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remove species rank
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wlangera committed Aug 1, 2024
1 parent c78ebec commit 7f36ea0
Showing 1 changed file with 3 additions and 41 deletions.
44 changes: 3 additions & 41 deletions source/markdown/dwc_mapping_mas.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -363,7 +363,6 @@ species_matching_mas_list <- lapply(
out_cols = c("scientificName", "family", "class"),
filter_cols = list(class = "dwc_class", kingdom = "dwc_kingdom"),
lang = "nld",
rank = "SPECIES",
status = c("ACCEPTED", "DOUBTFUL"),
limit = 1000)
Expand All @@ -374,27 +373,6 @@ species_matching_mas %>%
kable()
```

Voor meeste soorten komt het goed uit, maar voor een paar soorten niet.
We proberen apart voor de resterende soorten.
We verwijderen `rank = "SPECIES"` en verhogen de limit naar 5000.

```{r}
species_matching_mas_rest <- species_matching_mas %>%
filter(is.na(scientificName)) %>%
select(dwc_taxonID, dwc_vernacularName, dwc_class, dwc_kingdom) %>%
map_taxa_from_vernacular(
vernacular_name_col = "dwc_vernacularName",
out_cols = c("scientificName", "family", "class"),
filter_cols = list(class = "dwc_class", kingdom = "dwc_kingdom"),
lang = "nld",
status = c("ACCEPTED", "DOUBTFUL"),
limit = 5000) %>%
arrange(class, family, scientificName)
species_matching_mas_rest %>%
kable()
```

Nu hebben we namen voor alle taxa.
Enkel Veldmuis/Aardmuis niet, wat prima is.

Expand All @@ -406,28 +384,13 @@ species_matching_mas_list2 <- lapply(
"species", "authorship", "rank", "speciesKey"),
filter_cols = list(class = "dwc_class", kingdom = "dwc_kingdom"),
lang = "nld",
rank = "SPECIES",
status = c("ACCEPTED", "DOUBTFUL"),
limit = 1000)
species_matching_mas2 <- do.call(rbind.data.frame,
species_matching_mas_list2)
species_matching_mas_rest2 <- species_matching_mas2 %>%
filter(is.na(scientificName)) %>%
select(dwc_taxonID, dwc_vernacularName, dwc_class, dwc_kingdom) %>%
map_taxa_from_vernacular(
vernacular_name_col = "dwc_vernacularName",
out_cols = c("scientificName", "phylum", "order", "family", "genus",
"species", "authorship", "rank", "speciesKey"),
filter_cols = list(class = "dwc_class", kingdom = "dwc_kingdom"),
lang = "nld",
status = c("ACCEPTED", "DOUBTFUL"),
limit = 5000)
taxon_core <- rbind.data.frame(species_matching_mas2 %>%
filter(!is.na(scientificName)),
species_matching_mas_rest2) %>%
taxon_core <- species_matching_mas2 %>%
full_join(taxon_core,
relationship = "many-to-many",
by = join_by(dwc_taxonID, dwc_vernacularName, dwc_class,
Expand Down Expand Up @@ -491,10 +454,9 @@ Er zijn een aantal mismatches:

1. Species versus subspecies
- op zich geen probleem
- wel voor Stadsduif, want Columba livia is Rotsduif (?) --> hard coden?
2. Genera
2. Andere genera
- Braamsluiper: geen data van Curruca curruca in GBIF tax. backbone
- Fluiter: met 2 ll'en is correct (? op wikipedia ook met 1 l)
- Fluiter: met 2 ll'en is correct (? op wikipedia ook met 1 l ...)
- Grasmus: geen data van Curruca communis in GBIF tax. backbone
- Matkop: zowel Parus montanus als Poecile montanus zelfde info in GBIF tax. backbone

Expand Down

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