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dr. M.S. (Matthijs) Berends
2018-02-22 21:37:10 +01:00
parent d8da8daf9a
commit 10380bcfae
4 changed files with 117 additions and 58 deletions
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69
R/EUCAST.R
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@ -37,11 +37,19 @@
#' EUCAST Expert Rules Version 3.1: \cr
#' \url{http://www.eucast.org/expert_rules_and_intrinsic_resistance}
#' @examples
#' \dontrun{
#' tbl <- EUCAST_rules(tbl)
#' }
#' a <- data.frame(bactid = c("STAAUR", "ESCCOL", "KLEPNE", "PSEAER"),
#' vanc = "-",
#' amox = "-",
#' coli = "-",
#' cfta = "-",
#' cfur = "-",
#' stringsAsFactors = FALSE)
#' a
#'
#' b <- EUCAST_rules(a)
#' b
EUCAST_rules <- function(tbl,
col_bactcode = 'bacteriecode',
col_bactcode = 'bactid',
info = TRUE,
amcl = 'amcl',
amik = 'amik',
@ -232,61 +240,61 @@ EUCAST_rules <- function(tbl,
# Citrobacter
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium)'),
cols = c(ampi, tica))
cols = c(aminopenicillines, tica))
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae)'),
cols = c(ampi, amcl, czol, cfox))
cols = c(aminopenicillines, amcl, czol, cfox))
# Enterobacter
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Enterobacter cloacae'),
cols = c(ampi, amcl, czol, cfox))
cols = c(aminopenicillines, amcl, czol, cfox))
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Enterobacter aerogenes'),
cols = c(ampi, amcl, czol, cfox))
cols = c(aminopenicillines, amcl, czol, cfox))
# Escherichia
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Escherichia hermanni'),
cols = c(ampi, tica))
cols = c(aminopenicillines, tica))
# Hafnia
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Hafnia alvei'),
cols = c(ampi, amcl, czol, cfox))
cols = c(aminopenicillines, amcl, czol, cfox))
# Klebsiella
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Klebsiella'),
cols = c(ampi, tica))
cols = c(aminopenicillines, tica))
# Morganella / Proteus
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Morganella morganii'),
cols = c(ampi, amcl, czol, tetracyclines, polymyxines, nitr))
cols = c(aminopenicillines, amcl, czol, tetracyclines, polymyxines, nitr))
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Proteus mirabilis'),
cols = c(tetracyclines, tige, polymyxines, nitr))
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Proteus penneri'),
cols = c(ampi, czol, cfur, tetracyclines, tige, polymyxines, nitr))
cols = c(aminopenicillines, czol, cfur, tetracyclines, tige, polymyxines, nitr))
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Proteus vulgaris'),
cols = c(ampi, czol, cfur, tetracyclines, tige, polymyxines, nitr))
cols = c(aminopenicillines, czol, cfur, tetracyclines, tige, polymyxines, nitr))
# Providencia
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Providencia rettgeri'),
cols = c(ampi, amcl, czol, cfur, tetracyclines, tige, polymyxines, nitr))
cols = c(aminopenicillines, amcl, czol, cfur, tetracyclines, tige, polymyxines, nitr))
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Providencia stuartii'),
cols = c(ampi, amcl, czol, cfur, tetracyclines, tige, polymyxines, nitr))
cols = c(aminopenicillines, amcl, czol, cfur, tetracyclines, tige, polymyxines, nitr))
# Raoultella
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Raoultella'),
cols = c(ampi, tica))
cols = c(aminopenicillines, tica))
# Serratia
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Serratia marcescens'),
cols = c(ampi, amcl, czol, cfox, cfur, tetracyclines[tetracyclines != 'mino'], polymyxines, nitr))
cols = c(aminopenicillines, amcl, czol, cfox, cfur, tetracyclines[tetracyclines != 'mino'], polymyxines, nitr))
# Yersinia
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Yersinia enterocolitica'),
cols = c(ampi, amcl, tica, czol, cfox))
cols = c(aminopenicillines, amcl, tica, czol, cfox))
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Yersinia pseudotuberculosis'),
cols = c(poly, coli))
@ -313,32 +321,32 @@ EUCAST_rules <- function(tbl,
# Acinetobacter
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Acinetobacter (baumannii|pittii|nosocomialis|calcoaceticus)'),
cols = c(ampi, amcl, czol, cfot, cftr, aztr, erta, trim, fosf, tetracyclines[tetracyclines != 'mino']))
cols = c(aminopenicillines, amcl, czol, cfot, cftr, aztr, erta, trim, fosf, tetracyclines[tetracyclines != 'mino']))
# Achromobacter
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Achromobacter (xylosoxydans|xylosoxidans)'),
cols = c(ampi, czol, cfot, cftr, erta))
cols = c(aminopenicillines, czol, cfot, cftr, erta))
