mirror of
https://github.com/msberends/AMR.git
synced 2024-12-25 20:06:12 +01:00
1000 lines
44 KiB
R
1000 lines
44 KiB
R
# ==================================================================== #
|
|
# TITLE #
|
|
# Antimicrobial Resistance (AMR) Analysis #
|
|
# #
|
|
# SOURCE #
|
|
# https://github.com/msberends/AMR #
|
|
# #
|
|
# LICENCE #
|
|
# (c) 2018-2020 Berends MS, Luz CF et al. #
|
|
# #
|
|
# This R package is free software; you can freely use and distribute #
|
|
# it for both personal and commercial purposes under the terms of the #
|
|
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
|
|
# the Free Software Foundation. #
|
|
# #
|
|
# We created this package for both routine data analysis and academic #
|
|
# research and it was publicly released in the hope that it will be #
|
|
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
|
|
# Visit our website for more info: https://msberends.github.io/AMR. #
|
|
# ==================================================================== #
|
|
|
|
# Reproduction of the `microorganisms` data set
|
|
|
|
# Data retrieved from the Catalogue of Life (CoL) through the Encyclopaedia of Life:
|
|
# https://opendata.eol.org/dataset/catalogue-of-life/
|
|
# Data retrieved from the Global Biodiversity Information Facility (GBIF):
|
|
# https://doi.org/10.15468/rffz4x
|
|
#
|
|
# And from the Leibniz Institute: German Collection of Microorganisms and Cell Cultures (DSMZ)
|
|
# (register first at https://bacdive.dsmz.de/api/pnu/registration/register/ and use API as done below)
|
|
|
|
library(dplyr)
|
|
library(AMR)
|
|
# also needed: data.table, httr, jsonlite, cleaner, stringr
|
|
|
|
# unzip and extract taxa.txt (both around 1.5 GB, 3.7-3.9M rows) from Col and GBIF, then:
|
|
data_col_raw <- data.table::fread("data-raw/taxon.tab", quote = "")
|
|
data_gbif <- data.table::fread("data-raw/taxa.txt", quote = "")
|
|
|
|
# merge the two
|
|
data_col <- data_gbif %>%
|
|
rename(referenceID = identifier) %>%
|
|
bind_rows(data_col_raw) %>%
|
|
distinct(scientificName, kingdom, genus, specificEpithet, infraspecificEpithet, .keep_all = TRUE)
|
|
rm(data_col_raw)
|
|
rm(data_gbif)
|
|
|
|
|
|
# read the data from the DSMZ API (around 19000 rows)
|
|
dsmz_username <- ""
|
|
dsmz_password <- ""
|
|
GET_df <- function(url) {
|
|
result <- httr::GET(url, httr::authenticate(dsmz_username, dsmz_password))
|
|
httr::stop_for_status(result)
|
|
result %>%
|
|
httr::content(type = "text", encoding = "UTF-8") %>%
|
|
jsonlite::fromJSON(flatten = TRUE)
|
|
}
|
|
dsmz_first <- GET_df("https://bacdive.dsmz.de/api/pnu/species?page=1&format=json")
|
|
data_dsmz <- dsmz_first$results
|
|
# this next process will take appr. `dsmz_first$count / 100 * 5 / 60` minutes
|
|
for (i in 2:round((dsmz_first$count / 100) + 0.5)) {
|
|
data_dsmz <<- rbind(data_dsmz,
|
|
GET_df(paste0("https://bacdive.dsmz.de/api/pnu/species/?page=", i, "&format=json"))$results)
|
|
cat(i, "-", AMR:::percentage(i / round((dsmz_first$count / 100) + 0.5)), "\n")
|
|
}
|
|
rm(dsmz_first)
|
|
|
|
# the CoL data is over 3.7M rows:
|
|
data_col %>% cleaner::freq(kingdom)
|
|
# Item Count Percent Cum. Count Cum. Percent
|
|
# --- ---------- ---------- -------- ----------- -------------
|
|
# 1 Animalia 2,494,992 55.43% 2,494,992 55.43%
|
|
# 2 Plantae 1,379,674 30.65% 3,874,666 86.08%
|
|
# 3 Fungi 547,619 12.17% 4,422,285 98.24%
|
|
# 4 Chromista 51,475 1.14% 4,473,760 99.39%
|
|
# 5 Bacteria 14,442 0.32% 4,488,202 99.71%
|
|
# 6 Protozoa 8,750 0.19% 4,496,952 99.90%
|
|
# 7 Viruses 3,805 0.08% 4,500,757 99.99%
|
|
# 8 Archaea 609 0.01% 4,501,366 100.00%
|
|
|
|
# clean data_col
|
|
data_col.bak <- data_col
|
|
data_col_old <- data_col %>%
|
|
# filter: has new accepted name
|
|
filter(!is.na(acceptedNameUsageID)) %>%
|
|
as_tibble() %>%
|
|
transmute(fullname = trimws(stringr::str_replace(scientificName,
|
|
pattern = stringr::fixed(scientificNameAuthorship),
|
|
replacement = "")),
|
|
fullname_new = trimws(paste(ifelse(is.na(genus), "", genus),
|
|
ifelse(is.na(specificEpithet), "", specificEpithet),
|
|
ifelse(is.na(infraspecificEpithet), "", infraspecificEpithet))),
|
|
ref = scientificNameAuthorship,
|
|
prevalence = NA_integer_)
|
|
data_col <- data_col %>%
|
|
# filter: has no new accepted name
|
|
filter(is.na(acceptedNameUsageID)) %>%
|
|
as_tibble() %>%
|
|
transmute(fullname = "",
|
|
kingdom,
|
|
phylum,
|
|
class,
|
|
order,
|
|
family,
|
|
genus,
|
|
species = specificEpithet,
|
|
subspecies = infraspecificEpithet,
|
|
rank = taxonRank,
|
|
ref = scientificNameAuthorship,
|
|
species_id = referenceID,
|
|
source = "CoL")
|
|
|
|
# clean data_dsmz
|
|
data_dsmz.bak <- data_dsmz
|
|
data_dsmz_old <- data_dsmz %>%
|
|
# filter: correct name is not NULL
|
|
filter(!sapply(correct_name, is.null)) %>%
|
|
as_tibble() %>%
|
|
transmute(fullname = trimws(paste(ifelse(is.na(genus), "", genus),
|
|
ifelse(is.na(species_epithet), "", species_epithet),
|
|
ifelse(is.na(subspecies_epithet), "", subspecies_epithet))),
|
|
fullname_new = sapply(correct_name, function(x) x[2L]),
|
|
ref = authors,
|
|
