Merge pull request #166 from inbo/dev_nextrelease

Release version 0.8.0

.github/CONTRIBUTING.md

@@ -135,7 +135,7 @@ A tibble is a dataframe that makes working in the tidyverse a little [easier](ht
 We try to follow the [GitHub flow](https://guides.github.com/introduction/flow/) for development.
 
 1. Fork [this repo][repo] and clone it to your computer. To learn more about this process, see [this guide](https://guides.github.com/activities/forking/).
-2. If you have forked and cloned the project before and it has been a while since you worked on it, [pull changes from the original repo](https://help.github.com/articles/merging-an-upstream-repository-into-your-fork/) to your clone by using `git pull upstream master`.
+2. If you have forked and cloned the project before and it has been a while since you worked on it, [pull changes from the original repo](https://help.github.com/articles/merging-an-upstream-repository-into-your-fork/) to your clone by using `git pull upstream main`.
 3. Open the RStudio project file (`.Rproj`).
 5. Make your changes:
     * Write your code.
@@ -157,23 +157,23 @@ You will want to look at the file `src/manage_package.R` to get some useful pack
 **Releases, version numbering and the relation to git branches**
 
 - We follow the semantic version numbering as described [here](https://r-pkgs.org/description.html#version).
-- The commit referred to by `master` (branch tip) must always have a `<major>.<minor>.<patch>` version number in the `DESCRIPTION` file.
+- The commit referred to by `main` (branch tip) must always have a `<major>.<minor>.<patch>` version number in the `DESCRIPTION` file.
 It is the latest released package version.
-  - Subsequent commits on `master` which do not change the package code itself, but only website setup and repo documentation, must inherit the _same_ release version number.
+  - Subsequent commits on `main` which do not change the package code itself, but only website setup and repo documentation, must inherit the _same_ release version number.
   - **Commits which do change the package _must_ carry a development version number**; typically `<major>.<minor>.<patch>.9000`.
-It follows that they never appear at the tip of the `master` branch.
+It follows that they never appear at the tip of the `main` branch.
 Non-package commits _may_ follow this route as well: it is safe for all new commits.
 
   These conventions ensure that:
-  - a simple package installation with `remotes::install_github()`, which defaults to downloading from the `master` branch, will result in an installation of the latest release;
+  - a simple package installation with `remotes::install_github()`, which defaults to downloading from the `main` branch, will result in an installation of the latest release;
   - the `pkgdown` [website] shows the version number of the latest release.
 
-- Other branches than `master` can have various names.
+- Other branches than `main` can have various names.
 However, there is always at least one **development branch** whose name begins with `dev`.
 For example: `dev_nextrelease`, `dev_0.4.0`, ...
 It is the collector of new features and bugfixes that will lead to a later release, and its first commit should be to add a dev-suffix (`.9000`) to the current version number (don't increment `<major>.<minor>.<patch>`).
   - Especially when cooperating, it is counteradvised to push directly to this branch; better do so through pull requests from feature branches.
-- Eventually, the development branch's last commit before merging to `master` will be to increment at least one of `<major>`, `<minor>` or `<patch>` and to drop the dev-suffix from the version number (i.e. in the `DESCRIPTION` file).
+- Eventually, the development branch's last commit before merging to `main` will be to increment at least one of `<major>`, `<minor>` or `<patch>` and to drop the dev-suffix from the version number (i.e. in the `DESCRIPTION` file).
 Such final commits should happen directly on the development branch.
 No later than that commmit (but it can safely be done earlier), also the `.zenodo.json` metadata file must be updated to the new release version number.
 
@@ -196,7 +196,7 @@ This is needed to ensure a smooth merge of your branch to the base branch later
 1. Propose to merge your commits into the base branch: after pushing your branch to GitHub (which you can do repeatedly), this starts with making a **pull request** (PR; actually this is a merge request) and assign at least one reviewer before a merge can be decided.
 At that moment, open online discussion in the repo is possible on your changes (for other open discussion that you want to start, make an _issue_).
 As long as no merge is performed, more commits can be added to this PR with `git push`, e.g. to implement requested changes by others.
-    - make sure to correctly **set the base branch** in the pull request (because the default is `master`).
+    - make sure to correctly **set the base branch** in the pull request (because the default is `main`).
 1. After your PR is merged, pull the base branch and clean up your local repo in order to keep up with the remote.
 
