fix #68, fix #69 (#70)

* fix #68, fix #69 * slightly improve tests
prioritizr · Jul 16, 2023 · 506c420 · 506c420
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: wdpar
 Type: Package
-Version: 1.3.4
+Version: 1.3.5
 Title: Interface to the World Database on Protected Areas
 Description: Fetch and clean data from the World Database on Protected
     Areas (WDPA) and the World Database on Other Effective Area-Based
@@ -13,7 +13,6 @@ Authors@R: c(person(c('Jeffrey', 'O'), 'Hanson',
     email='jeffrey.hanson@uqconnect.edu.au', role = c('aut', 'cre')))
 Imports:
     utils,
-    sp,
     assertthat (>= 0.2.0),
     progress (>= 1.2.0),
     curl (>= 3.2),
@@ -39,7 +38,7 @@ Suggests:
     ps (>= 1.5.0)
 Depends:
     R (>= 3.5.0),
-    sf (>= 1.0-2)
+    sf (>= 1.0-13)
 License: GPL-3
 Encoding: UTF-8
 Language: en-US

diff --git a/NAMESPACE b/NAMESPACE
@@ -9,3 +9,4 @@ export(wdpa_latest_version)
 export(wdpa_read)
 export(wdpa_url)
 import(sf)
+importFrom(rappdirs,user_data_dir)
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,10 @@
+# wdpar 1.3.5
+
+- CRAN release.
+- Fix compatibility issues with Protected Planet (#69).
+- Upate `wdpa_clean()` to be more robust (#68).
+- Remove _sp_ package as dependency.
+
 # wdpar 1.3.4
 
 - CRAN release.

diff --git a/R/internal.R b/R/internal.R
@@ -92,12 +92,6 @@ extract_polygons_and_points <- function(x) {
   rbind(o, x[ind, , drop = FALSE])
 }
 
-# define dummy function to avoid CRAN notes for dependencies
-import_deps <- function() {
-  x <- rappdirs::user_data_dir
-  x <- sp::spTransform
-}
-
 # Empty WDPA data set
 #'
 #' This function creates an empty WDPA dataset.