prevalence = NA_integer_)
|
|
|
|
data_dsmz <- data_dsmz %>%
|
|
# filter: correct name is NULL
|
|
filter(sapply(correct_name, is.null)) %>%
|
|
as_tibble() %>%
|
|
transmute(fullname = "",
|
|
kingdom = regio,
|
|
phylum,
|
|
class = classis,
|
|
# order = "", # does not contain order, will add later based on CoL
|
|
family = familia,
|
|
genus = ifelse(is.na(genus), "", genus),
|
|
species = ifelse(is.na(species_epithet), "", species_epithet),
|
|
subspecies = ifelse(is.na(subspecies_epithet), "", subspecies_epithet),
|
|
rank = ifelse(species == "", "genus", "species"),
|
|
ref = authors,
|
|
species_id = as.character(pnu_no),
|
|
source = "DSMZ")
|
|
|
|
# DSMZ only contains genus/(sub)species, try to find taxonomic properties based on genus and data_col
|
|
ref_taxonomy <- data_col %>%
|
|
filter(family %in% data_dsmz$family & family != "") %>%
|
|
arrange(kingdom) %>%
|
|
distinct(family, .keep_all = TRUE) %>%
|
|
select(family, order)
|
|
|
|
data_dsmz <- data_dsmz %>%
|
|
left_join(ref_taxonomy, by = "family") # NAs will later become "(unknown ...)"
|
|
|
|
# combine everything
|
|
data_total <- data_col %>%
|
|
bind_rows(data_dsmz)
|
|
|
|
rm(data_col)
|
|
rm(data_dsmz)
|
|
rm(ref_taxonomy)
|
|
rm(data_col.bak)
|
|
rm(data_dsmz.bak)
|
|
|
|
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", "Blastocystis", "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", "Toxoplasma", "Treponema", "Trichinella", "Trichobilharzia", "Trichoderma",
|
|
"Trichomonas", "Trichophyton", "Trichosporon", "Trichostrongylus", "Trichuris", "Tritirachium",
|
|
"Trombicula", "Trypanosoma", "Tunga", "Ureaplasma", "Wuchereria")
|
|
|
|
MOs <- data_total %>%
|
|
filter(
|
|
(
|
|
# we only want all MICROorganisms and no viruses
|
|
!kingdom %in% c("Animalia", "Plantae", "Viruses")
|
|
# and not all fungi: Aspergillus, Candida, Trichphyton and Pneumocystis are the most important,
|
|
# so only keep these orders from the fungi:
|
|
& !(kingdom == "Fungi"
|
|
& !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% mo_found_in_NL
|
|
) %>%
|
|
# really no Plantae (e.g. Dracunculus exist both as worm and as plant)
|
|
filter(kingdom != "Plantae") %>%
|
|
filter(!rank %in% c("kingdom", "phylum", "class", "order", "family", "genus"))
|
|
|
|
# include all ranks other than species for the included species
|
|
MOs <- MOs %>% bind_rows(data_total %>%
|
|
filter((kingdom %in% MOs$kingdom & rank == "kingdom")
|
|
| (phylum %in% MOs$phylum & rank == "phylum")
|
|
| (class %in% MOs$class & rank == "class")
|
|
| (order %in% MOs$order & rank == "order")
|
|
| (family %in% MOs$family & rank == "family")
|
|
| (genus %in% MOs$genus & rank == "genus")))
|
|
|
|
get_author_year <- function(ref) {
|
|
# Only keep first author, e.g. transform 'Smith, Jones, 2011' to 'Smith et al., 2011'
|
|
|
|
authors2 <- iconv(ref, from = "UTF-8", to = "ASCII//TRANSLIT")
|
|
# remove leading and trailing brackets
|
|
authors2 <- gsub("^[(](.*)[)]$", "\\1", authors2)
|
|
# only take part after brackets if there's a name
|
|
authors2 <- ifelse(grepl(".*[)] [a-zA-Z]+.*", authors2),
|
|
gsub(".*[)] (.*)", "\\1", authors2),
|
|
authors2)
|
|
# get year from last 4 digits
|
|
lastyear = as.integer(gsub(".*([0-9]{4})$", "\\1", authors2))
|
|
# can never be later than now
|
|
lastyear = ifelse(lastyear > as.integer(format(Sys.Date(), "%Y")),
|
|
NA,
|
|
lastyear)
|
|
# get authors without last year
|
|
authors <- gsub("(.*)[0-9]{4}$", "\\1", authors2)
|
|
# remove nonsense characters from names
|
|
authors <- gsub("[^a-zA-Z,'& -]", "", authors)
|
|
# remove trailing and leading spaces
|
|
authors <- trimws(authors)
|
|
# only keep first author and replace all others by 'et al'
|
|
authors <- gsub("(,| and| et| &| ex| emend\\.?) .*", " et al.", authors)
|
|
# et al. always with ending dot
|
|
authors <- gsub(" et al\\.?", " et al.", authors)
|
|
authors <- gsub(" ?,$", "", authors)
|
|
# don't start with 'sensu' or 'ehrenb'
|
|
authors <- gsub("^(sensu|Ehrenb.?) ", "", authors, ignore.case = TRUE)
|
|
# no initials, only surname
|
|
authors <- gsub("^([A-Z]+ )+", "", authors, ignore.case = FALSE)
|
|
# combine author and year if year is available
|
|
ref <- ifelse(!is.na(lastyear),
|
|
paste0(authors, ", ", lastyear),
|
|
authors)
|
|
# fix beginning and ending
|
|
ref <- gsub(", $", "", ref)
|
|
ref <- gsub("^, ", "", ref)
|
|
ref <- gsub("^(emend|et al.,?)", "", ref)
|
|
ref <- trimws(ref)
|
|
|
|
# a lot start with a lowercase character - fix that
|
|
ref[!grepl("^d[A-Z]", ref)] <- gsub("^([a-z])", "\\U\\1", ref[!grepl("^d[A-Z]", ref)], perl = TRUE)
|
|
# specific one for the French that are named dOrbigny
|
|
ref[grepl("^d[A-Z]", ref)] <- gsub("^d", "d'", ref[grepl("^d[A-Z]", ref)])
|
|
ref <- gsub(" +", " ", ref)
|
|
ref
|
|
}
|
|
|
|
MOs <- MOs %>% mutate(ref = get_author_year(ref))
|
|
|
|
# Remove non-ASCII characters (these are not allowed by CRAN)
|
|
MOs <- MOs %>%
|
|
lapply(iconv, from = "UTF-8", to = "ASCII//TRANSLIT") %>%
|
|
as_tibble(stringsAsFactors = FALSE) %>%
|
|
# remove invalid characters
|
|
mutate_all(~gsub("[\"'`]+", "", .))