 **Git resources**

.zenodo.json

@@ -4,7 +4,7 @@
     "license": "GPL-3.0",
     "upload_type": "software",
     "access_right": "open",
-    "version": "0.7.0",
+    "version": "0.8.0",
     "creators": [
         {
             "name": "Vanderhaeghe, Floris",

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: n2khab
 Title: Providing Preprocessed Reference Data for Flemish Natura 2000 Habitat Analyses
-Version: 0.7.0
+Version: 0.8.0
 Authors@R: c(
     person("Floris", "Vanderhaeghe", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-6378-6229")), 
     person("Toon", "Westra", email = "[email protected]", role = c("aut"), comment = c(ORCID = "0000-0003-2478-9459")), 
@@ -45,7 +45,7 @@ Imports:
     withr
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.1
 Suggests: 
     bib2df,
     curl,

NEWS.md

@@ -1,3 +1,9 @@
+# n2khab 0.8.0 (2022-11-18)
+
+- Reference list `namelist` has been updated with improved type names (#163; thanks @jeroenvdborre).
+- Paper by De Saeger et al. (2017) is now referred in documentation of `read_habitatmap()` and derived functions (#165).
+- Git repository: branch `master` is replaced by `main` (#164).
+
 # n2khab 0.7.0 (2022-05-23)
 
 - Upgrade most [vc-formatted](https://ropensci.github.io/git2rdata) data sources to the format of **git2rdata** version 0.4.0. In this version, files not optimized for version control (but rather for readability), are saved as csv instead of tsv files. For **n2khab**, this applies to the `types` and `env_pressures` data sources. Since it is expected that this upgrade is not compatible with older **git2rdata** versions, the version dependency for **git2rdata** has been updated (#161).

