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(v2.1.1.9071) update veterinary SIR interpretation, add only_fungi

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dr. M.S. (Matthijs) Berends
2024-09-19 11:44:56 +02:00
parent 573c0346ed
commit ddb23b6e73
52 changed files with 290 additions and 162 deletions
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42
data-raw/reproduction_of_microorganisms.R
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@ -736,6 +736,8 @@ taxonomy_mycobank <- taxonomy_mycobank %>%
# Combine the datasets ----------------------------------------------------
# TODO !! check why e.g. Clavispora lusitaniae is gotten from GBIF, not MycoBank !!
taxonomy <- taxonomy_lpsn %>%
# add fungi
bind_rows(taxonomy_mycobank) %>%
@ -1237,9 +1239,9 @@ saveRDS(taxonomy, "data-raw/taxonomy2.rds")
# taxonomy <- readRDS("data-raw/taxonomy2.rds")
# Remove unwanted taxonomic entries from Protoza/Fungi --------------------
# Remove unwanted taxonomic entries ---------------------------------------
taxonomy <- taxonomy %>%
part1 <- taxonomy %>%
filter(
# keep all we added ourselves:
source == "manually added" |
@ -1259,10 +1261,7 @@ taxonomy <- taxonomy %>%
# kingdom of Protozoa:
(phylum %in% c("Choanozoa", "Mycetozoa") & prevalence < 2) |
# Fungi:
(kingdom == "Fungi" & (!rank %in% c("genus", "species", "subspecies") | prevalence < 2)) |
# !(phylum %in% c("Ascomycota", "Zygomycota", "Basidiomycota") & prevalence == 2 & rank %in% c("genus", "species", "subspecies")),
# !(genus %in% c("Leptosphaeria", "Physarum") & rank %in% c("species", "subspecies")), # keep only genus of this rare fungus, with resp. 850 and 500 species
# # (leave Alternaria in there, part of human mycobiome and opportunistic pathogen)
(kingdom == "Fungi" & (!rank %in% c("genus", "species", "subspecies") | prevalence < 2 | class == "Pichiomycetes")) |
# Animalia:
genus %in% c("Lucilia", "Lumbricus") |
(class == "Insecta" & !rank %in% c("species", "subspecies")) | # keep only genus of insects, not all of their (sub)species
@ -1272,6 +1271,29 @@ taxonomy <- taxonomy %>%
filter(kingdom != "Plantae",
!(genus %in% c("Aedes", "Anopheles") & rank %in% c("species", "subspecies")))
# now get the parents and old names
part2 <- taxonomy %>%
filter(gbif %in% c(part1$gbif_parent[!is.na(part1$gbif_parent)], part1$gbif_renamed_to[!is.na(part1$gbif_renamed_to)]) |
mycobank %in% c(part1$mycobank_parent[!is.na(part1$mycobank_parent)], part1$mycobank_renamed_to[!is.na(part1$mycobank_renamed_to)]) |
lpsn %in% c(part1$lpsn_parent[!is.na(part1$lpsn_parent)], part1$lpsn_renamed_to[!is.na(part1$lpsn_renamed_to)]))
parts <- bind_rows(part1, part2)
part3 <- taxonomy %>%
filter(gbif %in% c(parts$gbif_parent[!is.na(parts$gbif_parent)], parts$gbif_renamed_to[!is.na(parts$gbif_renamed_to)]) |
mycobank %in% c(parts$mycobank_parent[!is.na(parts$mycobank_parent)], parts$mycobank_renamed_to[!is.na(parts$mycobank_renamed_to)]) |
lpsn %in% c(parts$lpsn_parent[!is.na(parts$lpsn_parent)], parts$lpsn_renamed_to[!is.na(parts$lpsn_renamed_to)]))
parts <- bind_rows(part1, part2, part3)
part4 <- taxonomy %>%
filter(gbif %in% c(parts$gbif_parent[!is.na(parts$gbif_parent)], parts$gbif_renamed_to[!is.na(parts$gbif_renamed_to)]) |
mycobank %in% c(parts$mycobank_parent[!is.na(parts$mycobank_parent)], parts$mycobank_renamed_to[!is.na(parts$mycobank_renamed_to)]) |
lpsn %in% c(parts$lpsn_parent[!is.na(parts$lpsn_parent)], parts$lpsn_renamed_to[!is.na(parts$lpsn_renamed_to)]))
parts <- bind_rows(part1, part2, part3, part4)
taxonomy <- bind_rows(part1, part2, part3, part4) %>%
arrange(fullname) %>%
distinct(fullname, .keep_all = TRUE)
# no ghost families, orders classes, phyla
taxonomy <- taxonomy %>%
group_by(kingdom, family) %>%
@ -2005,7 +2027,7 @@ taxonomy <- taxonomy %>%
filter(!mo %in% groups$mo) %>%
bind_rows(groups)
# we added MO code, so make sure everything is still unique
# we added an MO code, so make sure everything is still unique
any(duplicated(taxonomy$mo))
any(duplicated(taxonomy$fullname))
@ -2018,13 +2040,17 @@ AMR::clinical_breakpoints %>% filter(!mo %in% taxonomy$mo)
AMR::example_isolates %>% filter(!mo %in% taxonomy$mo)
AMR::intrinsic_resistant %>% filter(!mo %in% taxonomy$mo)
# all our previously manually added names should be in it
all(microorganisms$fullname[microorganisms$source == "manually added"] %in% taxonomy$fullname)
microorganisms$fullname[!microorganisms$fullname[microorganisms$source == "manually added"] %in% taxonomy$fullname]
# put this one back
taxonomy <- taxonomy %>%
bind_rows(microorganisms %>%
filter(fullname == "Blastocystis hominis") %>%
mutate(mo = as.character(mo)))
# we added MO code, so make sure everything is still unique
# we added an MO code, so make sure everything is still unique
any(duplicated(taxonomy$mo))
any(duplicated(taxonomy$fullname))