|
|
|
|
# set new fullnames
|
|
MOs <- MOs %>%
|
|
mutate(fullname = trimws(case_when(rank == "family" ~ family,
|
|
rank == "order" ~ order,
|
|
rank == "class" ~ class,
|
|
rank == "phylum" ~ phylum,
|
|
rank == "kingdom" ~ kingdom,
|
|
TRUE ~ paste(genus, species, subspecies))),
|
|
fullname = gsub(" (var|f|subsp)[.]", "", fullname)) %>%
|
|
# remove text if it contains 'Not assigned', etc.
|
|
mutate_all(function(x) ifelse(x %like% "(not assigned|homonym|mistake)", NA, x)) %>%
|
|
# clean taxonomy
|
|
mutate(kingdom = ifelse(is.na(kingdom) | trimws(kingdom) == "", "(unknown kingdom)", trimws(kingdom)),
|
|
phylum = ifelse(is.na(phylum) | trimws(phylum) == "", "(unknown phylum)", trimws(phylum)),
|
|
class = ifelse(is.na(class) | trimws(class) == "", "(unknown class)", trimws(class)),
|
|
order = ifelse(is.na(order) | trimws(order) == "", "(unknown order)", trimws(order)),
|
|
family = ifelse(is.na(family) | trimws(family) == "", "(unknown family)", trimws(family)))
|
|
|
|
# Split old taxonomic names
|
|
MOs.old <- data_col_old %>%
|
|
filter(!gsub(" (var|f|subsp)[.]", "", fullname_new) %in% data_dsmz_old$fullname) %>%
|
|
bind_rows(data_dsmz_old) %>%
|
|
mutate(fullname_new = gsub(" (var|f|subsp)[.]", "", fullname_new),
|
|
fullname = gsub(" (var|f|subsp)[.]", "", fullname)) %>%
|
|
# for cases like Chlamydia pneumoniae -> Chlamydophila pneumoniae -> Chlamydia pneumoniae:
|
|
filter(!fullname %in% fullname_new &
|
|
fullname_new %in% MOs$fullname &
|
|
!is.na(fullname) &
|
|
fullname != fullname_new) %>%
|
|
distinct(fullname, .keep_all = TRUE) %>%
|
|
arrange(fullname) %>%
|
|
mutate(ref = get_author_year(ref))
|
|
|
|
MOs <- MOs %>%
|
|
# remove entries that are old and in MOs.old
|
|
filter(!fullname %in% MOs.old$fullname) %>%
|
|
# mark up
|
|
transmute(fullname,
|
|
kingdom,
|
|
phylum,
|
|
class,
|
|
order,
|
|
family,
|
|
genus,
|
|
species,
|
|
subspecies,
|
|
rank,
|
|
ref,
|
|
species_id = gsub("[^a-zA-Z0-9].*", "", species_id),
|
|
source) %>%
|
|
# prefer known taxonomy over unknown taxonomy, then DSMZ over CoL (= desc)
|
|
arrange(desc(kingdom, genus, species, source)) %>%
|
|
distinct(kingdom, fullname, .keep_all = TRUE)
|
|
|
|
# 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")) %>%
|
|
group_by(kingdom, genus) %>%
|
|
count() %>%
|
|
filter(n == 1) %>%
|
|
ungroup() %>%
|
|
mutate(kingdom_genus = paste(kingdom, genus)) %>%
|
|
pull(kingdom_genus)
|
|
MOs <- MOs %>% filter(!(paste(kingdom, genus) %in% to_remove))
|
|
rm(to_remove)
|
|
|
|
# add all mssing genera, families and orders
|
|
MOs <- MOs %>%
|
|
bind_rows(MOs %>%
|
|
arrange(genus, species) %>%
|
|
distinct(genus, .keep_all = TRUE) %>%
|
|
filter(rank == "species") %>%
|
|
mutate(fullname = genus,
|
|
species = "",
|
|
rank = "genus",
|
|
species_id = "",
|
|
ref = NA_character_)) %>%
|
|
bind_rows(MOs %>%
|
|
arrange(family, genus) %>%
|
|
distinct(family, .keep_all = TRUE) %>%
|
|
filter(rank == "genus") %>%
|
|
mutate(fullname = family,
|
|
genus = "",
|
|
rank = "family",
|
|
species_id = "",
|
|
ref = NA_character_)) %>%
|
|
bind_rows(MOs %>%
|
|
arrange(order, family) %>%
|
|
distinct(family, .keep_all = TRUE) %>%
|
|
filter(rank == "family") %>%
|
|
mutate(fullname = order,
|
|
family = "",
|
|
rank = "order",
|
|
species_id = "",
|
|
ref = NA_character_))
|
|
|
|
# remove the empty ones
|
|
MOs <- MOs %>%
|
|
mutate(fullname = gsub(",.*", "", fullname)) %>%
|
|
distinct(kingdom, fullname, .keep_all = TRUE) %>%
|
|
filter(fullname != "")
