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(v0.7.1.9076) mo codes

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dr. M.S. (Matthijs) Berends
2019-09-20 12:33:05 +02:00
parent e2aa4f996b
commit 3596adb295
41 changed files with 465 additions and 520 deletions
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data-raw/microorganisms.translation.rds
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data-raw/reproduction_of_microorganisms.R
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@ -91,6 +91,32 @@ rm(data_col)
rm(data_dsmz)
rm(ref_taxonomy)
mo_found_in_NL <- c("Absidia", "Acremonium", "Actinotignum", "Aedes", "Alternaria", "Anaerosalibacter", "Ancylostoma",
"Angiostrongylus", "Anisakis", "Anopheles", "Apophysomyces", "Arachnia", "Ascaris", "Aspergillus",
"Aureobacterium", "Aureobasidium", "Bacteroides", "Balantidum", "Basidiobolus", "Beauveria",
"Bilophilia", "Branhamella", "Brochontrix", "Brugia", "Calymmatobacterium", "Candida", "Capillaria",
"Capnocytophaga", "Catabacter", "Cdc", "Chaetomium", "Chilomastix", "Chryseobacterium",
"Chryseomonas", "Chrysonilia", "Cladophialophora", "Cladosporium", "Clonorchis", "Conidiobolus",
"Contracaecum", "Cordylobia", "Cryptococcus", "Curvularia", "Demodex", "Dermatobia", "Dicrocoelium",
"Dioctophyma", "Diphyllobothrium", "Dipylidium", "Dirofilaria", "Dracunculus", "Echinococcus",
"Echinostoma", "Elisabethkingia", "Enterobius", "Enteromonas", "Euascomycetes", "Exophiala",
"Exserohilum", "Fasciola", "Fasciolopsis", "Flavobacterium", "Fonsecaea", "Fusarium", "Fusobacterium",
"Giardia", "Gnathostoma", "Hendersonula", "Heterophyes", "Hymenolepis", "Hypomyces",
"Hysterothylacium", "Kloeckera", "Koserella", "Larva", "Lecythophora", "Leishmania", "Lelliottia",
"Leptomyxida", "Leptosphaeria", "Leptotrichia", "Loa", "Lucilia", "Lumbricus", "Malassezia",
"Malbranchea", "Mansonella", "Mesocestoides", "Metagonimus", "Metarrhizium", "Molonomonas",
"Mortierella", "Mucor", "Multiceps", "Mycocentrospora", "Mycoplasma", "Nanophetus", "Nattrassia",
"Necator", "Nectria", "Novospingobium", "Ochroconis", "Oesophagostomum", "Oidiodendron", "Onchocerca",
"Opisthorchis", "Opistorchis", "Paragonimus", "Paramyxovirus", "Pediculus", "Phlebotomus",
"Phocanema", "Phoma", "Phthirus", "Piedraia", "Pithomyces", "Pityrosporum", "Prevotella",
"Pseudallescheria", "Pseudoterranova", "Pulex", "Retortamonas", "Rhizomucor", "Rhizopus",
"Rhodotorula", "Salinococcus", "Sanguibacteroides", "Sarcophagidae", "Sarcoptes", "Schistosoma",
"Scolecobasidium", "Scopulariopsis", "Scytalidium", "Spirometra", "Sporobolomyces", "Stachybotrys",
"Stenotrophomononas", "Stomatococcus", "Strongyloides", "Syncephalastraceae", "Syngamus", "Taenia",
"Ternidens", "Torulopsis", "Toxocara", "Treponema", "Trichinella", "Trichobilharzia", "Trichoderma",
"Trichomonas", "Trichophyton", "Trichosporon", "Trichostrongylus", "Trichuris", "Tritirachium",
