P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-12 15:41:48 +02:00
Code Releases Activity

(v2.1.1.9068) fix for mo_url() and as.mo() for synonyms

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2024-07-17 14:29:55 +02:00
parent 63f6790c58
commit 7258a491b9
6 changed files with 79 additions and 56 deletions
Download Patch File Download Diff File Expand all files Collapse all files

17
data-raw/reproduction_of_microorganisms.R
View File

@ -559,6 +559,9 @@ taxonomy_mycobank <- taxonomy_mycobank %>%
TRUE ~ "")
)
# FOR 2025: use this to get all the genera with updated names from MO_PREVALENT_GENERA:
# AMR::microorganisms %>% filter(genus %in% MO_PREVALENT_GENERA) %>% pull(fullname) %>% mo_current() %>% mo_genus() %>% unique() %>% sort()
# keep only the relevant ones
taxonomy_mycobank <- taxonomy_mycobank %>%
filter(order %in% include_fungal_orders |
@ -1078,6 +1081,8 @@ taxonomy <- taxonomy %>%
rank == "genus" ~ lpsn[match(kingdom, fullname)],
# species, always has a genus
rank == "species" ~ lpsn[match(genus, fullname)],
# subspecies, always has a genus + species
rank == "subspecies" ~ lpsn[match(paste(genus, species), fullname)],
TRUE ~ NA_character_),
mycobank_parent = case_when(
rank == "phylum" ~ mycobank[match(kingdom, fullname)],
@ -1101,6 +1106,8 @@ taxonomy <- taxonomy %>%
rank == "genus" ~ mycobank[match(kingdom, fullname)],
# species
rank == "species" ~ mycobank[match(genus, fullname)],
# subspecies
rank == "subspecies" ~ mycobank[match(paste(genus, species), fullname)],
TRUE ~ NA_character_),
gbif_parent = case_when(
rank == "phylum" ~ gbif[match(kingdom, fullname)],
@ -1124,6 +1131,8 @@ taxonomy <- taxonomy %>%
rank == "genus" ~ gbif[match(kingdom, fullname)],
# species
rank == "species" ~ gbif[match(genus, fullname)],
# subspecies
rank == "subspecies" ~ gbif[match(paste(genus, species), fullname)],
TRUE ~ NA_character_))
# these still have no record in our data set:
@ -1699,6 +1708,8 @@ taxonomy <- taxonomy %>%
rank == "genus" ~ lpsn[match(kingdom, fullname)],
# species, always has a genus
rank == "species" ~ lpsn[match(genus, fullname)],
# subspecies, always has a genus + species
rank == "subspecies" ~ lpsn[match(paste(genus, species), fullname)],
TRUE ~ NA_character_),
mycobank_parent = case_when(
rank == "phylum" ~ mycobank[match(kingdom, fullname)],
@ -1722,6 +1733,8 @@ taxonomy <- taxonomy %>%
rank == "genus" ~ mycobank[match(kingdom, fullname)],
# species
rank == "species" ~ mycobank[match(genus, fullname)],
# subspecies
rank == "subspecies" ~ mycobank[match(paste(genus, species), fullname)],
TRUE ~ NA_character_),
gbif_parent = case_when(
rank == "phylum" ~ gbif[match(kingdom, fullname)],
@ -1745,6 +1758,8 @@ taxonomy <- taxonomy %>%
rank == "genus" ~ gbif[match(kingdom, fullname)],
# species
rank == "species" ~ gbif[match(genus, fullname)],
# subspecies
rank == "subspecies" ~ gbif[match(paste(genus, species), fullname)],
TRUE ~ NA_character_))
# check again
@ -1810,6 +1825,8 @@ taxonomy <- taxonomy %>%
rank == "genus" ~ lpsn[match(kingdom, fullname)],
# species, always has a genus
rank == "species" ~ lpsn[match(genus, fullname)],
# subspecies, always has a genus + species
rank == "subspecies" ~ lpsn[match(paste(genus, species), fullname)],
TRUE ~ NA_character_))