Merge pull request #159 from inbo/dev_nextrelease

Release version 0.6.0

.zenodo.json

@@ -4,7 +4,7 @@
     "license": "GPL-3.0",
     "upload_type": "software",
     "access_right": "open",
-    "version": "0.5.0",
+    "version": "0.6.0",
     "creators": [
         {
             "name": "Vanderhaeghe, Floris",

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: n2khab
 Title: Providing Preprocessed Reference Data for Flemish Natura 2000 Habitat Analyses
-Version: 0.5.0
+Version: 0.6.0
 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")), 
@@ -45,7 +45,7 @@ Imports:
     withr
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
 Suggests: 
     bib2df,
     curl,

NAMESPACE

@@ -24,6 +24,7 @@ export(read_namelist)
 export(read_raster_runif)
 export(read_scheme_types)
 export(read_schemes)
+export(read_shallowgroundwater)
 export(read_soilmap)
 export(read_types)
 export(read_watercourse_100mseg)

NEWS.md

@@ -1,6 +1,22 @@
-## n2khab 0.5.0 (2021-05-12)
+# n2khab 0.6.0 (2022-02-03)
 
-#### Support for new data source versions
+## New features
+
+- Function `read_shallowgroundwater()` to return the `shallowgroundwater` data source (#156).
+  - The raw data source `shallowgroundwater` represents the areas in
+the Flemish region of Belgium where the mean lowest groundwater level is estimated to be less than approximately 2 m below soil surface ([inbo/n2khab-preprocessing/pull/61](https://github.com/inbo/n2khab-preprocessing/pull/61); <https://doi.org/10.5281/zenodo.5902880>).
+- Reference lists `types`, `schemes`, `scheme_types`, `namelist` were updated (#150, #151, #154, #158):
+  - a few type name updates (thanks S. De Saeger);
+  - updated value of `groundw_dep` for type `91F0`;
+  - environmental pressures `ep_07.2` and `ep_07.4` received updated (Dutch) explanations;
+  - scheme `HQ2190` has been replaced by two schemes `HQ2190_terr` and `HQ2190_aq`;
+  - typegroups were defined for scheme `GW_05.1_aq` (with contributions from L. Denys & A. Leyssen).
+- Readme (homepage): a **new installation method** using [inbo.r-universe.dev](https://inbo.r-universe.dev) has been added and is recommended (#153, 746fb81).
+
+
+# n2khab 0.5.0 (2021-05-12)
+
+## Support for new data source versions
 
 The following new data source versions are now supported by their associated reading functions:
 
@@ -13,38 +29,38 @@ The following new data source versions are now supported by their associated rea
 
 Function documentation was updated accordingly and refined.
 
-#### New functions
+## New functions
 
 - Function `read_raster_runif()` to return the `raster_runif` data source (#136, #138)
   - The raw data source `raster_runif` is a raster with cells matching those of `GRTSmaster_habitats`.
   Their values are uniformly distributed random numbers between 0 and 1
   ([inbo/n2khab-preprocessing/pull/55](https://github.com/inbo/n2khab-preprocessing/pull/55) and following pull requests; <https://doi.org/10.5281/zenodo.4745983>).
 - Function `checksum()` and associated shortcut functions to calculate file checksums (#122)
 
-#### Other updates & internal changes
+## Other updates & internal changes
 
 Including:
 
 - `scheme_types` data source: updates in typegroup memberships of MNE scheme `GW_05.1_terr` (#116)
 - `expand_types()` now also supports expanding `5130_hei` to `5130` (#143)
 
 
-## n2khab 0.4.0 (2021-02-10)
+# n2khab 0.4.0 (2021-02-10)
 
-#### New feature
+## New feature
 
 - Function `read_watercourse_100mseg()` (#105) to return the `watercourse_100mseg` data source or one of its elements.
 `watercourse_100mseg` is a new processed data source ([inbo/n2khab-preprocessing/pull/44](https://github.com/inbo/n2khab-preprocessing/pull/44); <https://doi.org/10.5281/zenodo.4452577>).
 