"Trombicula", "Trypanosoma", "Tunga", "Ureaplasma", "Wuchereria")
MOs <- data_total %>%
filter(
(
@ -102,23 +128,7 @@ MOs <- data_total %>%
& !order %in% c("Eurotiales", "Microascales", "Mucorales", "Saccharomycetales", "Schizosaccharomycetales", "Tremellales", "Onygenales", "Pneumocystales"))
)
# or the genus has to be one of the genera we found in our hospitals last decades (Northern Netherlands, 2002-2018)
| genus %in% c("Absidia", "Acremonium", "Actinotignum", "Aedes", "Alternaria", "Anaerosalibacter", "Ancylostoma", "Angiostrongylus",
"Anisakis", "Anopheles", "Apophysomyces", "Arachnia", "Ascaris", "Aureobacterium", "Aureobasidium", "Balantidum", "Basidiobolus",
"Beauveria", "Bilophilia", "Branhamella", "Brochontrix", "Brugia", "Calymmatobacterium", "Capillaria", "Catabacter", "Cdc", "Chaetomium",
"Chilomastix", "Chryseomonas", "Chrysonilia", "Cladophialophora", "Cladosporium", "Clonorchis", "Conidiobolus", "Contracaecum",
"Cordylobia", "Curvularia", "Demodex", "Dermatobia", "Dicrocoelium", "Dioctophyma", "Diphyllobothrium", "Dipylidium", "Dirofilaria",
"Dracunculus", "Echinococcus", "Echinostoma", "Enterobius", "Enteromonas", "Euascomycetes", "Exophiala", "Exserohilum", "Fasciola",
"Fasciolopsis", "Fonsecaea", "Fusarium", "Gnathostoma", "Hendersonula", "Heterophyes", "Hymenolepis", "Hypomyces", "Hysterothylacium",
"Kloeckera", "Koserella", "Larva", "Lecythophora", "Leishmania", "Lelliottia", "Leptomyxida", "Leptosphaeria", "Loa", "Lucilia",
"Lumbricus", "Malassezia", "Malbranchea", "Mansonella", "Mesocestoides", "Metagonimus", "Metarrhizium", "Molonomonas", "Mortierella",
"Mucor", "Multiceps", "Mycocentrospora", "Nanophetus", "Nattrassia", "Necator", "Nectria", "Novospingobium", "Ochroconis",
"Oesophagostomum", "Oidiodendron", "Onchocerca", "Opisthorchis", "Opistorchis", "Paragonimus", "Paramyxovirus", "Pediculus",
"Phlebotomus", "Phocanema", "Phoma", "Phthirus", "Piedraia", "Pithomyces", "Pityrosporum", "Pseudallescheria", "Pseudoterranova",
"Pulex", "Retortamonas", "Rhizomucor", "Rhizopus", "Rhodotorula", "Salinococcus", "Sanguibacteroides", "Sarcophagidae", "Sarcoptes",
"Schistosoma", "Scolecobasidium", "Scopulariopsis", "Scytalidium", "Spirometra", "Sporobolomyces", "Stachybotrys", "Stenotrophomononas",
"Stomatococcus", "Strongyloides", "Syncephalastraceae", "Syngamus", "Taenia", "Ternidens", "Torulopsis", "Toxocara", "Trichinella",
"Trichobilharzia", "Trichoderma", "Trichomonas", "Trichosporon", "Trichostrongylus", "Trichuris", "Tritirachium", "Trombicula",
"Trypanosoma", "Tunga", "Wuchereria")
| genus %in% mo_found_in_NL
# or the taxonomic entry is old - the species was renamed
| !is.na(col_id_new)
) %>%
@ -209,11 +219,6 @@ MOs.old <- MOs %>%
distinct(fullname, .keep_all = TRUE) %>%
arrange(col_id)
MO.bak <- MOs
MOold.bak <- MOs.old
MOs <- MO.bak
MOs.old <- MOold.bak
MOs <- MOs %>%
filter(is.na(col_id_new) | source == "DSMZ") %>%
