From db5a0d32a5ecc88b262fda01861158dc84fc3001 Mon Sep 17 00:00:00 2001 From: "Matthijs S. Berends" Date: Fri, 3 Aug 2018 10:58:48 +0200 Subject: [PATCH] typos of Becker algorithm --- R/bactid.R | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/R/bactid.R b/R/bactid.R index 07218704..ea50d61a 100644 --- a/R/bactid.R +++ b/R/bactid.R @@ -126,23 +126,24 @@ as.bactid <- function(x, Becker = FALSE, Lancefield = FALSE) { # https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4187637/figure/F3/ species <- left_join_microorganisms(mo)$species if (species %in% c("arlettae", "auricularis", "capitis", - "caprae", "carnosus", "cohnii", "condimene", + "caprae", "carnosus", "cohnii", "condimenti", "devriesei", "epidermidis", "equorum", "fleurettii", "gallinarum", "haemolyticus", "hominis", "jettensis", "kloosii", "lentus", "lugdunensis", "massiliensis", "microti", - "muscae", "nepalensis", "pasteuri", "perrasii", - "pettenkoleri", "piscifermentans", "rostri", - "saccharott", "saprophyticus", "sciuri", - "siepanovicii", "simulans", "succinus", + "muscae", "nepalensis", "pasteuri", "petrasii", + "pettenkoferi", "piscifermentans", "rostri", + "saccharolyticus", "saprophyticus", "sciuri", + "stepanovicii", "simulans", "succinus", "vitulinus", "warneri", "xylosus")) { x[i] <- "STACNS" next } else if ((Becker == "all" & species == "aureus") | species %in% c("simiae", "agnetis", "chromogenes", - "delphirul", "felis", "futrae", + "delphini", "felis", "lutrae", "hyicus", "intermedius", - "pseudointermedius", "schleiferi")) { + "pseudintermedius", "pseudointermedius", + "schleiferi")) { x[i] <- "STACPS" next }