diff --git a/R/package.R b/R/package.R
@@ -35,3 +35,7 @@ NULL
 
 #' @import sf
 NULL
+
+# avoid false positive NOTEs during CRAN checks
+#' @importFrom rappdirs user_data_dir
+NULL
diff --git a/R/st_erase_overlaps.R b/R/st_erase_overlaps.R
@@ -60,37 +60,54 @@ st_erase_overlaps <- function(x, verbose = FALSE) {
     if (length(ovr) > 0) {
       ## create union
       ### run union
-      u <- sf::st_union(sf::st_set_precision(
-        suppressWarnings(sf::st_collection_extract(sf::st_buffer(o[ovr], 0))),
-        precision))
+      u <- sf::st_union(
+        sf::st_set_precision(
+          suppressWarnings(sf::st_collection_extract(sf::st_buffer(o[ovr], 0))),
+          precision
+        )
+      )
       ### buffer the union to fix any geometry issues
       u <- sf::st_buffer(u, dist = 0)
       ### repair the geometry if there are any issues
       if (!all(sf::st_is_valid(u))) {
         #nocov start
-        u <- suppressWarnings(sf::st_collection_extract(
-          sf::st_make_valid(sf::st_set_precision(u, precision)),
-          "POLYGON"))
+        u <- suppressWarnings(
+          sf::st_collection_extract(
+            sf::st_make_valid(sf::st_set_precision(u, precision)),
+            "POLYGON"
+          )
+        )
         #nocov end
       }
       ## calculate difference
       ### run difference
       d <- sf::st_difference(
-        suppressWarnings(sf::st_collection_extract(
-          sf::st_make_valid(sf::st_set_precision(g[i], precision)),
-          "POLYGON")),
-        suppressWarnings(sf::st_collection_extract(
-          sf::st_make_valid(sf::st_set_precision(u, precision)),
-          "POLYGON")))
-      if (length(d) == 0L)
-        d[[1]] <- sf::st_polygon() #nocov
+        suppressWarnings(
+          sf::st_collection_extract(
+            sf::st_make_valid(sf::st_set_precision(g[i], precision)),
+            "POLYGON"
+          )
+        ),
+        suppressWarnings(
+          sf::st_collection_extract(
+            sf::st_make_valid(sf::st_set_precision(u, precision)),
+            "POLYGON"
+          )
+        )
+      )
+      if (length(d) == 0L) {
+        d <- sf::st_sfc(sf::st_geometrycollection(), crs = sf::st_crs(d)) #nocov
+      }
       d <- suppressWarnings(sf::st_collection_extract(d, "POLYGON"))
       ### repair the geometry if there are any issues
       if (!all(sf::st_is_valid(d))) {
         #nocov start
-        d <- suppressWarnings(sf::st_collection_extract(
-          sf::st_make_valid(sf::st_set_precision(d, precision)),
-          "POLYGON"))
+        d <- suppressWarnings(
+          sf::st_collection_extract(
+            sf::st_make_valid(sf::st_set_precision(d, precision)),
+            "POLYGON"
+          )
+        )
         #nocov end
       }
     } else {
@@ -106,16 +123,19 @@ st_erase_overlaps <- function(x, verbose = FALSE) {
       d <- d[as.numeric(sf::st_area(d)) > 1]
       d <- sf::st_cast(d, "MULTIPOLYGON")
       if (length(d) == 0) {
-        d[[1]] <- sf::st_polygon() #nocov
+        d <- sf::st_sfc(sf::st_geometrycollection(), crs = sf::st_crs(d)) #nocov
       }
       d <- suppressWarnings(sf::st_collection_extract(d, "POLYGON"))
     }
     ## if d contains multiple geometries, then union them
     if (length(d) > 1) {
       d <- sf::st_union(d)
-      d <- suppressWarnings(sf::st_collection_extract(
-        sf::st_make_valid(sf::st_set_precision(d, precision)),
-        "POLYGON"))
+      d <- suppressWarnings(
+        sf::st_collection_extract(
+          sf::st_make_valid(sf::st_set_precision(d, precision)),
+          "POLYGON"
+        )
+      )
     }
     ## create empty geometry if empty
     if (length(d) == 0) {

diff --git a/R/wdpa_url.R b/R/wdpa_url.R
@@ -79,7 +79,7 @@ wdpa_url <- function(x, wait = FALSE, page_wait = 2) {
       pjs <- start_phantomjs()
       rd <- webdriver::Session$new(port = pjs$port)
       ## navigate to download web page
-      rd$go(paste0("https://protectedplanet.net/country/", x))
+      rd$go(paste0("https://www.protectedplanet.net/country/", x))
       Sys.sleep(page_wait) # wait for page to load
       elem <- rd$findElement(css = ".download__trigger")
       elem$click()