-#### Updates & internal changes
+## Updates & internal changes
 
 Including:
 
 - Update `namelist` data source: Dutch shortname of one type changed (#102).
 - Drop dependency on `sp`, which was used for CRS handling in a few functions (#103).
 - Minor updates in documentation and vignettes to solve newly encountered errors and notes in `R CMD check` (#107).
 
-#### Repo and website maintenance
+## Repo and website maintenance
 
 - Update and extend Readme (homepage) and Contributing Guide (#97, #110), including:
     - instruction for upgrading the package;
@@ -53,37 +69,37 @@ Including:
 - Continuous integration: leave Travis CI; add new GitHub Actions workflows (#108).
 - Website: larger fontsize; Ubuntu Mono font for code; consistent colouring of hyperlinks (#110).
 
-## n2khab 0.3.1 (2020-10-26)
+# n2khab 0.3.1 (2020-10-26)
 
-#### Minor patch
+## Minor patch
 
 - `read_watersurfaces()` has been limited explicitly to using data source version 'watersurfaces_v1.0'.
 Accommodation of the newer 'watersurfaces_v1.1' is planned for later.
 
-## n2khab 0.3.0 (2020-10-16)
+# n2khab 0.3.0 (2020-10-16)
 
-#### Breaking change
+## Breaking change
 
 - Functions that preprocess (non-included) N2KHAB data sources have been simplified by dropping their `path` argument (#92).
 Existing R code will continue to run normally if you complied with the recommended file organization (see `vignette("v020_datastorage")` and `vignette("v022_example")`) and did not set the `path` and `file` arguments.
 
-#### New features
+## New features
 
 - New function `read_habitatquarries()` for reading the `habitatquarries` data source (#83, #94,  [inbo/n2khab-preprocessing/pull/41](https://github.com/inbo/n2khab-preprocessing/pull/41)).
 - Updates in reference lists (#88, #93, [7ce3b32](https://github.com/inbo/n2khab/commit/7ce3b32)):
     - `schemes` & `scheme_types`: updates of spatial restrictions, names and typegroup names of MNE schemes (for defining the schemes' target populations);
     - `types`: update groundwater dependency of type `2170`.
 
-#### Internal changes
+## Internal changes
 
 - Harden CRS representations (#84)
 - Re-integrate `download_zenodo()` (from `inborutils`) (#89)
 - Drop some package dependencies to speed up package loading (#89, #90)
 
 
-## n2khab 0.2.0 (2020-05-08)
+# n2khab 0.2.0 (2020-05-08)
 
-#### New features
+## New features
 
 - Updates in reference lists (#64, #65, #69, [e69cd52](https://github.com/inbo/n2khab/pull/73/commits/e69cd52)):
     - `types`: updates of flood dependency scores and hydrological class of several types, following several expert discussions and checks
@@ -101,21 +117,21 @@ Existing R code will continue to run normally if you complied with the recommend
 
 Further, a number of smaller fixes and enhancements were made.
 
-## n2khab 0.1.2 (2020-03-04)
+# n2khab 0.1.2 (2020-03-04)
 
-#### Hotfix
+## Hotfix
 
 - `read_GRTSmh()`, `read_GRTSmh_base4frac()`, `read_GRTSmh_diffres()`: avoided CRS error with more recent GDAL/PROJ.4 installations (#61)
 
-## n2khab 0.1.1 (2020-02-26)
+# n2khab 0.1.1 (2020-02-26)
 
-#### Hotfix
+## Hotfix
 
 - `read_habitatmap_terr()`: fixed non-functioning argument `keep_aq_types=FALSE` (#60)
 
-## n2khab 0.1.0 (2020-01-30)
+# n2khab 0.1.0 (2020-01-30)
 
-#### Features of the first stable release
+## Features of the first stable release
 
 - Core reading and preprocessing functions
 - Several built-in checklists (among which: `types` and `env_pressures`)
@@ -124,7 +140,7 @@ Further, a number of smaller fixes and enhancements were made.
 - A reexport of `download_zenodo()` from `inborutils`
 - Website built with `pkgdown`
 
-#### Historical note
+## Historical note
 
 This package is the successor of the 'n2khabutils' package.
 Previous to commit `c8608d9`, the code was part of the [n2khab-monitoring](https://github.com/inbo/n2khab-monitoring) repo (formerly 'n2khab-inputs'), where the original version history remains stored.