|
|
|
|
# what characters are in the fullnames?
|
|
table(sort(unlist(strsplit(x = paste(MOs$fullname, collapse = ""), split = ""))))
|
|
MOs %>% filter(!fullname %like% "^[a-z ]+$") %>% arrange(fullname) %>% View()
|
|
|
|
table(MOs$kingdom, MOs$rank)
|
|
table(AMR::microorganisms$kingdom, AMR::microorganisms$rank)
|
|
|
|
# set prevalence per species
|
|
MOs <- MOs %>%
|
|
mutate(prevalence = case_when(
|
|
class == "Gammaproteobacteria"
|
|
| genus %in% c("Enterococcus", "Staphylococcus", "Streptococcus")
|
|
~ 1,
|
|
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
|
|
))
|
|
|
|
# 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, genus, species, subspecies) %>%
|
|
group_by(kingdom) %>%
|
|
mutate(abbr_other = case_when(
|
|
rank == "family" ~ paste0("[FAM]_",
|
|
abbreviate(family,
|
|
minlength = 8,
|
|
use.classes = TRUE,
|
|
method = "both.sides",
|
|
strict = FALSE)),
|
|
rank == "order" ~ paste0("[ORD]_",
|
|
abbreviate(order,
|
|
minlength = 8,
|
|
use.classes = TRUE,
|
|
method = "both.sides",
|
|
strict = FALSE)),
|
|
rank == "class" ~ paste0("[CLS]_",
|
|
abbreviate(class,
|
|
minlength = 8,
|
|
use.classes = TRUE,
|
|
method = "both.sides",
|
|
strict = FALSE)),
|
|
rank == "phylum" ~ paste0("[PHL]_",
|
|
abbreviate(phylum,
|
|
minlength = 8,
|
|
use.classes = TRUE,
|
|
method = "both.sides",
|
|
strict = FALSE)),
|
|
rank == "kingdom" ~ paste0("[KNG]_", kingdom),
|
|
TRUE ~ NA_character_
|
|
)) %>%
|
|
# 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(gsub("^ae", "\u00E6\u00E6", genus, ignore.case = TRUE), # keep a starting Latin ae
|
|
minlength = 5,
|
|
use.classes = TRUE,
|
|
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(gsub("^ae", "\u00E6\u00E6", species),
|
|
minlength = 4,
|
|
use.classes = TRUE,
|
|
method = "both.sides")) %>%
|
|
ungroup() %>%
|
|
group_by(genus, species) %>%
|
|
mutate(abbr_subspecies = abbreviate(gsub("^ae", "\u00E6\u00E6", subspecies),
|
|
minlength = 4,
|
|
use.classes = TRUE,
|
|
method = "both.sides")) %>%
|
|
ungroup() %>%
|
|
# remove trailing underscores
|
|
mutate(mo = gsub("_+$", "",
|
|
toupper(paste(ifelse(kingdom %in% c("Animalia", "Plantae"),
|
|
substr(kingdom, 1, 2),
|
|
substr(kingdom, 1, 1)),
|
|
ifelse(is.na(abbr_other),
|
|
paste(abbr_genus,
|
|
abbr_species,
|
|
abbr_subspecies,
|
|
sep = "_"),
|
|
abbr_other),
|
|
sep = "_"))),
|
|
mo = gsub("(\u00C6|\u00E6)+", "AE", mo)) %>%
|
|
mutate(mo = ifelse(duplicated(.$mo),
|
|
# these one or two must be unique too
|
|
paste0(mo, "1"),
|
|
mo),
|
|
fullname = ifelse(fullname == "",
|
|
trimws(paste(genus, species, subspecies)),
|
|
fullname)) %>%
|
|
# put `mo` in front, followed by the rest
|
|
select(mo, everything(), -abbr_other, -abbr_genus, -abbr_species, -abbr_subspecies)
|
|
|
|
# add non-taxonomic entries
|
|
MOs <- MOs %>%
|
|
bind_rows(
|
|
# Unknowns
|
|
data.frame(mo = "UNKNOWN",
|
|
fullname = "(unknown name)",
|
|
kingdom = "(unknown kingdom)",
|
|
phylum = "(unknown phylum)",
|
|
class = "(unknown class)",
|
|
order = "(unknown order)",
|
|
family = "(unknown family)",
|
|
genus = "(unknown genus)",
|
|
species = "(unknown species)",
|
|
subspecies = "(unknown subspecies)",
|
|
rank = "(unknown rank)",
|
|
ref = NA_character_,
|
|
species_id = "",
|
|
source = "manually added",
|
|
prevalence = 1,
|
|
stringsAsFactors = FALSE),
|
|
data.frame(mo = "B_GRAMN",
|
|
fullname = "(unknown Gram-negatives)",
|
|
kingdom = "Bacteria",
|
|
phylum = "(unknown phylum)",
|
|
class = "(unknown class)",
|
|
order = "(unknown order)",
|
|
family = "(unknown family)",
|
|
genus = "(unknown Gram-negatives)",
|
|
species = "(unknown species)",
|
|
subspecies = "(unknown subspecies)",
|
|
rank = "species",
|
|
ref = NA_character_,
|
|
species_id = "",
|
|
source = "manually added",
|
|
prevalence = 1,
|
|
stringsAsFactors = FALSE),
|
|
data.frame(mo = "B_GRAMP",
|
|
fullname = "(unknown Gram-positives)",
|
|
kingdom = "Bacteria",
|
|
phylum = "(unknown phylum)",
|
|
class = "(unknown class)",
|
|
order = "(unknown order)",
|
|
family = "(unknown family)",
|
|
genus = "(unknown Gram-positives)",
|
|
species = "(unknown species)",
|
|
subspecies = "(unknown subspecies)",
|
|
rank = "species",
|
|
ref = NA_character_,
|
|
species_id = "",
|
|
source = "manually added",
|
|
prevalence = 1,
|
|
stringsAsFactors = FALSE),
|
|
data.frame(mo = "F_YEAST",
|
|
fullname = "(unknown yeast)",
|
|
kingdom = "Fungi",
|
|
phylum = "(unknown phylum)",
|
|
class = "(unknown class)",
|
|
order = "(unknown order)",
|
|
family = "(unknown family)",
|
|
genus = "(unknown genus)",
|
|
species = "(unknown species)",
|
|
subspecies = "(unknown subspecies)",
|
|
rank = "species",
|
|
ref = NA_character_,
|
|
