Merge pull request #189 from inbo/dev_nextrelease

Preparing version 0.11.0

.github/workflows/R-CMD-check-latest.yaml

@@ -33,14 +33,13 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
-          http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: false
 
       - name: Add ubuntugis-unstable PPA (Linux)

.github/workflows/R-CMD-check.yaml

@@ -27,14 +27,13 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
-          http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2

.github/workflows/site-deploy.yaml

@@ -12,7 +12,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/site-devel.yaml

@@ -12,7 +12,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -31,7 +31,7 @@ jobs:
           Rscript -e 'options(rmarkdown.html_vignette.check_title = FALSE); pkgdown::build_site()'
 
       - name: Upload pkgdown-site as artifact
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: pkgdown-site
           path: docs

.zenodo.json

@@ -4,7 +4,7 @@
     "license": "GPL-3.0",
     "upload_type": "software",
     "access_right": "open",
-    "version": "0.10.1",
+    "version": "0.11.0",
     "creators": [
         {
             "name": "Vanderhaeghe, Floris",

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: n2khab
 Title: Providing Preprocessed Reference Data for Flemish Natura 2000 Habitat Analyses
-Version: 0.10.1
+Version: 0.11.0
 Authors@R: c(
     person("Floris", "Vanderhaeghe", email = "floris.vanderhaeghe@inbo.be", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-6378-6229")), 
     person("Toon", "Westra", email = "toon.westra@inbo.be", role = c("aut"), comment = c(ORCID = "0000-0003-2478-9459")), 
@@ -46,7 +46,7 @@ Imports:
     tidyr (>= 1.0.0),
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Suggests: 
     bib2df,
     digest,

NEWS.md

@@ -1,3 +1,34 @@
+# n2khab 0.11.0 (2024-10-03)
+
+## Support for new data source versions
+
+The following new data source versions are now supported by the corresponding functions (#184):
+
+- `habitatmap_2023` (`read_habitatmap()`)
+- `habitatmap_stdized_2023_v1` (`read_habitatmap_stdized()`)
+- `habitatmap_terr_2023_v1` (`read_habitatmap_terr()`)
+- `habitatstreams_2023` (`read_habitatstreams()`)
+- `watersurfaces_hab_v5` (`read_watersurfaces_hab()`)
+
+Function documentation was updated accordingly.
+
+## Drop `rbbvos+` from built-in data sources
+
+- Type `rbbvos+` has been considered too loosely defined, as an intermediate between `rbbvos` and `6510_hua`, and it has not been mapped consistently.
+Hence this type is considered obsolete and it has been dropped from the `types` and `namelist` data sources (#182).
+However do note that it exists in versions of `habitatmap` and derived data sources.
+- `expand_types()` has been adjusted accordingly (#182).
+
+## Other updates
+
+Including:
+
+- the `fix_geom` implementation in `read_watersurfaces()` is now more efficient (#185);
+- `read_habitatmap()` also gained a `fix_geom` argument (#184);
+- `read_habitatsprings()` now returns integer IDs as integers (#180);
+- `expand_types()` with a grouped data frame is now more efficient ([13d05ec](https://github.com/inbo/n2khab/commit/13d05ec));
+- several fixes (#186, [88f0e19](https://github.com/inbo/n2khab/commit/88f0e19)).
+
 # n2khab 0.10.1 (2023-12-04)
 
 - Silently ignore errors from package {remotes} during package loading ([56e9c06](https://github.com/inbo/n2khab/commit/56e9c06)).