R/GRTSmh.R

@@ -225,7 +225,7 @@ convert_base4frac_to_dec <-
 #' with the decimal integer ranking numbers of 10 hierarchical levels of the
 #' GRTS cell addresses, including the one from \code{GRTSmaster_habitats}
 #' (with GRTS cell addresses at the resolution level).
-#' The coordinate reference system is 'Belge 72 / Belgian Lambert 72'
+#' The coordinate reference system is 'BD72 / Belgian Lambert 72'
 #' (EPSG-code \href{https://epsg.io/31370}{31370}).
 #'
 #' The data source \code{GRTSmaster_habitats}, provided and documented in
@@ -470,7 +470,7 @@ read_GRTSmh_base4frac <-
 #' The function returns one selected level, either as a RasterLayer or as an
 #' \code{sf} polygon layer (in the latter case, only levels 4 to 9 are
 #' provided).
-#' The coordinate reference system is 'Belge 72 / Belgian Lambert 72'
+#' The coordinate reference system is 'BD72 / Belgian Lambert 72'
 #' (EPSG-code \href{https://epsg.io/31370}{31370}).
 #'
 #' The \code{GRTSmh_diffres} data source file is a file collection (available

R/read_admin_areas.R

@@ -2,7 +2,7 @@
 #' administrative areas
 #'
 #' Returns an administrative geospatial data source.
-#' The coordinate reference system is 'Belge 72 / Belgian Lambert 72'
+#' The coordinate reference system is 'BD72 / Belgian Lambert 72'
 #' (EPSG-code \href{https://epsg.io/31370}{31370}).
 #'
 #' @details See section \emph{Usage} to see which N2KHAB data sources are

R/read_ecoregions.R

@@ -3,7 +3,7 @@
 #' Returns the raw data source \code{ecoregions}, with unique polygon
 #' identifiers \code{polygon_code} and \code{polygon_id}.
 #' Multiple polygons can have the same \code{region_name}.
-#' The coordinate reference system is 'Belge 72 / Belgian Lambert 72'
+#' The coordinate reference system is 'BD72 / Belgian Lambert 72'
 #' (EPSG-code \href{https://epsg.io/31370}{31370}).
 #'
 #' Original columns of the raw data source were mapped as:

R/read_habitatdata.R

@@ -471,7 +471,7 @@ read_watersurfaces_hab <-
 #' }
 #'
 #' @family functions involved in processing the 'watersurfaces' data source
-#' @family functions returning important environmental data sets
+#' @family functions returning environmental data sets
 #'
 #' @references
 #'
@@ -1540,7 +1540,7 @@ read_habitatsprings <-
 #'     \item \code{polygon_id}: a unique number per polygon.
 #'     \item \code{unit_id}: a unique number for each quarry unit. Quarry units
 #'     consisting of several polygons (= partly outside the Flemish region)
-#'     have a number greater than 100.
+#'     have a number greater than or equal to 100.
 #'     \item \code{name}: site name.
 #'     \item \code{code_orig}: original 'habitattype' code in the raw data
 #'     source \code{habitatquarries}.

R/read_raster_runif.R

@@ -8,7 +8,7 @@
 #' with a small buffer added.
 #' Every raster cell has a random value between 0 and 1 according to the
 #' uniform distribution.
-#' The coordinate reference system is 'Belge 72 / Belgian Lambert 72'
+#' The coordinate reference system is 'BD72 / Belgian Lambert 72'
 #' (EPSG-code \href{https://epsg.io/31370}{31370}).
 #'
 #' The \code{raster_runif} data source is a GeoTIFF file (available at