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typos of Becker algorithm

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dr. M.S. (Matthijs) Berends 2018-08-03 10:58:48 +02:00
parent bd9bcfef78
commit db5a0d32a5
1 changed files with 8 additions and 7 deletions
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15
R/bactid.R
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@ -126,23 +126,24 @@ as.bactid <- function(x, Becker = FALSE, Lancefield = FALSE) {
# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4187637/figure/F3/ # https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4187637/figure/F3/
species <- left_join_microorganisms(mo)$species species <- left_join_microorganisms(mo)$species
if (species %in% c("arlettae", "auricularis", "capitis", if (species %in% c("arlettae", "auricularis", "capitis",
"caprae", "carnosus", "cohnii", "condimene", "caprae", "carnosus", "cohnii", "condimenti",
"devriesei", "epidermidis", "equorum", "devriesei", "epidermidis", "equorum",
"fleurettii", "gallinarum", "haemolyticus", "fleurettii", "gallinarum", "haemolyticus",
"hominis", "jettensis", "kloosii", "lentus", "hominis", "jettensis", "kloosii", "lentus",
"lugdunensis", "massiliensis", "microti", "lugdunensis", "massiliensis", "microti",
"muscae", "nepalensis", "pasteuri", "perrasii", "muscae", "nepalensis", "pasteuri", "petrasii",
"pettenkoleri", "piscifermentans", "rostri", "pettenkoferi", "piscifermentans", "rostri",
"saccharott", "saprophyticus", "sciuri", "saccharolyticus", "saprophyticus", "sciuri",
"siepanovicii", "simulans", "succinus", "stepanovicii", "simulans", "succinus",
"vitulinus", "warneri", "xylosus")) { "vitulinus", "warneri", "xylosus")) {
x[i] <- "STACNS" x[i] <- "STACNS"
next next
} else if ((Becker == "all" & species == "aureus") } else if ((Becker == "all" & species == "aureus")
| species %in% c("simiae", "agnetis", "chromogenes", | species %in% c("simiae", "agnetis", "chromogenes",
"delphirul", "felis", "futrae", "delphini", "felis", "lutrae",
"hyicus", "intermedius", "hyicus", "intermedius",
"pseudointermedius", "schleiferi")) { "pseudintermedius", "pseudointermedius",
"schleiferi")) {
x[i] <- "STACPS" x[i] <- "STACPS"
next next
} }