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new MOs, cleanup
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128
R/mo.R
128
R/mo.R
@ -91,7 +91,6 @@
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#' }
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as.mo <- function(x, Becker = FALSE, Lancefield = FALSE) {
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if (NCOL(x) == 2) {
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# support tidyverse selection like: df %>% select(colA, colB)
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# paste these columns together
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@ -131,74 +130,11 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE) {
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x_species <- paste(x, 'species')
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# add start en stop regex
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x <- paste0('^', x, '$')
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x_withspaces_all <- x_withspaces
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x_withspaces <- paste0('^', x_withspaces, '$')
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for (i in 1:length(x)) {
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if (Becker == TRUE | Becker == "all") {
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mo <- suppressWarnings(guess_mo(x_backup[i]))
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if (mo %like% '^STA') {
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# See Source. It's this figure:
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# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4187637/figure/F3/
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species <- left_join_microorganisms(mo)$species
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if (species %in% c("arlettae", "auricularis", "capitis",
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"caprae", "carnosus", "cohnii", "condimenti",
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"devriesei", "epidermidis", "equorum",
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"fleurettii", "gallinarum", "haemolyticus",
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"hominis", "jettensis", "kloosii", "lentus",
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"lugdunensis", "massiliensis", "microti",
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"muscae", "nepalensis", "pasteuri", "petrasii",
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"pettenkoferi", "piscifermentans", "rostri",
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"saccharolyticus", "saprophyticus", "sciuri",
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"stepanovicii", "simulans", "succinus",
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"vitulinus", "warneri", "xylosus")) {
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x[i] <- "STACNS"
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next
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} else if ((Becker == "all" & species == "aureus")
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| species %in% c("simiae", "agnetis", "chromogenes",
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"delphini", "felis", "lutrae",
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"hyicus", "intermedius",
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"pseudintermedius", "pseudointermedius",
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"schleiferi")) {
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x[i] <- "STACPS"
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next
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}
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}
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}
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if (Lancefield == TRUE) {
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mo <- suppressWarnings(guess_mo(x_backup[i]))
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if (mo %like% '^STC') {
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# See Source
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species <- left_join_microorganisms(mo)$species
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if (species == "pyogenes") {
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x[i] <- "STCGRA"
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next
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}
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if (species == "agalactiae") {
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x[i] <- "STCGRB"
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next
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}
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if (species %in% c("equisimilis", "equi",
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"zooepidemicus", "dysgalactiae")) {
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x[i] <- "STCGRC"
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next
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}
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if (species == "anginosus") {
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x[i] <- "STCGRF"
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next
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}
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if (species == "sanguis") {
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x[i] <- "STCGRH"
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next
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}
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if (species == "salivarius") {
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x[i] <- "STCGRK"
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next
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}
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}
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}
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if (identical(x_trimmed[i], "")) {
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# empty values
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x[i] <- NA
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@ -206,12 +142,12 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE) {
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next
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}
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if (x_backup[i] %in% AMR::microorganisms$mo) {
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# is already a valid mo
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# is already a valid MO code
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x[i] <- x_backup[i]
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next
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}
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if (x_trimmed[i] %in% AMR::microorganisms$mo) {
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# is already a valid mo
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# is already a valid MO code
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x[i] <- x_trimmed[i]
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next
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}
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@ -303,6 +239,13 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE) {
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next
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}
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# try fullname without start and stop regex, to also find subspecies, like "K. pneu rhino"
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found <- MOs[which(gsub("[\\(\\)]", "", MOs$fullname) %like% x_withspaces_all[i]),]$mo
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if (length(found) > 0) {
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x[i] <- found[1L]
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next
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}
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# search for GLIMS code
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found <- AMR::microorganisms.umcg[which(toupper(AMR::microorganisms.umcg$umcg) == toupper(x_trimmed[i])),]$mo
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if (length(found) > 0) {
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@ -352,6 +295,57 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE) {
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call. = FALSE)
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}
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if (Becker == TRUE | Becker == "all") {
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# See Source. It's this figure:
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# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4187637/figure/F3/
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CoNS <- MOs %>%
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filter(genus == "Staphylococcus",
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species %in% c("arlettae", "auricularis", "capitis",
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"caprae", "carnosus", "cohnii", "condimenti",
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"devriesei", "epidermidis", "equorum",
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"fleurettii", "gallinarum", "haemolyticus",
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"hominis", "jettensis", "kloosii", "lentus",
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"lugdunensis", "massiliensis", "microti",
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"muscae", "nepalensis", "pasteuri", "petrasii",
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"pettenkoferi", "piscifermentans", "rostri",
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"saccharolyticus", "saprophyticus", "sciuri",
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"stepanovicii", "simulans", "succinus",
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"vitulinus", "warneri", "xylosus")) %>%
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pull(mo)
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CoPS <- MOs %>%
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filter(genus == "Staphylococcus",
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species %in% c("simiae", "agnetis", "chromogenes",
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"delphini", "felis", "lutrae",
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"hyicus", "intermedius",
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"pseudintermedius", "pseudointermedius",
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"schleiferi")) %>%
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pull(mo)
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x[x %in% CoNS] <- "STACNS"
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x[x %in% CoPS] <- "STACPS"
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if (Becker == "all") {
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x[x == "STAAUR"] <- "STACPS"
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}
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}
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if (Lancefield == TRUE) {
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# group A
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x[x == "STCPYO"] <- "STCGRA" # S. pyogenes
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# group B
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x[x == "STCAGA"] <- "STCGRB" # S. agalactiae
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# group C
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S_groupC <- MOs %>% filter(genus == "Streptococcus",
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species %in% c("equisimilis", "equi",
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"zooepidemicus", "dysgalactiae")) %>%
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pull(mo)
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x[x %in% S_groupC] <- "STCGRC" # S. agalactiae
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# group F
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x[x == "STCANG"] <- "STCGRF" # S. anginosus
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# group H
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x[x == "STCSAN"] <- "STCGRH" # S. sanguis
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# group K
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x[x == "STCSAL"] <- "STCGRK" # S. salivarius
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}
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# left join the found results to the original input values (x_input)
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df_found <- data.frame(input = as.character(unique(x_input)),
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found = x,
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