species_id = "",
|
|
source = "manually added",
|
|
prevalence = 2,
|
|
stringsAsFactors = FALSE),
|
|
data.frame(mo = "F_FUNGUS",
|
|
fullname = "(unknown fungus)",
|
|
kingdom = "Fungi",
|
|
phylum = "(unknown phylum)",
|
|
class = "(unknown class)",
|
|
order = "(unknown order)",
|
|
family = "(unknown family)",
|
|
genus = "(unknown genus)",
|
|
species = "(unknown species)",
|
|
subspecies = "(unknown subspecies)",
|
|
rank = "species",
|
|
ref = NA_character_,
|
|
species_id = "",
|
|
source = "manually added",
|
|
prevalence = 2,
|
|
stringsAsFactors = FALSE),
|
|
# CoNS
|
|
MOs %>%
|
|
filter(genus == "Staphylococcus", species == "epidermidis") %>% .[1,] %>%
|
|
mutate(mo = gsub("(.*)_(.*)_.*", "\\1_\\2_CONS", mo),
|
|
species = "coagulase-negative",
|
|
fullname = "Coagulase-negative Staphylococcus (CoNS)",
|
|
ref = NA_character_,
|
|
species_id = "",
|
|
source = "manually added"),
|
|
# CoPS
|
|
MOs %>%
|
|
filter(genus == "Staphylococcus", species == "epidermidis") %>% .[1,] %>%
|
|
mutate(mo = gsub("(.*)_(.*)_.*", "\\1_\\2_COPS", mo),
|
|
species = "coagulase-positive",
|
|
fullname = "Coagulase-positive Staphylococcus (CoPS)",
|
|
ref = NA_character_,
|
|
species_id = "",
|
|
source = "manually added"),
|
|
# Streptococci groups A, B, C, F, H, K
|
|
MOs %>%
|
|
filter(genus == "Streptococcus", species == "pyogenes") %>% .[1,] %>%
|
|
# we can keep all other details, since S. pyogenes is the only member of group A
|
|
mutate(mo = gsub("(.*)_(.*)_.*", "\\1_\\2_GRPA", mo),
|
|
species = "group A" ,
|
|
fullname = "Streptococcus group A",
|
|
source = "manually added"),
|
|
MOs %>%
|
|
filter(genus == "Streptococcus", species == "agalactiae") %>% .[1,] %>%
|
|
# we can keep all other details, since S. agalactiae is the only member of group B
|
|
mutate(mo = gsub("(.*)_(.*)_.*", "\\1_\\2_GRPB", mo),
|
|
species = "group B" ,
|
|
fullname = "Streptococcus group B",
|
|
source = "manually added"),
|
|
MOs %>%
|
|
filter(genus == "Streptococcus", species == "dysgalactiae") %>% .[1,] %>%
|
|
mutate(mo = gsub("(.*)_(.*)_.*", "\\1_\\2_GRPC", mo),
|
|
species = "group C" ,
|
|
fullname = "Streptococcus group C",
|
|
ref = NA_character_,
|
|
species_id = "",
|
|
source = "manually added"),
|
|
MOs %>%
|
|
filter(genus == "Streptococcus", species == "agalactiae") %>% .[1,] %>%
|
|
mutate(mo = gsub("(.*)_(.*)_.*", "\\1_\\2_GRPD", mo),
|
|
species = "group D" ,
|
|
fullname = "Streptococcus group D",
|
|
ref = NA_character_,
|
|
species_id = "",
|
|
source = "manually added"),
|
|
MOs %>%
|
|
filter(genus == "Streptococcus", species == "agalactiae") %>% .[1,] %>%
|
|
mutate(mo = gsub("(.*)_(.*)_.*", "\\1_\\2_GRPF", mo),
|
|
species = "group F" ,
|
|
fullname = "Streptococcus group F",
|
|
ref = NA_character_,
|
|
species_id = "",
|
|
source = "manually added"),
|
|
MOs %>%
|
|
filter(genus == "Streptococcus", species == "agalactiae") %>% .[1,] %>%
|
|
mutate(mo = gsub("(.*)_(.*)_.*", "\\1_\\2_GRPG", mo),
|
|
species = "group G" ,
|
|
fullname = "Streptococcus group G",
|
|
ref = NA_character_,
|
|
species_id = "",
|
|
source = "manually added"),
|
|
MOs %>%
|
|
filter(genus == "Streptococcus", species == "agalactiae") %>% .[1,] %>%
|
|
mutate(mo = gsub("(.*)_(.*)_.*", "\\1_\\2_GRPH", mo),
|
|
species = "group H" ,
|
|
fullname = "Streptococcus group H",
|
|
ref = NA_character_,
|
|
species_id = "",
|
|
source = "manually added"),
|
|
MOs %>%
|
|
filter(genus == "Streptococcus", species == "agalactiae") %>% .[1,] %>%
|
|
mutate(mo = gsub("(.*)_(.*)_.*", "\\1_\\2_GRPK", mo),
|
|
species = "group K" ,
|
|
fullname = "Streptococcus group K",
|
|
ref = NA_character_,
|
|
species_id = "",
|
|
source = "manually added"),
|
|
# Beta haemolytic Streptococci
|
|
MOs %>%
|
|
filter(genus == "Streptococcus", species == "agalactiae") %>% .[1,] %>%
|
|
mutate(mo = gsub("(.*)_(.*)_.*", "\\1_\\2_HAEM", mo),
|
|
species = "beta-haemolytic" ,
|
|
fullname = "Beta-haemolytic Streptococcus",
|
|
ref = NA_character_,
|
|
species_id = "",
|
|
source = "manually added"),
|
|
# Viridans Streptococci
|
|
MOs %>%
|
|
filter(genus == "Streptococcus", species == "agalactiae") %>% .[1,] %>%
|
|
mutate(mo = gsub("(.*)_(.*)_.*", "\\1_\\2_VIRI", mo),
|
|
species = "viridans" ,
|
|
fullname = "Viridans Group Streptococcus (VGS)",
|
|
ref = NA_character_,
|
|
species_id = "",
|
|
source = "manually added"),
|
|
# Milleri Streptococci
|
|
MOs %>%
|
|
filter(genus == "Streptococcus", species == "agalactiae") %>% .[1,] %>%
|
|
mutate(mo = gsub("(.*)_(.*)_.*", "\\1_\\2_MILL", mo),
|
|
species = "milleri" ,
|
|
fullname = "Milleri Group Streptococcus (MGS)",
|
|
ref = NA_character_,
|
|
species_id = "",
|
|
source = "manually added"),
|
|
# Candida krusei
|
