diff --git a/.zenodo.json b/.zenodo.json index fd1bbb8..50cf457 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -4,7 +4,7 @@ "license": "GPL-3.0", "upload_type": "software", "access_right": "open", - "version": "0.2.0", + "version": "0.3.0", "creators": [ { "name": "Vanderhaeghe, Floris", diff --git a/DESCRIPTION b/DESCRIPTION index 07258c8..85fc167 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: n2khabmon Title: Prepare and Manage N2KHAB Monitoring Schemes -Version: 0.2.0 +Version: 0.3.0 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 index 8539ee2..25f654f 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +# n2khabmon 0.3.0 (2024-06-21) + +- `namelist` data source: update names of some schemes (#13). + # n2khabmon 0.2.0 (2024-05-06) - `schemes` & `scheme_types` data sources: drop scheme `HQ6120`; add type for scheme `HQ2330` (#10). diff --git a/inst/textdata/namelist.tsv b/inst/textdata/namelist.tsv index 10dc747..e774fbd 100644 --- a/inst/textdata/namelist.tsv +++ b/inst/textdata/namelist.tsv @@ -26,14 +26,14 @@ GW_03.3_group2 en types from mesotrophic environments mesotrophic GW_03.3_group3 en types from weakly eutrophic environments weakly eutrophic GW_03.3_group4 en types from moderately eutrophic to eutrophic environments (moderately) eutrophic GW_04.2 en Groundwater monitoring: 4.2 Acidification through groundwater GW: 04.2_acidif_gw -GW_05.1_aq en Groundwater monitoring: 5.1 Desiccation through groundwater: partim aquatic GW: 05.1_des_gw: aq +GW_05.1_aq en Groundwater monitoring: 5.1 Desiccation through groundwater: scheme section aquatic GW: 05.1_des_gw: aq GW_05.1_aq_group1 en types from spring-fed brooks spring-fed brooks GW_05.1_aq_group2 en types from lakes with stable groundwater table stable lakes GW_05.1_aq_group3 en types from lowland rivers lowland rivers GW_05.1_aq_group4 en types from dune lakes (moderate groundwater dynamics) dune lakes GW_05.1_aq_group5 en types from softwater lakes with dynamic groundwater table dynamic softwater lakes -GW_05.1_quarries en Groundwater monitoring: 5.1 Desiccation through groundwater: partim marl quarries GW: 05.1_des_gw: quarries -GW_05.1_terr en Groundwater monitoring: 5.1 Desiccation through groundwater: partim terrestrial GW: 05.1_des_gw: terr +GW_05.1_quarries en Groundwater monitoring: 5.1 Desiccation through groundwater: scheme section marl quarries GW: 05.1_des_gw: quarries +GW_05.1_terr en Groundwater monitoring: 5.1 Desiccation through groundwater: scheme section terrestrial GW: 05.1_des_gw: terr GW_05.1_terr_group1 en types from very wet environments very wet GW_05.1_terr_group2 en types from wet environments wet GW_05.1_terr_group3 en types from moderately wet environments moderately wet @@ -98,12 +98,12 @@ SOIL_08.2 en Soil monitoring: 8.2 Pollution through soil SOIL: 08.2_poll_soil SURF en Surfacewater monitoring NA SURF_012 en Surfacewater monitoring: 12 Soil dynamics increase (erosion, soil turbation, sand drift) SURF: 012_soildyn_incr SURF_03.2 en Surfacewater monitoring: 3.2 Eutrophication through soil SURF: 03.2_eutr_soil -SURF_03.4_lentic en Surfacewater