<dbl>[39m[23m
-#> [90m1[39m     1 landscape    [31mNA[39m    [31mNA[39m ta      0.09
+#>   <int> <chr>     <int> <int> <chr>  <dbl>
+#> 1     1 landscape    NA    NA ta      0.09
 lsm_c_te(landscape)
-#> [90m# A tibble: 3 x 6[39m
+#> # A tibble: 3 x 6
 #>   layer level class    id metric value
-#>   [3m[90m<int>[39m[23m [3m[90m<chr>[39m[23m [3m[90m<int>[39m[23m [3m[90m<int>[39m[23m [3m[90m<chr>[39m[23m  [3m[90m<dbl>[39m[23m
-#> [90m1[39m     1 class     1    [31mNA[39m te       180
-#> [90m2[39m     1 class     2    [31mNA[39m te       227
-#> [90m3[39m     1 class     3    [31mNA[39m te       321
+#>   <int> <chr> <int> <int> <chr>  <dbl>
+#> 1     1 class     1    NA te       180
+#> 2     1 class     2    NA te       227
+#> 3     1 class     3    NA te       321
 ```
 
 There is also a wrapper around every metric in the package to quickly
@@ -156,20 +156,20 @@ calculate a bunch of metrics:
 # calculate all metrics on patch level
 calculate_lsm(landscape, level = "patch")
 #> Warning: Please use 'check_landscape()' to ensure the input data is valid.
-#> [90m# A tibble: 324 x 6[39m
+#> # A tibble: 324 x 6
 #>    layer level class    id metric  value
-#>    [3m[90m<int>[39m[23m [3m[90m<chr>[39m[23m [3m[90m<int>[39m[23m [3m[90m<int>[39m[23m [3m[90m<chr>[39m[23m   [3m[90m<dbl>[39m[23m
-#> [90m 1[39m     1 patch     1     1 area   0.000[4m1[24m
-#> [90m 2[39m     1 patch     1     2 area   0.000[4m5[24m
-#> [90m 3[39m     1 patch     1     3 area   0.014[4m8[24m
-#> [90m 4[39m     1 patch     1     4 area   0.000[4m1[24m
-#> [90m 5[39m     1 patch     1     5 area   0.000[4m1[24m
-#> [90m 6[39m     1 patch     1     6 area   0.001[4m4[24m
-#> [90m 7[39m     1 patch     1     7 area   0.000[4m3[24m
-#> [90m 8[39m     1 patch     1     8 area   0.000[4m5[24m
-#> [90m 9[39m     1 patch     1     9 area   0.000[4m1[24m
-#> [90m10[39m     1 patch     2    10 area   0.003[4m5[24m
-#> [90m# … with 314 more rows[39m
+#>    <int> <chr> <int> <int> <chr>   <dbl>
+#>  1     1 patch     1     1 area   0.0001
+#>  2     1 patch     1     2 area   0.0005
+#>  3     1 patch     1     3 area   0.0148
+#>  4     1 patch     1     4 area   0.0001
+#>  5     1 patch     1     5 area   0.0001
+#>  6     1 patch     1     6 area   0.0014
+#>  7     1 patch     1     7 area   0.0003
+#>  8     1 patch     1     8 area   0.0005
+#>  9     1 patch     1     9 area   0.0001
+#> 10     1 patch     2    10 area   0.0035
+#> # … with 314 more rows
 ```
 
 ### Utility functions