|
MOs %>%
|
|
filter(genus == "Candida", species == "glabrata") %>% .[1,] %>%
|
|
mutate(mo = gsub("(.*)_(.*)_.*", "\\1_\\2_KRUS", mo),
|
|
species = "krusei" ,
|
|
fullname = "Candida krusei",
|
|
ref = NA_character_,
|
|
species_id = "",
|
|
source = "manually added"),
|
|
# Blastocystis hominis does not exist (it means 'got a Blastocystis from humans', PMID 15634993)
|
|
# but let's be nice to the clinical people in microbiology
|
|
MOs %>%
|
|
filter(fullname == "Blastocystis") %>%
|
|
mutate(mo = paste0(mo, "_HMNS"),
|
|
fullname = paste(fullname, "hominis"),
|
|
species = "hominis",
|
|
source = "manually added",
|
|
ref = NA_character_,
|
|
species_id = ""),
|
|
# Trichomonas vaginalis is missing, same order as Dientamoeba
|
|
MOs %>%
|
|
filter(fullname == "Dientamoeba") %>%
|
|
mutate(mo = gsub("(.*?)_.*", "\\1_THMNS", mo),
|
|
fullname = "Trichomonas",
|
|
family = "Trichomonadidae",
|
|
genus = "Trichomonas",
|
|
source = "manually added",
|
|
ref = "Donne, 1836",
|
|
species_id = ""),
|
|
MOs %>%
|
|
filter(fullname == "Dientamoeba fragilis") %>%
|
|
mutate(mo = gsub("(.*?)_.*", "\\1_THMNS_VAG", mo),
|
|
fullname = "Trichomonas vaginalis",
|
|
family = "Trichomonadidae",
|
|
genus = "Trichomonas",
|
|
species = "vaginalis",
|
|
source = "manually added",
|
|
ref = "Donne, 1836",
|
|
species_id = ""),
|
|
MOs %>% # add family as such too
|
|
filter(fullname == "Monocercomonadidae") %>%
|
|
mutate(mo = gsub("(.*)_(.*)_.*", "\\1_\\2_TRCHMNDD", mo),
|
|
fullname = "Trichomonadidae",
|
|
family = "Trichomonadidae",
|
|
rank = "family",
|
|
genus = "",
|
|
species = "",
|
|
source = "manually added",
|
|
ref = "",
|
|
species_id = ""),
|
|
)
|
|
|
|
# Incorporate new microbial order for Gammaproteobacteria - Adeolu et al. (2016), PMID 27620848
|
|
MOs[which(MOs$family == "Enterobacteriaceae"), "family"] <- ""
|
|
MOs[which(MOs$genus %in% c("Escherichia",
|
|
"Atlantibacter",
|
|
"Biostraticola",
|
|
"Buttiauxella",
|
|
"Cedecea",
|
|
"Citrobacter",
|
|
"Cronobacter",
|
|
"Enterobacillus",
|
|
"Enterobacter",
|
|
"Franconibacter",
|
|
"Gibbsiella",
|
|
"Izhakiella",
|
|
"Klebsiella",
|
|
"Kluyvera",
|
|
"Kosakonia",
|
|
"Leclercia",
|
|
"Lelliottia",
|
|
"Mangrovibacter",
|
|
"Pluralibacter",
|
|
"Pseudocitrobacter",
|
|
"Raoultella",
|
|
"Rosenbergiella",
|
|
"Saccharobacter",
|
|
"Salmonella",
|
|
"Shigella",
|
|
"Shimwellia",
|
|
"Siccibacter",
|
|
"Trabulsiella",
|
|
"Yokenella")), "family"] <- "Enterobacteriaceae"
|
|
MOs[which(MOs$genus %in% c("Erwinia",
|
|
"Buchnera",
|
|
"Pantoea",
|
|
"Phaseolibacter",
|
|
"Tatumella",
|
|
"Wigglesworthia")), "family"] <- "Erwiniaceae"
|
|
MOs[which(MOs$genus %in% c("Pectobacterium",
|
|
"Brenneria",
|
|
"Dickeya",
|
|
"Lonsdalea",
|
|
"Sodalis")), "family"] <- "Pectobacteriaceae"
|
|
MOs[which(MOs$genus %in% c("Yersinia",
|
|
"Chania",
|
|
"Ewingella",
|
|
"Rahnella",
|
|
"Rouxiella",
|
|
"Samsonia",
|
|
"Serratia")), "family"] <- "Yersiniaceae"
|
|
MOs[which(MOs$genus %in% c("Hafnia",
|
|
"Edwardsiella",
|
|
"Obesumbacterium")), "family"] <- "Hafniaceae"
|
|
MOs[which(MOs$genus %in% c("Morganella",
|
|
"Arsenophonus",
|
|
"Cosenzaea",
|
|
"Moellerella",
|
|
"Photorhabdus",
|
|
"Proteus",
|
|
"Providencia",
|
|
"Xenorhabdus")), "family"] <- "Morganellaceae"
|
|
MOs[which(MOs$genus %in% c("Budvicia",
|
|
"Leminorella",
|
|
"Pragia")), "family"] <- "Budviciaceae"
|
|
MOs[which(MOs$family %in% c("Enterobacteriaceae",
|
|
"Erwiniaceae",
|
|
"Pectobacteriaceae",
|
|
"Yersiniaceae",
|
|
"Hafniaceae",
|
|
"Morganellaceae",
|
|
"Budviciaceae")), "order"] <- "Enterobacterales"
|
|
new_families <- MOs %>%
|
|
filter(order == "Enterobacterales") %>%
|
|
pull(family) %>%
|
|
unique()
|
|
|
|
MOs <- MOs %>%
|
|
filter(!(rank == "family" & fullname %in% new_families)) %>%
|
|
bind_rows(tibble(mo = paste0("B_[FAM]_",
|
|
toupper(abbreviate(new_families,
|
|
minlength = 8,
|
|
use.classes = TRUE,
|
|
method = "both.sides",
|
|
strict = FALSE))),
|
|
fullname = new_families,
|
|
kingdom = "Bacteria",
|
|
phylum = "Proteobacteria",
|
|
class = "Gammaproteobacteria",
|
|
order = "Enterobacterales",
|
|
family = new_families,
|
|
genus = "",
|
|
species = "",
|
|
subspecies = "",
|
|
rank = "family",
|
|
ref = "Adeolu et al., 2016",
|
|
species_id = NA_character_,
|
|
source = "manually added",
|
|
prevalence = 1))
|
|
|
|
MOs[which(MOs$order == "Enterobacteriales"), "order"] <- "Enterobacterales"
|
|
MOs[which(MOs$fullname == "Enterobacteriales"), "fullname"] <- "Enterobacterales"
|
|
|
|
# add prevalence to old taxonomic names
|
|
MOs.old <- MOs.old %>%
|
|
select(-prevalence) %>%
|
|
left_join(MOs %>% select(fullname, prevalence), by = c("fullname_new" = "fullname"))