transmute(col_id,
@ -241,12 +246,6 @@ MOs <- MOs %>%
arrange(desc(source)) %>%
distinct(kingdom, fullname, .keep_all = TRUE)
# # Filter out the DSMZ records that were renamed and are now in MOs.old
# MOs <- MOs %>%
# filter(!(source == "DSMZ" & fullname %in% MOs.old$fullname)) %>%
# distinct(kingdom, fullname, .keep_all = TRUE) %>%
# filter(fullname != "")
# remove all genera that have no species - they are irrelevant for microbiology and almost all from the kingdom of Animalia
to_remove <- MOs %>%
filter(!kingdom %in% c("Bacteria", "Protozoa")) %>%
@ -259,15 +258,19 @@ to_remove <- MOs %>%
MOs <- MOs %>% filter(!(paste(kingdom, genus) %in% to_remove))
rm(to_remove)
# add CoL ID from MOs.bak, for the cases where DSMZ took preference
# add CoL's col_id, source and ref from MOs.bak, for the cases where DSMZ took preference
MOs <- MOs %>%
mutate(kingdom_fullname = paste(kingdom, fullname)) %>%
select(-col_id) %>%
left_join(MO.bak %>%
filter(is.na(col_id_new), !is.na(col_id)) %>%
transmute(col_id, kingdom_fullname = trimws(paste(kingdom, genus, species, subspecies))),
by = "kingdom_fullname") %>%
select(col_id, everything(), -kingdom_fullname)
transmute(col_id, species_id, source, ref, kingdom_fullname = trimws(paste(kingdom, genus, species, subspecies))),
by = "kingdom_fullname",
suffix = c("_dsmz", "_col")) %>%
mutate(col_id = col_id_col,
species_id = ifelse(!is.na(species_id_col), gsub(".*/(.*)$", "\\1", species_id_col), species_id_dsmz),
source = ifelse(!is.na(species_id_col), source_col, source_dsmz),
ref = ifelse(!is.na(species_id_col) & ref_col != "", ref_col, ref_dsmz)) %>%
select(-matches("(_col|_dsmz|kingdom_fullname)"))
MOs.old <- MOs.old %>%
@ -279,7 +282,9 @@ MOs.old <- MOs.old %>%
select(col_id = col_id.x, col_id_new, fullname, ref = ref.x)
# remove the records that are in MOs.old
sum(MOs.old$fullname %in% MOs$fullname)
MOs <- MOs %>% filter(!fullname %in% MOs.old$fullname)
sum(MOs.old$fullname %in% MOs$fullname)
# what characters are in the fullnames?
table(sort(unlist(strsplit(x = paste(MOs$fullname, collapse = ""), split = ""))))
@ -293,28 +298,13 @@ MOs <- MOs %>%
class == "Gammaproteobacteria"
| genus %in% c("Enterococcus", "Staphylococcus", "Streptococcus")
~ 1,
phylum %in% c("Proteobacteria",
"Firmicutes",
"Actinobacteria",
"Sarcomastigophora")
| genus %in% c("Aspergillus",
"Bacteroides",
"Candida",
"Capnocytophaga",
"Chryseobacterium",
"Cryptococcus",
"Elisabethkingia",
"Flavobacterium",
"Fusobacterium",
"Giardia",
"Leptotrichia",
"Mycoplasma",
"Prevotella",
"Rhodotorula",
"Treponema",
"Trichophyton",
"Ureaplasma")
| rank %in% c("kingdom", "phylum", "class", "order", "family")
kingdom %in% c("Archaea", "Bacteria", "Chromista", "Fungi")
& (phylum %in% c("Proteobacteria",
"Firmicutes",
"Actinobacteria",
"Sarcomastigophora")
| genus %in% mo_found_in_NL
| rank %in% c("kingdom", "phylum", "class", "order", "family"))
~ 2,
TRUE ~ 3
))
