P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-16 09:43:13 +02:00
Code Releases Activity

(v1.5.0.9029) added missing families and orders

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-03-05 01:31:46 +01:00
parent ddf88345f1
commit 0e0e3c4ffa
30 changed files with 61003 additions and 60523 deletions
Download Patch File Download Diff File Expand all files Collapse all files

73
data-raw/reproduction_of_microorganisms_update.R
View File

@ -296,6 +296,79 @@ MOs <- MOs %>%
# clean up
df_remove_nonASCII()
# add all mssing genera, families and orders
MOs <- MOs %>%
bind_rows(
MOs %>%
arrange(genus, species) %>%
distinct(genus, .keep_all = TRUE) %>%
filter(rank == "species", source != "manually added") %>%
mutate(mo = gsub("^([A-Z]_[A-Z]+)_.*", "\\1", mo),
fullname = genus,
species = "",
subspecies = "",
rank = "genus",
species_id = "",
snomed = NA,
ref = NA_character_),
MOs %>%
group_by(family) %>%
filter(!any(rank == "family") & n() > 1) %>%
ungroup() %>%
arrange(family) %>%
distinct(family, .keep_all = TRUE) %>%
filter(!family %in% c("", NA), source != "manually added") %>%
mutate(mo = paste0(substr(kingdom, 1, 1), "_[FAM]_",
abbreviate(family,
minlength = 8,
use.classes = TRUE,
method = "both.sides",
strict = FALSE)),
mo = toupper(mo),
fullname = family,
genus = "",
species = "",
subspecies = "",
rank = "family",
species_id = "",
snomed = NA,
ref = NA_character_),
MOs %>%
group_by(order) %>%
filter(!any(rank == "order") & n() > 1) %>%
ungroup() %>%
arrange(order) %>%
distinct(order, .keep_all = TRUE) %>%
filter(!order %in% c("", NA), source != "manually added") %>%
mutate(mo = paste0(substr(kingdom, 1, 1), "_[ORD]_",
abbreviate(order,
minlength = 8,
use.classes = TRUE,
method = "both.sides",
strict = FALSE)),
mo = toupper(mo),
fullname = order,
family = "",
genus = "",
species = "",
subspecies = "",
rank = "order",
species_id = "",
snomed = NA,
ref = NA_character_)
) %>%
arrange(fullname)
# clean snomed
for (i in 1:nrow(MOs)) {
sno <- as.character(sort(unique(tolower(MOs[i, "snomed"][[1]]))))
if (length(sno) > 0) {
MOs[i, "snomed"][[1]] <- ifelse(length(sno[!sno == ""]) == 0, list(""), list(sno))
}
}
# Merge synonyms ----------------------------------------------------------
# remove synonyms that are now valid names