|
|
|
|
# everything distinct?
|
|
sum(duplicated(MOs$mo))
|
|
sum(duplicated(MOs$fullname))
|
|
colnames(MOs)
|
|
|
|
# add the ones we would delete now, that have unexisting codes and names (also in the old names)
|
|
MOs <- MOs %>%
|
|
mutate(mo = as.character(mo)) %>%
|
|
bind_rows(
|
|
AMR::microorganisms %>%
|
|
mutate(mo = as.character(mo)) %>%
|
|
filter(genus %in% gen & !fullname %in% AMR::microorganisms$fullname &
|
|
!fullname %in% AMR::microorganisms.old$fullname &
|
|
!mo %in% microorganisms$mo) %>%
|
|
select(all_of(colnames(AMR::microorganisms)))
|
|
)
|
|
|
|
# here we welcome the new ones:
|
|
MOs %>% arrange(fullname) %>% filter(!fullname %in% AMR::microorganisms$fullname) %>% View()
|
|
MOs.old %>% arrange(fullname) %>% filter(!fullname %in% AMR::microorganisms.old$fullname) %>% View()
|
|
# and the ones we lost:
|
|
# AMR::microorganisms %>% filter(!fullname %in% MOs$fullname) %>% View() # based on fullname
|
|
AMR::microorganisms %>% filter(!fullname %in% c(MOs$fullname, MOs.old$fullname)) %>% View() # excluding renamed ones
|
|
# AMR::microorganisms %>% filter(!mo %in% MOs$mo) %>% View() # based on mo
|
|
# AMR::microorganisms %>% filter(!mo %in% MOs$mo & !fullname %in% MOs$fullname) %>% View()
|
|
# and these IDs have changed:
|
|
old_new <- MOs %>%
|
|
mutate(kingdom_fullname = paste(kingdom, fullname)) %>%
|
|
filter(kingdom_fullname %in% (AMR::microorganisms %>%
|
|
mutate(kingdom_fullname = paste(kingdom, fullname)) %>%
|
|
pull(kingdom_fullname))) %>%
|
|
left_join(AMR::microorganisms %>%
|
|
mutate(kingdom_fullname = paste(kingdom, fullname)) %>%
|
|
select(mo, kingdom_fullname), by = "kingdom_fullname", suffix = c("_new", "_old")) %>%
|
|
filter(mo_new != mo_old) %>%
|
|
select(mo_old, mo_new, everything())
|
|
View(old_new)
|
|
|
|
# set new MO codes as names to existing data sets
|
|
rsi_translation$mo <- mo_name(rsi_translation$mo, language = NULL)
|
|
microorganisms.codes$mo <- mo_name(microorganisms.codes$mo, language = NULL)
|
|
microorganisms.translation <- AMR:::microorganisms.translation %>%
|
|
bind_rows(tibble(mo_old = AMR:::microorganisms.translation$mo_new, mo_new = mo_old)) %>%
|
|
filter(!mo_old %in% MOs$mo) %>%
|
|
mutate(mo_new = mo_name(mo_new, language = NULL)) %>%
|
|
bind_rows(old_new %>% select(mo_old, mo_new)) %>%
|
|
distinct(mo_old, .keep_all = TRUE)
|
|
|
|
# arrange the data sets to save
|
|
MOs <- MOs %>% arrange(fullname)
|
|
MOs.old <- MOs.old %>% arrange(fullname)
|
|
|
|
# transform
|
|
MOs <- as.data.frame(MOs, stringsAsFactors = FALSE)
|
|
MOs.old <- as.data.frame(MOs.old, stringsAsFactors = FALSE)
|
|
microorganisms.codes <- as.data.frame(microorganisms.codes, stringsAsFactors = FALSE)
|
|
class(MOs$mo) <- c("mo", "character")
|
|
|
|
# SAVE
|
|
### for same server
|
|
microorganisms <- dataset_UTF8_to_ASCII(MOs)
|
|
microorganisms.old <- dataset_UTF8_to_ASCII(MOs.old)
|
|
### for other server
|
|
saveRDS(MOs, "microorganisms.rds")
|
|
saveRDS(MOs.old, "microorganisms.old.rds")
|
|
saveRDS(microorganisms.codes, "microorganisms.codes.rds")
|
|
|
|
# on the server, do:
|
|
usethis::use_data(microorganisms, overwrite = TRUE, version = 2)
|
|
usethis::use_data(microorganisms.old, overwrite = TRUE, version = 2)
|
|
rm(microorganisms)
|
|
rm(microorganisms.old)
|
|
|
|
# load new data sets
|
|
devtools::load_all(".")
