Merge pull request #11 from inbo/dev_nextrelease

Preparing version 0.2.0
inbo · May 6, 2024 · cb014b9 · cb014b9
2 parents 5713ed6 + f2fad15
commit cb014b9
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Showing 20 changed files with 416 additions and 343 deletions.
diff --git a/.github/workflows/R-CMD-check-latest.yaml b/.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)

diff --git a/.github/workflows/R-CMD-check.yaml b/.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

diff --git a/.github/workflows/site-deploy.yaml b/.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
 

diff --git a/.github/workflows/site-devel.yaml b/.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
diff --git a/.zenodo.json b/.zenodo.json
@@ -4,7 +4,7 @@
     "license": "GPL-3.0",
     "upload_type": "software",
     "access_right": "open",
-    "version": "0.1.3",
+    "version": "0.2.0",
     "creators": [
         {
             "name": "Vanderhaeghe, Floris",

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: n2khabmon
 Title: Prepare and Manage N2KHAB Monitoring Schemes
-Version: 0.1.3
+Version: 0.2.0
 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("ctb"), comment = c(ORCID = "0000-0003-2478-9459")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+# n2khabmon 0.2.0 (2024-05-06)
+
+- `schemes` & `scheme_types` data sources: drop scheme `HQ6120`; add type for scheme `HQ2330` (#10).
+- `scheme_types` data source: define typegroups for schemes `SOIL_03.2` & `SURF_03.4_lotic` (#10).
+- `namelist` data source: use longer names for MNE schemes (#10).
+
 # n2khabmon 0.1.3 (2024-02-06)
 
 - `read_scheme_types()`: fix the call to `n2khab::read_types()` when running `read_scheme_types(extended = TRUE)` ([995b32b](https://github.com/inbo/n2khabmon/commit/995b32b)).

diff --git a/R/textdata.R b/R/textdata.R
@@ -164,7 +164,7 @@ NULL
 #'   }
 #' \itemize{
 #'     \item{More information on the MHQ-schemes can be found in
-#'     \href{https://pureportal.inbo.be/portal/files/4339795/Westra_etal_2014_MonitoringNatura2000Habitats.pdf}{Westra \emph{et al.} (2014)}.
+#'     \href{https://doi.org/10.21436/inbor.85829488}{Westra \emph{et al.} (2022)}.
 #'   }
 #'  }
 #'
@@ -257,7 +257,7 @@ NULL
 #'
 #' \itemize{
 #'     \item{For the MHQ-schemes, the list of sampled types is based on the report of
-#'     \href{https://pureportal.inbo.be/portal/files/4339795/Westra_etal_2014_MonitoringNatura2000Habitats.pdf}{Westra \emph{et al.} (2014)}.
+#'     \href{https://doi.org/10.21436/inbor.85829488}{Westra \emph{et al.} (2022)}.
 #'   }
 #'  }
 #'

diff --git a/inst/textdata/namelist.tsv b/inst/textdata/namelist.tsv
diff --git a/inst/textdata/namelist.yml b/inst/textdata/namelist.yml
@@ -6,7 +6,7 @@
   - lang
   - code
   hash: 3345146f5a5902a684bc1b965f00486c82952d94
-  data_hash: 5651825f61a8cf829fd3437ae195ed719f518b75
+  data_hash: 7c3bb83b09e5613712999d40029af0170cbbd90e
 code:
   class: character
 lang:

diff --git a/inst/textdata/scheme_types.tsv b/inst/textdata/scheme_types.tsv
@@ -585,70 +585,70 @@ scheme	type	typegroup
 24	35	NA
 24	36	NA
 24	76	NA
-25	2	NA
-25	7	NA
-25	8	NA
-25	9	NA
-25	10	NA
-25	11	NA
-25	12	NA
-25	17	NA
-25	18	NA
-25	19	NA
-25	20	NA
-25	21	NA
-25	31	NA
-25	32	NA
-25	33	NA
-25	34	NA
-25	35	NA
-25	36	NA
-25	37	NA
-25	38	NA
-25	39	NA
-25	40	NA
-25	41	NA
-25	42	NA
-25	43	NA
-25	44	NA
-25	45	NA
-25	46	NA
-25	49	NA
-25	50	NA
-25	51	NA
-25	52	NA
-25	53	NA
-25	54	NA
-25	55	NA
-25	57	NA
-25	58	NA
-25	59	NA
-25	60	NA
-25	61	NA
-25	62	NA
-25	63	NA
-25	64	NA
-25	65	NA
-25	67	NA
-25	68	NA
-25	69	NA
-25	70	NA
-25	72	NA
-25	73	NA
-25	74	NA
-25	75	NA
-25	76	NA
-25	77	NA
-25	78	NA
-25	79	NA
-25	80	NA
-25	81	NA
-25	82	NA
-25	84	NA
-25	86	NA
-25	87	NA
-25	88	NA
-25	89	NA
+25	2	33
+25	7	33
+25	8	32
+25	9	32
+25	10	30
+25	11	31
+25	12	30
+25	17	31
+25	18	31
+25	19	30
+25	20	30
+25	21	30
+25	31	30
+25	32	30
+25	33	31
+25	34	31
+25	35	30
+25	36	31
+25	37	31
+25	38	31
+25	39	30
+25	40	30
+25	41	30
+25	42	31
+25	43	31
+25	44	31
+25	45	33
+25	46	33
+25	49	32
+25	50	32
+25	51	32
+25	52	32
+25	53	31
+25	54	32
+25	55	33
+25	57	32
+25	58	33
+25	59	33
+25	60	31
+25	61	31
+25	62	32
+25	63	30
+25	64	30
+25	65	31
+25	67	31
+25	68	33
+25	69	33
+25	70	31
+25	72	32
+25	73	31
+25	74	32
+25	75	32
+25	76	33
+25	77	32
+25	78	31
+25	79	33
+25	80	33
+25	81	33
+25	82	32
+25	84	31
+25	86	32
+25	87	33
+25	88	32
+25	89	33
 26	2	NA
 26	7	NA
 26	36	NA
@@ -696,8 +696,8 @@ scheme	type	typegroup
 62	26	24
 62	27	21
 62	30	24
-63	28	NA
-63	66	NA
+63	28	37
+63	66	35
 30	28	NA
 30	66	NA
 31	23	NA
@@ -731,6 +731,7 @@ scheme	type	typegroup
 65	18	NA
 41	19	NA
 42	20	NA
+42	21	NA
 43	22	NA
 44	23	NA
 44	24	NA
@@ -740,7 +741,6 @@ scheme	type	typegroup
 40	28	NA
 49	31	NA
 50	32	NA
-51	36	NA
 52	39	NA
 52	40	NA
 52	41	NA