diff --git a/README.md b/README.md
@@ -181,24 +181,24 @@ head(mlt_pa_data)
     ## Geometry type: MULTIPOLYGON
     ## Dimension:     XY
     ## Bounding box:  xmin: 1382584 ymin: 4280853 xmax: 1399759 ymax: 4299615
-    ## CRS:           +proj=cea +lon_0=0 +lat_ts=30 +x_0=0 +y_0=0 +datum=WGS84 +ellps=WGS84 +units=m +no_defs
+    ## Projected CRS: +proj=cea +lon_0=0 +lat_ts=30 +x_0=0 +y_0=0 +datum=WGS84 +ellps=WGS84 +units=m +no_defs
     ## Precision:     1500 
     ## # A tibble: 6 × 33
-    ##      WDPAID WDPA_PID  PA_DEF NAME  ORIG_…¹ DESIG DESIG…² DESIG…³ IUCN_…⁴ INT_C…⁵
-    ##       <dbl> <chr>     <chr>  <chr> <chr>   <chr> <chr>   <chr>   <chr>   <chr>  
-    ## 1    194425 194425    PA     'Il-… 'Il-Gż… Rise… Nature… Nation… Ia      Not Ap…
-    ## 2    194420 194420    PA     Filf… Filfla  Rise… Nature… Nation… Ia      Not Ap…
-    ## 3 555588631 555588631 PA     Il-M… Il-Maj… Park… Nation… Nation… II      Not Ap…
-    ## 4    174757 174757    PA     Il-Ġ… Il-Ġon… List… List o… Nation… III     Not Ap…
-    ## 5    174758 174758    PA     Bidn… Bidnij… List… List o… Nation… III     Not Ap…
-    ## 6    194415 194415    PA     'Il-… 'Il-Ġo… List… List o… Nation… III     Not Ap…
-    ## # … with 23 more variables: MARINE <chr>, REP_M_AREA <dbl>, GIS_M_AREA <dbl>,
-    ## #   REP_AREA <dbl>, GIS_AREA <dbl>, NO_TAKE <chr>, NO_TK_AREA <dbl>,
-    ## #   STATUS <chr>, STATUS_YR <dbl>, GOV_TYPE <chr>, OWN_TYPE <chr>,
-    ## #   MANG_AUTH <chr>, MANG_PLAN <chr>, VERIF <chr>, METADATAID <int>,
-    ## #   SUB_LOC <chr>, PARENT_ISO <chr>, ISO3 <chr>, SUPP_INFO <chr>,
-    ## #   CONS_OBJ <chr>, GEOMETRY_TYPE <chr>, AREA_KM2 <dbl>,
-    ## #   geometry <MULTIPOLYGON [m]>, and abbreviated variable names ¹ORIG_NAME, …
+    ##      WDPAID WDPA_PID  PA_DEF NAME  ORIG_NAME DESIG DESIG_ENG DESIG_TYPE IUCN_CAT
+    ##       <dbl> <chr>     <chr>  <chr> <chr>     <chr> <chr>     <chr>      <chr>   
+    ## 1    194425 194425    PA     'Il-… 'Il-Gżej… Rise… Nature R… National   Ia      
+    ## 2    194420 194420    PA     Filf… Filfla    Rise… Nature R… National   Ia      
+    ## 3 555588631 555588631 PA     Il-M… Il-Majji… Park… National… National   II      
+    ## 4    174757 174757    PA     Il-Ġ… Il-Ġonna… List… List of … National   III     
+    ## 5    174758 174758    PA     Bidn… Bidnija,… List… List of … National   III     
+    ## 6    194415 194415    PA     'Il-… 'Il-Ġonn… List… List of … National   III     
+    ## # ℹ 24 more variables: INT_CRIT <chr>, MARINE <chr>, REP_M_AREA <dbl>,
+    ## #   GIS_M_AREA <dbl>, REP_AREA <dbl>, GIS_AREA <dbl>, NO_TAKE <chr>,
+    ## #   NO_TK_AREA <dbl>, STATUS <chr>, STATUS_YR <dbl>, GOV_TYPE <chr>,
+    ## #   OWN_TYPE <chr>, MANG_AUTH <chr>, MANG_PLAN <chr>, VERIF <chr>,
+    ## #   METADATAID <int>, SUB_LOC <chr>, PARENT_ISO <chr>, ISO3 <chr>,
+    ## #   SUPP_INFO <chr>, CONS_OBJ <chr>, GEOMETRY_TYPE <chr>, AREA_KM2 <dbl>,
+    ## #   geometry <MULTIPOLYGON [m]>
 
 Finally, after cleaning the data, let’s plot a map showing Malta’s
 protected areas and color each area according to its management category

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/CONTRIBUTING.html b/docs/CONTRIBUTING.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/articles/index.html b/docs/articles/index.html