@ -322,7 +312,7 @@ MOs <- MOs %>%
# Add abbreviations so we can easily know which ones are which ones.
# These will become valid and unique microbial IDs for the AMR package.
MOs <- MOs %>%
arrange(prevalence, fullname) %>%
arrange(prevalence, genus, species, subspecies) %>%
group_by(kingdom) %>%
mutate(abbr_other = case_when(
rank == "family" ~ paste0("[FAM]_",
@ -354,22 +344,21 @@ MOs <- MOs %>%
)) %>%
# abbreviations may be same for genera between kingdoms,
# because each abbreviation starts with the the first character(s) of the kingdom
mutate(abbr_genus = abbreviate(genus,
mutate(abbr_genus = abbreviate(gsub("^ae", "\u00E6\u00E6", genus, ignore.case = TRUE), # keep a starting Latin ae
minlength = 5,
use.classes = TRUE,
method = "both.sides",
strict = FALSE)) %>%
method = "both.sides")) %>%
ungroup() %>%
group_by(genus) %>%
# species abbreviations may be the same between genera
# because the genus abbreviation is part of the abbreviation
mutate(abbr_species = abbreviate(species,
mutate(abbr_species = abbreviate(gsub("^ae", "\u00E6\u00E6", species),
minlength = 4,
use.classes = TRUE,
method = "both.sides")) %>%
ungroup() %>%
group_by(genus, species) %>%
mutate(abbr_subspecies = abbreviate(subspecies,
mutate(abbr_subspecies = abbreviate(gsub("^ae", "\u00E6\u00E6", subspecies),
minlength = 4,
use.classes = TRUE,
method = "both.sides")) %>%
@ -385,7 +374,8 @@ MOs <- MOs %>%
abbr_subspecies,
sep = "_"),
abbr_other),
sep = "_")))) %>%
sep = "_"))),
mo = gsub("(\u00C6|\u00E6)+", "AE", mo)) %>%
mutate(mo = ifelse(duplicated(.$mo),
# these one or two must be unique too
paste0(mo, "1"),
@ -643,7 +633,8 @@ MOs <- MOs %>%
MOs <- MOs %>%
group_by(kingdom) %>%
distinct(fullname, .keep_all = TRUE) %>%
ungroup()
ungroup() %>%
filter(fullname != "")
# everything distinct?
sum(duplicated(MOs$mo))
@ -693,10 +684,11 @@ MOs$col_id <- as.integer(MOs$col_id)
MOs.old$col_id <- as.integer(MOs.old$col_id)
MOs.old$col_id_new <- as.integer(MOs.old$col_id_new)
# save
# SAVE
### for other server
saveRDS(MOs, "microorganisms.rds")
saveRDS(MOs.old, "microorganisms.old.rds")
saveRDS(microorganisms.codes, "microorganisms.codes.rds")
### for same server
microorganisms <- MOs
microorganisms.old <- MOs.old
@ -708,9 +700,14 @@ class(microorganisms.translation$mo_new) <- "mo"
usethis::use_data(microorganisms, overwrite = TRUE, version = 2)
usethis::use_data(microorganisms.old, overwrite = TRUE, version = 2)
usethis::use_data(microorganisms.codes, overwrite = TRUE, version = 2)
saveRDS(AMR::microorganisms.translation, file = "microorganisms.translation.rds", version = 2) # this one will be covered in data-raw/internals.R
saveRDS(microorganisms.translation, file = "data-raw/microorganisms.translation.rds", version = 2) # this one will be covered in data-raw/internals.R
rm(microorganisms)
rm(microorganisms.old)
rm(microorganisms.codes)
rm(microorganisms.translation)
# and update the year and dimensions in R/data.R
devtools::load_all(".")
# TO DO AFTER THIS
# * Update the year and dim()s in R/data.R
# * Rerun data-raw/reproduction_of_rsi_translation.R
# * Run unit tests

6
data-raw/reproduction_of_microorganisms_new.R
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@ -654,4 +654,8 @@ usethis::use_data(microorganisms, overwrite = TRUE, version = 2)
usethis::use_data(microorganisms.old, overwrite = TRUE, version = 2)
rm(microorganisms)
rm(microorganisms.old)
# and update the year in R/data.R
# TO DO AFTER THIS
# * Update the year and dim()s in R/data.R
# * Rerun data-raw/reproduction_of_rsi_translation.R
# * Run unit tests

1
data-raw/reproduction_of_rsi_translation.R
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@ -52,3 +52,4 @@ rsi_translation <- tbl_mic %>%
# save to package
usethis::use_data(rsi_translation, overwrite = TRUE)
rm(rsi_translation)
devtools::load_all(".")