|
|
|
|
# reset previously changed mo codes
|
|
rsi_translation$mo <- as.mo(rsi_translation$mo)
|
|
microorganisms.codes$mo <- as.mo(microorganisms.codes$mo)
|
|
class(microorganisms.codes$mo) <- c("mo", "character")
|
|
microorganisms.translation <- microorganisms.translation %>%
|
|
# (to do: add last package version to column pkg_version)
|
|
left_join(microorganisms.old[, c("fullname", "fullname_new")], # microorganisms.old is now new and loaded
|
|
by = c("mo_new" = "fullname")) %>%
|
|
mutate(name = ifelse(!is.na(fullname_new), fullname_new, mo_new)) %>%
|
|
left_join(microorganisms[, c("fullname", "mo")], # as is microorganisms
|
|
by = c("name" = "fullname")) %>%
|
|
select(mo_old, mo_new = mo) %>%
|
|
filter(!is.na(mo_old), !is.na(mo_new))
|
|
class(microorganisms.translation$mo_old) <- "character" # no class <mo> since those aren't valid MO codes
|
|
class(microorganisms.translation$mo_new) <- c("mo", "character")
|
|
# save those to the package
|
|
usethis::use_data(rsi_translation, overwrite = TRUE, version = 2)
|
|
usethis::use_data(microorganisms.codes, overwrite = TRUE, version = 2)
|
|
saveRDS(microorganisms.translation, file = "data-raw/microorganisms.translation.rds", version = 2)
|
|
# to save microorganisms.translation internally to the package
|
|
source("data-raw/internals.R")
|
|
|
|
# load new data sets again
|
|
devtools::load_all(".")
|
|
|
|
# and check: these codes should not be missing (will otherwise throw a unit test error):
|
|
AMR::microorganisms.codes %>% filter(!mo %in% MOs$mo)
|
|
AMR::rsi_translation %>% filter(!mo %in% MOs$mo)
|
|
AMR:::microorganisms.translation %>% filter(!mo_new %in% MOs$mo)
|
|
|
|
# update the example_isolates data set
|
|
example_isolates$mo <- as.mo(example_isolates$mo)
|
|
usethis::use_data(example_isolates, overwrite = TRUE)
|
|
|
|
# Don't forget to add SNOMED codes! (data-raw/snomed.R)
|
|
|
|
# run the unit tests
|
|
testthat::test_file("tests/testthat/test-data.R")
|
|
testthat::test_file("tests/testthat/test-mo.R")
|
|
testthat::test_file("tests/testthat/test-mo_property.R")
|
|
|
|
# edit 2020-05-28
|
|
# Not sure why it now says M. tuberculosis was renamed to M. africanum (B_MYCBC_AFRC), but that's not true
|
|
microorganisms <- microorganisms %>%
|
|
bind_rows(microorganisms %>%
|
|
filter(mo == "B_MYCBC_AFRC") %>%
|
|
mutate(mo = "B_MYCBC_TBRC", snomed = list(c("113861009", "113858008")),
|
|
ref = "Lehmann et al., 2018",species_id = "778540",
|
|
source = "DSMZ", species = "tuberculosis",
|
|
fullname = "Mycobacterium tuberculosis")) %>%
|
|
arrange(fullname)
|
|
class(microorganisms$mo) <- c("mo", "character")
|
|
microorganisms.old <- microorganisms.old %>% filter(fullname != "Mycobacterium tuberculosis")
|
|
|
|
usethis::use_data(microorganisms, overwrite = TRUE, version = 2, compress = "xz")
|
|
usethis::use_data(microorganisms.old, overwrite = TRUE, version = 2)
|
|
|
|
|
|
# OLD CODE ----------------------------------------------------------------
|
|
|
|
# to keep all the old IDs:
|
|
# MOs <- MOs %>% filter(!mo %in% old_new$mo_new) %>%
|
|
# rbind(microorganisms %>%
|
|
# filter(mo %in% old_new$mo_old) %>%
|
|
# select(mo, fullname) %>%
|
|
# left_join(MOs %>%
|
|
# select(-mo), by = "fullname"))
|
|
# this is how to fix it
|
|
# microorganisms.codes <- AMR::microorganisms.codes %>%
|
|
# left_join(MOs %>%
|
|
# mutate(kingdom_fullname = paste(kingdom, fullname)) %>%
|
|
# left_join(AMR::microorganisms %>%
|
|
# transmute(mo, kingdom_fullname = paste(kingdom, fullname)),
|
|
# by = "kingdom_fullname", suffix = c("_new", "_old")) %>%
|
|
# select(mo_old, mo_new),
|
|
# by = c("mo" = "mo_old")) %>%
|
|
# select(code, mo = mo_new) %>%
|
|
# filter(!is.na(mo))
|
|
# microorganisms.codes %>% filter(!mo %in% MOs$mo)
|
|
# # and for microorganisms.translation:
|
|
# microorganisms.translation <- AMR:::microorganisms.translation %>%
|
|
# select(mo = mo_new) %>%
|
|
# left_join(AMR::microorganisms %>%
|
|
# transmute(mo, kingdom_fullname = paste(kingdom, fullname)),
|
|
# by = "kingdom_fullname", suffix = c("_new", "_old")) %>%
|
|
# select(mo_old, mo_new)
|
|
# left_join(MOs %>%
|
|
# mutate(kingdom_fullname = paste(kingdom, fullname)) %>%
|
|
# left_join(AMR::microorganisms %>%
|
|
# transmute(mo, kingdom_fullname = paste(kingdom, fullname)),
|
|
# by = "kingdom_fullname", suffix = c("_new", "_old")) %>%
|
|
# select(mo_old, mo_new),
|
|
# by = c("mo" = "mo_old")) %>%
|
|
# select(code, mo = mo_new) %>%
|
|
# filter(!is.na(mo))
|
|
# microorganisms.codes %>% filter(!mo %in% MOs$mo)
|