R/datawrangling.R

@@ -31,22 +31,22 @@
 #' \item{for 2330: both subtype codes must be present}
 #' \item{for 5130: 5130_hei must be present (note that only the main type code
 #' occurs in the targeted data sources)}
-#' \item{for 6230: 6230_ha, 6230_hmo and 6230_hnk must be present
+#' \item{for 6230: 6230_ha, 6230_hmo and 6230_hn must be present
 #' (not the rare 6230_hnk)}
 #' \item{for 91E0: 91E0_va, 91E0_vm and 91E0_vn must be present
 #' (not the rarer 91E0_sf, 91E0_vc and 91E0_vo)}
 #' }
 #' However, it is possible to relax this requirement by setting
 #' \code{strict = FALSE}.
-#' This will add the main type code whenever \emph{one} corresponding subtype
-#' code is present.
+#' This will add the main type code whenever \emph{one} of the above required
+#' subtype codes is present.
 #' In all cases no other main type codes are added apart from
 #' 2330, 5130, 6230 and 91E0.
 #' This is because the data sources with which the result
 #' is to be matched (see Description) don't contain certain main type codes,
 #' and because it makes no sense in other cases
-#' (rbbkam, rbbvos, rbbzil & 9120 in the \code{habitatmap} do not refer to a
-#' main type but to an non-defined subtype with no specific code).
+#' (rbbkam, rbbzil & 9120 in the \code{habitatmap} do not refer to a
+#' main type but to a non-defined subtype with no specific code).
 #'
 #'
 #' @param x An object of class \code{data.frame}.
@@ -130,11 +130,26 @@ expand_types <- function(x,
   assert_that(is.flag(use_grouping), noNA(use_grouping))
   assert_that(is.flag(strict), noNA(strict))
 
+  types <-
+    read_types() %>%
+    select(1:3)
+
+  subtypes <-
+    types %>%
+    filter(.data$typelevel == "subtype") %>%
+    select(1, 3)
+
+  if (!all(unique(x[[type_var]]) %in% types$type)) {
+    warning("The data frame contains type codes which are not standard.")
+  }
+
   if (!use_grouping) {
     expand_types_plain(
       x = x,
       type_var = type_var,
-      strict = strict
+      strict = strict,
+      types = types,
+      subtypes = subtypes
     )
   } else {
     x %>%
@@ -143,7 +158,9 @@ expand_types <- function(x,
       mutate(newdata = map(.data$data,
         expand_types_plain,
         type_var = type_var,
-        strict = strict
+        strict = strict,
+        types = types,
+        subtypes = subtypes
       )) %>%
       select(-.data$data) %>%
       unnest(cols = .data$newdata) %>%
@@ -186,31 +203,20 @@ expand_types <- function(x,
 #' @keywords internal
 expand_types_plain <- function(x,
                                type_var = "type",
-                               strict = TRUE) {
-  types <-
-    read_types() %>%
-    select(1:3)
-
-  subtypes <-
-    types %>%
-    filter(.data$typelevel == "subtype") %>%
-    select(1, 3)
-
+                               strict = TRUE,
+                               types,
+                               subtypes) {
   orig_types <-
     x[, type_var] %>%
     rename(orig_abcd = type_var)
 
-  if (!all(unique(orig_types$orig_abcd) %in% types$type)) {
-    warning("The data frame contains type codes which are not standard.")
-  }
-
   # main types to add:
   suppressWarnings(
     join_main_types <-
       subtypes %>%
       filter(.data$main_type == "2330" |
         .data$type %in% c(
-          "6230_ha", "6230_hmo", "6230_hnk",
+          "6230_ha", "6230_hmo", "6230_hn",
           "5130_hei",
           "91E0_va", "91E0_vm", "91E0_vn"
         )) %>%

R/n2khab-deprecated.R

@@ -5,7 +5,14 @@
 #' - [`read_scheme_types()`] has moved to package `n2khabmon`.
 #' Use [`n2khabmon::read_scheme_types()`] instead.
 #'
-#' @param ... arguments passed to the new function
+#' An efficient way with base R to avoid function masking and conflict warnings
+#' when attaching both `{n2khab}` and `{n2khabmon}`, regardless of the order
+#' in which they're loaded, is by specifying something as below in your
+#' script, at least _before_ loading `{n2khab}`:
+#'
+#' `conflictRules("n2khab", exclude = c("read_schemes", "read_scheme_types"))`
+#'
+#' @param ... Arguments passed to the new function.
 #'
 #' @md
 #'

R/options.R

@@ -77,7 +77,7 @@ n2khab_options <- function() {
     ),
     "n2khab_use_raster",
     tryCatch(
-      n2khab_using_raster(),
+      as.character(n2khab_using_raster()),
       error = function(e) {
         message(as.character(e))
         NA
@@ -125,5 +125,7 @@ n2khab_using_raster <- function() {
   if (identical(opt, "")) {
     opt <- NA
   }
-  opt || grepl("TRUE|true", opt)
+  (is.logical(opt) && length(opt) == 1 && opt) ||
+    identical(opt, "TRUE") ||
+    identical(opt, "true")
 }