R/read_habitatdata.R

@@ -110,12 +110,20 @@
 #'
 #' @references
 #'
-#' De Saeger, S., Guelinckx, R., Oosterlynck, P., De Bruyn, A., Debusschere, K.,
+#' \itemize{
+#' \item De Saeger, S., Guelinckx, R., Oosterlynck, P., De Bruyn, A.,
+#' Debusschere, K.,
 #' Dhaluin, P., Erens, R., Hendrickx, P., Hennebel, D., Jacobs, I., Kumpen, M.,
-#' Op De Beeck, J., Spanhove, T., Tamsyn, W., Van Oost, F., Van Dam, G.,
+#' Opdebeeck, J., Spanhove, T., Tamsyn, W., Van Oost, F., Van Dam, G.,
 #' Van Hove, M., Wils, C., Paelinckx, D. (2020). Biologische Waarderingskaart
 #' en Natura 2000 Habitatkaart, uitgave 2020. (Rapporten van het Instituut voor Natuur- en Bosonderzoek; Nr. 35). Instituut voor Natuur- en Bosonderzoek (INBO).
 #' \doi{10.21436/inbor.18840851}.
+#' \item De Saeger, S., Oosterlynck, P. & Paelinckx, D. (2017). The Biological
+#' Valuation Map (BVM): a field-driven survey of land cover and vegetation in
+#' the Flemish Region of Belgium. Documents phytosociologiques - Actes du
+#' colloque de Saint-Mandé 2012 - Prodrome et cartographie des végétations de
+#' France - 2017. Vol. 6: 372-382.
+#' }
 #'
 #' @examples
 #' \dontrun{
@@ -768,12 +776,20 @@ read_watersurfaces <-
 #'
 #' @references
 #'
-#' De Saeger, S., Guelinckx, R., Oosterlynck, P., De Bruyn, A., Debusschere, K.,
+#' \itemize{
+#' \item De Saeger, S., Guelinckx, R., Oosterlynck, P., De Bruyn, A.,
+#' Debusschere, K.,
 #' Dhaluin, P., Erens, R., Hendrickx, P., Hennebel, D., Jacobs, I., Kumpen, M.,
-#' Op De Beeck, J., Spanhove, T., Tamsyn, W., Van Oost, F., Van Dam, G.,
+#' Opdebeeck, J., Spanhove, T., Tamsyn, W., Van Oost, F., Van Dam, G.,
 #' Van Hove, M., Wils, C., Paelinckx, D. (2020). Biologische Waarderingskaart
 #' en Natura 2000 Habitatkaart, uitgave 2020. (Rapporten van het Instituut voor Natuur- en Bosonderzoek; Nr. 35). Instituut voor Natuur- en Bosonderzoek (INBO).
 #' \doi{10.21436/inbor.18840851}.
+#' \item De Saeger, S., Oosterlynck, P. & Paelinckx, D. (2017). The Biological
+#' Valuation Map (BVM): a field-driven survey of land cover and vegetation in
+#' the Flemish Region of Belgium. Documents phytosociologiques - Actes du
+#' colloque de Saint-Mandé 2012 - Prodrome et cartographie des végétations de
+#' France - 2017. Vol. 6: 372-382.
+#' }
 #'
 #' @examples
 #' \dontrun{
@@ -914,7 +930,9 @@ read_habitatmap <-
 #' Lambert 72 CRS (EPSG-code \href{https://epsg.io/31370}{31370}), and
 #' \code{habitatmap_terr_types}.
 #' \code{habitatmap_terr} is the further interpreted, terrestrial part of
-#' \code{habitatmap_stdized} (see \code{\link{read_habitatmap_stdized}}).
+#' \code{habitatmap_stdized} (see \code{\link{read_habitatmap_stdized}}),
+#' which, in turn, is derived from the raw data source \code{habitatmap}
+#' (De Saeger et al., 2020).
 #' By default, occurrences of type \code{7220} are dropped because a more
 #' reliable data source is available for this habitat type (see \code{drop_7220}
 #' argument).
@@ -1016,6 +1034,23 @@ read_habitatmap <-
 #'
 #' @family functions involved in processing the 'habitatmap' data source
 #'
+#' @references
+#'
+#' \itemize{
+#' \item De Saeger, S., Guelinckx, R., Oosterlynck, P., De Bruyn, A.,
+#' Debusschere, K.,
+#' Dhaluin, P., Erens, R., Hendrickx, P., Hennebel, D., Jacobs, I., Kumpen, M.,
+#' Opdebeeck, J., Spanhove, T., Tamsyn, W., Van Oost, F., Van Dam, G.,
+#' Van Hove, M., Wils, C., Paelinckx, D. (2020). Biologische Waarderingskaart
+#' en Natura 2000 Habitatkaart, uitgave 2020. (Rapporten van het Instituut voor Natuur- en Bosonderzoek; Nr. 35). Instituut voor Natuur- en Bosonderzoek (INBO).
+#' \doi{10.21436/inbor.18840851}.
+#' \item De Saeger, S., Oosterlynck, P. & Paelinckx, D. (2017). The Biological
+#' Valuation Map (BVM): a field-driven survey of land cover and vegetation in
+#' the Flemish Region of Belgium. Documents phytosociologiques - Actes du
+#' colloque de Saint-Mandé 2012 - Prodrome et cartographie des végétations de
+#' France - 2017. Vol. 6: 372-382.
+#' }
+#'
 #' @examples
 #' \dontrun{
 #' # This example supposes that your working directory or a directory up to 10

README.md

@@ -17,7 +17,7 @@ The standard reference data include: checklists, spatial habitat distribution, a
 
 ## Installing and using the _n2khab_ package
 
-To install the current package version from the `master` branch (latest stable release), run:
+To install the current package version from the `main` branch (latest stable release), run:
 
 ```r
 install.packages("n2khab", repos = c(inbo = "https://inbo.r-universe.dev", 
@@ -36,7 +36,7 @@ remotes::install_github("inbo/n2khab",
                         upgrade = TRUE)
 ```
 
-Note that this will install the package from the `master` branch.
+Note that this will install the package from the `main` branch.
 If you need a version from another branch, add the `ref` argument in the above function to provide the branch name.
 
 Repeat the installation when you wish to upgrade.