monitoring: 3.4 Eutrophication through surface water (including inundation): partim lentic waters SURF: 03.4_eutr_sw: lentic +SURF_03.4_lentic en Surfacewater monitoring: 3.4 Eutrophication through surface water (including inundation): scheme section lentic waters SURF: 03.4_eutr_sw: lentic SURF_03.4_lentic_group1 en types from oligotrophic environments oligotrophic SURF_03.4_lentic_group2 en types from mesotrophic environments mesotrophic SURF_03.4_lentic_group3 en types from weakly eutrophic environments weakly eutrophic SURF_03.4_lentic_group4 en types from moderately eutrophic to eutrophic environments (moderately) eutrophic -SURF_03.4_lotic en Surfacewater monitoring: 3.4 Eutrophication through surface water (including inundation): partim lotic waters SURF: 03.4_eutr_sw: lotic +SURF_03.4_lotic en Surfacewater monitoring: 3.4 Eutrophication through surface water (including inundation): scheme section lotic waters SURF: 03.4_eutr_sw: lotic SURF_03.4_lotic_group1 en types from oligotrophic environments oligotrophic SURF_03.4_lotic_group2 en types from mesotrophic environments mesotrophic SURF_03.4_lotic_group3 en types from weakly eutrophic environments weakly eutrophic @@ -141,14 +141,14 @@ GW_03.3_group2 nl types van mesotroof milieu mesotroof GW_03.3_group3 nl types van zwak eutroof milieu zwak eutroof GW_03.3_group4 nl types van matig eutroof tot eutroof milieu (matig) eutroof GW_04.2 nl Grondwatermeetnet: 4.2 Verzuring via het grondwater GW: 04.2_verzu_gw -GW_05.1_aq nl Grondwatermeetnet: 5.1 Verdroging via het grondwater: partim aquatisch GW: 05.1_verdro_gw: aq +GW_05.1_aq nl Grondwatermeetnet: 5.1 Verdroging via het grondwater: deelmeetnet aquatisch GW: 05.1_verdro_gw: aq GW_05.1_aq_group1 nl types van bronbeken bronbeken GW_05.1_aq_group2 nl types van stilstaand water met stabiel grondwaterregime stabiele plassen GW_05.1_aq_group3 nl types van laaglandbeken laaglandbeken GW_05.1_aq_group4 nl types van duinplassen (middelmatig grondwaterregime) duinplassen GW_05.1_aq_group5 nl types van vennen met dynamisch grondwaterregime dynamische vennen -GW_05.1_quarries nl Grondwatermeetnet: 5.1 Verdroging via het grondwater: partim mergelgroeven GW: 05.1_verdro_gw: quarries -GW_05.1_terr nl Grondwatermeetnet: 5.1 Verdroging via het grondwater: partim terrestrisch GW: 05.1_verdro_gw: terr +GW_05.1_quarries nl Grondwatermeetnet: 5.1 Verdroging via het grondwater: deelmeetnet mergelgroeven GW: 05.1_verdro_gw: quarries +GW_05.1_terr nl Grondwatermeetnet: 5.1 Verdroging via het grondwater: deelmeetnet terrestrisch GW: 05.1_verdro_gw: terr GW_05.1_terr_group1 nl types van zeer nat milieu zeer nat GW_05.1_terr_group2 nl types van nat milieu nat GW_05.1_terr_group3 nl types van matig nat milieu matig nat @@ -184,17 +184,17 @@ HQ9130 nl Meetnet habitatkwaliteit: eiken-beukenbossen met wilde hyacint en pare HQ9160 nl Meetnet habitatkwaliteit: eiken-haagbeukenbossen Meetnet habitatkwaliteit 9160 HQ9190 nl Meetnet habitatkwaliteit: oude eiken-berkenbossen Meetnet habitatkwaliteit 9190 HQ91E0 nl Meetnet habitatkwaliteit: vochtige alluviale bossen Meetnet