# Burkholderia
edit_rsi(to = 'R',
# onder 'Burkholderia cepacia complex' vallen deze species allemaal: PMID 16217180.
rows = which(tbl$fullname %like% '^Burkholderia (cepacia|multivorans|cenocepacia|stabilis|vietnamiensis|dolosa|ambifaria|anthina|pyrrocinia|ubonensis)'),
cols = c(ampi, amcl, tica, pita, czol, cfot, cftr, aztr, erta, cipr, chlo, aminoglycosiden, trim, fosf, polymyxines))
cols = c(aminopenicillines, amcl, tica, pita, czol, cfot, cftr, aztr, erta, cipr, chlo, aminoglycosiden, trim, fosf, polymyxines))
# Elizabethkingia
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Elizabethkingia meningoseptic(a|um)'),
cols = c(ampi, amcl, tica, czol, cfot, cftr, cfta, cfep, aztr, erta, imip, mero, polymyxines))
cols = c(aminopenicillines, amcl, tica, czol, cfot, cftr, cfta, cfep, aztr, erta, imip, mero, polymyxines))
# Ochrobactrum
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Ochrobactrum anthropi'),
cols = c(ampi, amcl, tica, pita, czol, cfot, cftr, cfta, cfep, aztr, erta))
cols = c(aminopenicillines, amcl, tica, pita, czol, cfot, cftr, cfta, cfep, aztr, erta))
# Pseudomonas
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Pseudomonas aeruginosa'),
cols = c(ampi, amcl, czol, cfot, cftr, erta, chlo, kana, neom, trim, trsu, tetracyclines, tige))
cols = c(aminopenicillines, amcl, czol, cfot, cftr, erta, chlo, kana, neom, trim, trsu, tetracyclines, tige))
# Stenotrophomonas
edit_rsi(to = 'R',
rows = which(tbl$fullname %like% '^Stenotrophomonas maltophilia'),
cols = c(ampi, amcl, tica, pita, czol, cfot, cftr, cfta, aztr, erta, imip, mero, aminoglycosiden, trim, fosf, tetr))
cols = c(aminopenicillines, amcl, tica, pita, czol, cfot, cftr, cfta, aztr, erta, imip, mero, aminoglycosiden, trim, fosf, tetr))
# Table 3: Intrinsic resistance in other Gram-negative bacteria ----
@ -448,6 +456,12 @@ EUCAST_rules <- function(tbl,
& tbl[, ampi] == 'R'),
cols = c(ureidopenicillines, carbapenems))
}
if (!is.na(amox)) {
edit_rsi(to = 'R',
rows = which(tbl$genus == 'Enterococcus'
& tbl[, amox] == 'R'),
cols = c(ureidopenicillines, carbapenems))
}
# Table 9: Interpretive rules for B-lactam agents and Gram-negative rods ----
if (info == TRUE) {
@ -579,7 +593,7 @@ EUCAST_rules <- function(tbl,
cols = trim)
}
if (!is.na(ampi) & !is.na(amox)) {
tbl[, amox] <- tbl[, ampi]
tbl[, amox] <- tbl %>% pull(ampi)
}
# Toegevoegde kolommen weer verwijderen
@ -596,6 +610,7 @@ EUCAST_rules <- function(tbl,
tbl
}
#' @name EUCAST
#' @rdname EUCAST
#' @export
interpretive_reading <- function(...) {