diff --git a/inst/textdata/scheme_types.yml b/inst/textdata/scheme_types.yml
@@ -5,8 +5,8 @@
   sorting:
   - scheme
   - type
-  hash: f524df97d6a2338298f54d28479a4dd150c04492
-  data_hash: 15566cc555458d0a9108c0d9bec43950db66e6f3
+  hash: fd5e35e7671efa6e0d9a6fc691da0ac4c745d2fe
+  data_hash: fc922afef448dda550b49c0d0ac2debc985de441
 scheme:
   class: factor
   labels:
@@ -64,7 +64,6 @@ scheme:
   - HQ3260
   - HQ4010
   - HQ4030
-  - HQ6120
   - HQ6230
   - HQ6410
   - HQ6510
@@ -129,7 +128,6 @@ scheme:
   - 40
   - 49
   - 50
-  - 51
   - 52
   - 53
   - 54
@@ -395,10 +393,18 @@ typegroup:
   - GW_05.1_terr_group3
   - GW_05.1_terr_group4
   - GW_05.1_terr_group5
+  - SOIL_03.2_group1
+  - SOIL_03.2_group2
+  - SOIL_03.2_group3
+  - SOIL_03.2_group4
   - SURF_03.4_lentic_group1
   - SURF_03.4_lentic_group2
   - SURF_03.4_lentic_group3
   - SURF_03.4_lentic_group4
+  - SURF_03.4_lotic_group1
+  - SURF_03.4_lotic_group2
+  - SURF_03.4_lotic_group3
+  - SURF_03.4_lotic_group4
   index:
   - 1
   - 2
@@ -425,8 +431,16 @@ typegroup:
   - 18
   - 19
   - 20
+  - 30
+  - 31
+  - 32
+  - 33
   - 21
   - 22
   - 23
   - 24
+  - 34
+  - 35
+  - 36
+  - 37
   ordered: no
diff --git a/inst/textdata/schemes.tsv b/inst/textdata/schemes.tsv
@@ -53,7 +53,6 @@ scheme	programme	attribute_1	attribute_2	attribute_3	spatial_restriction	notes	t
 40	2	34	NA	NA	NA	NA	3	NA	NA
 49	2	20	NA	NA	NA	NA	4	NA	NA
 50	2	21	NA	NA	NA	NA	4	NA	NA
-51	2	22	NA	NA	NA	NA	4	NA	NA
 52	2	23	NA	NA	NA	NA	4	NA	NA
 53	2	24	NA	NA	NA	NA	4	NA	NA
 54	2	25	NA	NA	NA	NA	4	NA	NA

diff --git a/inst/textdata/schemes.yml b/inst/textdata/schemes.yml
@@ -5,8 +5,8 @@
   sorting:
   - programme
   - scheme
-  hash: 0d1cc8555f417924aa8c7c08feb9b52c8eb2e212
-  data_hash: 81182a48ef9d6facf38a0d31fb372ee66882e4da
+  hash: 673425b8d121998f9d991046eddebbfd25143a4a
+  data_hash: 75eca4b595176f155b23af80a8fde2ea537ce6a7
 scheme:
   class: factor
   labels:
@@ -64,7 +64,6 @@ scheme:
   - HQ3260
   - HQ4010
   - HQ4030
-  - HQ6120
   - HQ6230
   - HQ6410
   - HQ6510
@@ -129,7 +128,6 @@ scheme:
   - 40
   - 49
   - 50
-  - 51
   - 52
   - 53
   - 54
@@ -175,7 +173,6 @@ attribute_1:
   - '3260'
   - '4010'
   - '4030'
-  - '6120'
   - '6230'
   - '6410'
   - '6510'
@@ -209,7 +206,6 @@ attribute_1:
   - 34
   - 20
   - 21
-  - 22
   - 23
   - 24
   - 25

diff --git a/man/scheme_types.Rd b/man/scheme_types.Rd