habitatkwaliteit 91E0 -INUN nl Inundatiemeetnet NA -INUN_03.4 nl Inundatiemeetnet: 3.4 Eutrofiëring via het oppervlaktewater (incl. overstromingswater en afspoeling) INUN: 03.4_eutr_ow -INUN_061 nl Inundatiemeetnet: 61 Toename overstromingsduur of -frequentie (incl. getijden) INUN: 061_overstr_plus -INUN_062 nl Inundatiemeetnet: 62 Afname overstromingsduur of -frequentie (incl. getijden) INUN: 062_overstr_min -INUN_063 nl Inundatiemeetnet: 63 Toename van stroomsnelheid, waterpeil en/of de fluctuatie ervan INUN: 063_owpeil_plus -INUN_064 nl Inundatiemeetnet: 64 Afname van stroomsnelheid, waterpeil en/of de fluctuatie ervan INUN: 064_owpeil_min -INUN_065 nl Inundatiemeetnet: 65 Toename golfslagwerking INUN: 065_golf_plus -INUN_066 nl Inundatiemeetnet: 66 Afname golfslagwerking INUN: 066_golf_min -INUN_07.2 nl Inundatiemeetnet: 7.2 Verzoeting via het oppervlaktewater (incl. overstromingswater) INUN: 07.2_verzoet_ow -INUN_08.4 nl Inundatiemeetnet: 8.4 Verontreiniging via het oppervlaktewater (incl. overstromingswater) INUN: 08.4_verontr_ow -INUN_103 nl Inundatiemeetnet: 103 Klimaatverandering: zeespiegelstijging INUN: 103_klim_zee +INUN nl Inundatiewatermeetnet NA +INUN_03.4 nl Inundatiewatermeetnet: 3.4 Eutrofiëring via het oppervlaktewater (incl. overstromingswater en afspoeling) INUN: 03.4_eutr_ow +INUN_061 nl Inundatiewatermeetnet: 61 Toename overstromingsduur of -frequentie (incl. getijden) INUN: 061_overstr_plus +INUN_062 nl Inundatiewatermeetnet: 62 Afname overstromingsduur of -frequentie (incl. getijden) INUN: 062_overstr_min +INUN_063 nl Inundatiewatermeetnet: 63 Toename van stroomsnelheid, waterpeil en/of de fluctuatie ervan INUN: 063_owpeil_plus +INUN_064 nl Inundatiewatermeetnet: 64 Afname van stroomsnelheid, waterpeil en/of de fluctuatie ervan INUN: 064_owpeil_min +INUN_065 nl Inundatiewatermeetnet: 65 Toename golfslagwerking INUN: 065_golf_plus +INUN_066 nl Inundatiewatermeetnet: 66 Afname golfslagwerking INUN: 066_golf_min +INUN_07.2 nl Inundatiewatermeetnet: 7.2 Verzoeting via het oppervlaktewater (incl. overstromingswater) INUN: 07.2_verzoet_ow +INUN_08.4 nl Inundatiewatermeetnet: 8.4 Verontreiniging via het oppervlaktewater (incl. overstromingswater) INUN: 08.4_verontr_ow +INUN_103 nl Inundatiewatermeetnet: 103 Klimaatverandering: zeespiegelstijging INUN: 103_klim_zee lentic nl stilstaande wateren NA lotic nl stromende wateren NA MHQ nl Monitoringprogramma biotische habitatkwaliteit NA @@ -213,12 +213,12 @@ SOIL_08.2 nl Bodemmeetnet: 8.2 Verontreiniging via de bodem SOIL: 08.2_verontr_b SURF nl Oppervlaktewatermeetnet NA SURF_012 nl Oppervlaktewatermeetnet: 12 Toename bodemdynamiek (erosie, omwoeling, verstuiving) SURF: 012_boddyn_plus SURF_03.2 nl Oppervlaktewatermeetnet: 3.2 Eutrofiëring via de bodem SURF: 03.2_eutr_bod -SURF_03.4_lentic nl Oppervlaktewatermeetnet: 3.4 Eutrofiëring via het oppervlaktewater (incl. overstromingswater en afspoeling): partim stilstaande wateren SURF: 03.4_eutr_ow: lentic +SURF_03.4_lentic nl Oppervlaktewatermeetnet: 3.4 Eutrofiëring via het oppervlaktewater (incl. overstromingswater en afspoeling): deelmeetnet stilstaande wateren SURF: 03.4_eutr_ow: lentic SURF_03.4_lentic_group1 nl types van oligotroof milieu oligotroof SURF_03.4_lentic_group2 nl types van mesotroof milieu mesotroof SURF_03.4_lentic_group3 nl types van zwak eutroof milieu zwak eutroof SURF_03.4_lentic_group4 nl types van matig eutroof tot eutroof milieu (matig) eutroof -SURF_03.4_lotic nl Oppervlaktewatermeetnet: 3.4 Eutrofiëring via het oppervlaktewater (incl. overstromingswater en afspoeling): partim stromende wateren SURF: 03.4_eutr_ow: lotic +SURF_03.4_lotic nl Oppervlaktewatermeetnet: 3.4 Eutrofiëring via het oppervlaktewater (incl. overstromingswater en afspoeling): deelmeetnet stromende wateren SURF: 03.4_eutr_ow: lotic SURF_03.4_lotic_group1 nl types van oligotroof milieu oligotroof SURF_03.4_lotic_group2 nl types van mesotroof milieu mesotroof SURF_03.4_lotic_group3 nl types van zwak eutroof milieu zwak eutroof diff --git a/inst/textdata/namelist.yml b/inst/textdata/namelist.yml index adb6104..5ebc022 100644 --- a/inst/textdata/namelist.yml +++ b/inst/textdata/namelist.yml @@ -6,7 +6,7 @@ - lang - code hash: 3345146f5a5902a684bc1b965f00486c82952d94 - data_hash: 7c3bb83b09e5613712999d40029af0170cbbd90e + data_hash: f070e7c2d9a0782eda2000df4152e435895db638 code: class: character lang: diff --git a/misc/generate_textdata/10_schemes_and_scheme_types.Rmd b/misc/generate_textdata/10_schemes_and_scheme_types.Rmd index 8648814..77045c1 100644 --- a/misc/generate_textdata/10_schemes_and_scheme_types.Rmd +++ b/misc/generate_textdata/10_schemes_and_scheme_types.Rmd @@ -23,7 +23,14 @@ Reading data frame coming from the [n2khab-mne-selections](https://gitlab.com/fl ```{r} schemes_types_nl <- - read_vc("rawraw_data/10_compmeetnet_types_milieudrukken") + read_vc("rawraw_data/10_compmeetnet_types_milieudrukken") %>% + # fix terms on the fly: still to be implemented in n2khab-mne-selections repo! + mutate( + Comp_meetnet = fct_recode( + Comp_meetnet, + Inundatiewatermeetnet = "Inundatiemeetnet" + ) + ) ``` Reading a link between older Dutch codes of environmental pressures and the current ep_codes: @@ -81,7 +88,7 @@ schemes_schemetypes <- "Bodemmeetnet" = "SOIL", "Grondwatermeetnet" = "GW", "Oppervlaktewatermeetnet" = "SURF", - "Inundatiemeetnet" = "INUN"), + "Inundatiewatermeetnet" = "INUN"), attribute_2 = factor(attribute_2, levels = ep_codes %>% @@ -370,7 +377,7 @@ cbind(code = c("ATM", "SOIL", "GW", "SURF", "INUN"), "Bodemmeetnet", "Grondwatermeetnet", "Oppervlaktewatermeetnet", - "Inundatiemeetnet")) %>% + "Inundatiewatermeetnet")) %>% rbind(matrix(c("aq", "en", "aquatic", "terr", "en", "terrestrial", "quarries", "en", "marl quarries", @@ -423,13 +430,17 @@ schemes %>% left_join(namelist %>% select(-shortname), by = c("attribute_3" = "code", "lang")) %>% rename(name_4 = name) %>% - mutate(name = str_c(name_1, + mutate(partim = case_when( + is.na(name_4) ~ NA_character_, + lang == "en" ~ ": scheme section ", + lang == "nl" ~ ": deelmeetnet " + ), + name = str_c(name_1, ": ", name_3, ifelse(is.na(name_4), "", - str_c(": partim ", - name_4) + str_c(partim, name_4) ) ), shortname = str_c(attribute_1, diff --git a/misc/generate_textdata/index.Rmd b/misc/generate_textdata/index.Rmd index f3ef16e..2014b86 100644 --- a/misc/generate_textdata/index.Rmd +++ b/misc/generate_textdata/index.Rmd @@ -52,6 +52,7 @@ library(knitr) library(googlesheets4) local_gs4_quiet() library(git2rdata) +library(forcats) library(n2khab) opts_chunk$set( echo = TRUE, diff --git a/misc/generate_textdata/renv.lock b/misc/generate_textdata/renv.lock index e85d1be..ecd3434 100644 --- a/misc/generate_textdata/renv.lock +++ b/misc/generate_textdata/renv.lock @@ -1,6 +1,6 @@ { "R": { - "Version": "4.4.0", + "Version": "4.4.1", "Repositories": [ { "Name": "P3M", @@ -23,29 +23,29 @@ "Packages": { "DBI": { "Package": "DBI", - "Version": "1.2.2", + "Version": "1.2.3", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "methods" ], - "Hash": "164809cd72e1d5160b4cb3aa57f510fe" + "Hash": "065ae649b05f1ff66bb0c793107508f5" }, "KernSmooth": { "Package": "KernSmooth", - "Version": "2.23-22", + "Version": "2.23-24", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "stats" ], - "Hash": "2fecebc3047322fa5930f74fae5de70f" + "Hash": "9f33a1ee37bbe8919eb2ec4b9f2473a5" }, "MASS": { "Package": "MASS", - "Version": "7.3-60.2", + "Version": "7.3-61", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -56,7 +56,7 @@ "stats", "utils" ], - "Hash": "2f342c46163b0b54d7b64d1f798e2c78" + "Hash": "0cafd6f0500e5deba33be22c46bf6055" }, "R6": { "Package": "R6", @@ -167,14 +167,14 @@ }, "cachem": { "Package": "cachem", - "Version": "1.0.8", + "Version": "1.1.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "fastmap", "rlang" ], - "Hash": "c35768291560ce302c0a6589f92e837d" + "Hash": "cd9a672193789068eb5a2aad65a0dedf" }, "callr": { "Package": "callr", @@ -379,7 +379,7 @@ }, "downlit": { "Package": "downlit", - "Version": "0.4.3", + "Version": "0.4.4", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -395,7 +395,7 @@ "withr", "yaml" ], - "Hash": "14fa1f248b60ed67e1f5418391a17b14" + "Hash": "45a6a596bf0108ee1ff16a040a2df897" }, "dplyr": { "Package": "dplyr", @@ -449,14 +449,14 @@ }, "evaluate": { "Package": "evaluate", - "Version": "0.23", + "Version": "0.24.0", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "methods" ], - "Hash": "daf4a1246be12c1fa8c7705a0935c1a0" + "Hash": "a1066cbc05caee9a4bf6d90f194ff4da" }, "fansi": { "Package": "fansi", @@ -472,10 +472,10 @@ }, "fastmap": { "Package": "fastmap", - "Version": "1.1.1", + "Version": "1.2.0", "Source": "Repository", - "Repository": "RSPM", - "Hash": "f7736a18de97dea803bde0a2daaafb27" + "Repository": "CRAN", + "Hash": "aa5e1cd11c2d15497494c5292d7ffcc8" }, "fontawesome": { "Package": "fontawesome", @@ -684,14 +684,14 @@ }, "highr": { "Package": "highr", - "Version": "0.10", + "Version": "0.11", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "xfun" ], - "Hash": "06230136b2d2b9ba5805e1963fa6e890" + "Hash": "d65ba49117ca223614f71b60d85b8ab7" }, "htmltools": { "Package": "htmltools", @@ -815,9 +815,14 @@ }, "knitr": { "Package": "knitr", - "Version": "1.46", - "Source": "Repository", - "Repository": "RSPM", + "Version": "1.47.2", + "Source": "GitHub", + "RemoteType": "github", + "RemoteHost": "api.github.com", + "RemoteRepo": "knitr", + "RemoteUsername": "yihui", + "RemoteRef": "HEAD", + "RemoteSha": "f50b75b6feadb625ab0b3f76f21f5777e3c53232", "Requirements": [ "R", "evaluate", @@ -827,7 +832,7 @@ "xfun", "yaml" ], - "Hash": "6e008ab1d696a5283c79765fa7b56b47" + "Hash": "871ca8f9bb61c5e646bdb62c90348dd8" }, "later": { "Package": "later", @@ -935,13 +940,13 @@ }, "openssl": { "Package": "openssl", - "Version": "2.1.2", + "Version": "2.2.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "askpass" ], - "Hash": "ea2475b073243d9d338aa8f086ce973e" + "Hash": "2bcca3848e4734eb3b16103bc9aa4b8e" }, "pander": { "Package": "pander", @@ -1242,7 +1247,7 @@ "Package": "renv", "Version": "1.0.7", "Source": "Repository", - "Repository": "P3M", + "Repository": "RSPM", "Requirements": [ "utils" ], @@ -1250,20 +1255,20 @@ }, "rlang": { "Package": "rlang", - "Version": "1.1.3", + "Version": "1.1.4", "Source": "Repository", "Repository": "RSPM", "Requirements": [ "R", "utils" ], - "Hash": "42548638fae05fd9a9b5f3f437fbbbe2" + "Hash": "3eec01f8b1dee337674b2e34ab1f9bc1" }, "rmarkdown": { "Package": "rmarkdown", - "Version": "2.26", + "Version": "2.27", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "bslib", @@ -1280,7 +1285,7 @@ "xfun", "yaml" ], - "Hash": "9b148e7f95d33aac01f31282d49e4f44" + "Hash": "27f9502e1cdbfa195f94e03b0f517484" }, "roxygen2": { "Package": "roxygen2", @@ -1444,16 +1449,16 @@ }, "stringi": { "Package": "stringi", - "Version": "1.8.3", + "Version": "1.8.4", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "stats", "tools", "utils" ], - "Hash": "058aebddea264f4c99401515182e656a" + "Hash": "39e1144fd75428983dc3f63aa53dfa91" }, "stringr": { "Package": "stringr", @@ -1481,14 +1486,15 @@ }, "systemfonts": { "Package": "systemfonts", - "Version": "1.0.6", + "Version": "1.1.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", - "cpp11" + "cpp11", + "lifecycle" ], - "Hash": "6d538cff441f0f1f36db2209ac7495ac" + "Hash": "213b6b8ed5afbf934843e6c3b090d418" }, "testthat": { "Package": "testthat", @@ -1521,15 +1527,16 @@ }, "textshaping": { "Package": "textshaping", - "Version": "0.3.7", + "Version": "0.4.0", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "R", "cpp11", + "lifecycle", "systemfonts" ], - "Hash": "997aac9ad649e0ef3b97f96cddd5622b" + "Hash": "5142f8bc78ed3d819d26461b641627ce" }, "tibble": { "Package": "tibble", @@ -1602,13 +1609,13 @@ }, "tinytex": { "Package": "tinytex", - "Version": "0.50", + "Version": "0.51", "Source": "Repository", - "Repository": "RSPM", + "Repository": "CRAN", "Requirements": [ "xfun" ], - "Hash": "be7a76845222ad20adb761f462eed3ea" + "Hash": "d44e2fcd2e4e076f0aac540208559d1d" }, "units": { "Package": "units", @@ -1749,7 +1756,7 @@ }, "xfun": { "Package": "xfun", - "Version": "0.43", + "Version": "0.45", "Source": "Repository", "Repository": "RSPM", "Requirements": [ @@ -1757,7 +1764,7 @@ "stats", "tools" ], - "Hash": "ab6371d8653ce5f2f9290f4ec7b42a8e" + "Hash": "ca59c87fe305b16a9141a5874c3a7889" }, "xml2": { "Package": "xml2",