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AMR
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eucast updates

This commit is contained in:
dr. M.S. (Matthijs) Berends 2018-11-01 17:06:08 +01:00
parent d3f5236690
commit f7687557c9
5 changed files with 147 additions and 76 deletions
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1
NEWS.md
View File

@ -13,6 +13,7 @@
* Better error handling when rules cannot be applied (i.e. new values could not be inserted)
* The number of affected values will now only be measured once per row/column combination
* Data set `septic_patients` now reflects these changes
* Small fixes to EUCAST clinical breakpoint rules
* Tremendous speed improvement for `as.mo` (and subsequently all `mo_*` functions), as empty values wil be ignored *a priori*
* Fewer than 3 characters as input for `as.mo` will return NA
* Added parameter `combine_IR` (TRUE/FALSE) to functions `portion_df` and `count_df`, to indicate that all values of I and R must be merged into one, so the output only consists of S vs. IR (susceptible vs. non-susceptible)

188
R/eucast.R
View File

@ -23,7 +23,7 @@
#' @param col_mo column name of the microbial ID in \code{tbl} - values in this column should be present in \code{microorganisms$mo}, see \code{\link{microorganisms}}
#' @param info print progress
#' @param rules a character vector that specifies which rules should be applied - one or more of \code{c("breakpoints", "expert", "other", "all")}
#' @param amcl,amik,amox,ampi,azit,azlo,aztr,cefa,cfep,cfot,cfox,cfra,cfta,cftr,cfur,chlo,cipr,clar,clin,clox,coli,czol,dapt,doxy,erta,eryt,fosf,fusi,gent,imip,kana,levo,linc,line,mero,mezl,mino,moxi,nali,neom,neti,nitr,norf,novo,oflo,oxac,peni,pita,poly,pris,qida,rifa,roxi,siso,teic,tetr,tica,tige,tobr,trim,trsu,vanc column name of an antibiotic, see Details
#' @param amcl,amik,amox,ampi,azit,azlo,aztr,cefa,cfep,cfot,cfox,cfra,cfta,cftr,cfur,chlo,cipr,clar,clin,clox,coli,czol,dapt,doxy,erta,eryt,fosf,fusi,gent,imip,kana,levo,linc,line,mero,mezl,mino,moxi,nali,neom,neti,nitr,norf,novo,oflo,oxac,peni,pipe,pita,poly,pris,qida,rifa,roxi,siso,teic,tetr,tica,tige,tobr,trim,trsu,vanc column name of an antibiotic, see Details
#' @param col_bactid Deprecated. Use \code{col_mo} instead.
#' @param verbose a logical to indicate whether extensive info should be returned as a \code{data.frame} with info about which rows and columns are effected
#' @param ... parameters that are passed on to \code{EUCAST_rules}
@ -77,6 +77,7 @@
#' \strong{novo}: novobiocin (an ATCvet code: \emph{QJ01XX95}),
#' \strong{oflo}: ofloxacin (\emph{J01MA01}),
#' \strong{peni}: penicillin (\emph{J01RA01}),
#' \strong{pipe}: piperacillin (\emph{J01CA12}),
#' \strong{pita}: piperacillin+tazobactam (\emph{J01CR05}),
#' \strong{poly}: polymyxin B (\emph{J01XB02}),
#' \strong{pris}: pristinamycin (\emph{J01FG01}),
@ -199,6 +200,7 @@ EUCAST_rules <- function(tbl,
oflo = 'oflo',
oxac = 'oxac',
peni = 'peni',
pipe = 'pipe',
pita = 'pita',
poly = 'poly',
pris = 'pris',
@ -257,8 +259,8 @@ EUCAST_rules <- function(tbl,
cfox, cfta, cftr, cfur, chlo, cipr, clar, clin, clox, coli,
czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana,
levo, linc, line, mero, mezl, mino, moxi, nali, neom, neti, nitr,
novo, norf, oflo, oxac, peni, pita, poly, pris, qida, rifa, roxi, siso,
teic, tetr, tica, tige, tobr, trim, trsu, vanc)
novo, norf, oflo, oxac, peni, pipe, pita, poly, pris, qida, rifa,
roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu, vanc)
col.list <- check_available_columns(tbl = tbl, col.list = col.list, info = info)
amcl <- col.list[amcl]
amik <- col.list[amik]
@ -307,6 +309,7 @@ EUCAST_rules <- function(tbl,
oflo <- col.list[oflo]
oxac <- col.list[oxac]
peni <- col.list[peni]
pipe <- col.list[pipe]
pita <- col.list[pita]
poly <- col.list[poly]
pris <- col.list[pris]
@ -404,7 +407,7 @@ EUCAST_rules <- function(tbl,
cephalosporins <- c(cfep, cfot, cfox, cfra, cfta, cftr, cfur, czol)
carbapenems <- c(erta, imip, mero)
aminopenicillins <- c(ampi, amox)
ureidopenicillins <- c(pita, azlo, mezl)
ureidopenicillins <- c(pipe, pita, azlo, mezl)
fluoroquinolones <- c(oflo, cipr, norf, levo, moxi)
all_betalactam <- c(aminopenicillins, ureidopenicillins, cephalosporins, carbapenems, amcl, oxac, clox, peni)
@ -483,7 +486,7 @@ EUCAST_rules <- function(tbl,
rows = which(tbl$genus == "Staphylococcus"
& tbl[, peni] == 'S'
& tbl[, cfox] == 'S'),
cols = c(ampi, amox, pita, tica))
cols = c(ampi, amox, pipe, tica))
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Staphylococcus"
@ -503,7 +506,7 @@ EUCAST_rules <- function(tbl,
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Staphylococcus saprophyticus"
& tbl[, ampi] == 'S'),
cols = c(ampi, amox, amcl, pita))
cols = c(amox, amcl, pipe, pita))
}
if (!is.na(cfox)) {
# inferred from cefoxitin
@ -564,11 +567,11 @@ EUCAST_rules <- function(tbl,
changed_results <- 0
cat(rule)
}
if (!is.na(peni)) {
if (!is.na(ampi)) { # penicillin group
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Enterococcus faecium"
& tbl[, peni] == 'R'),
& tbl[, ampi] == 'R'),
cols = all_betalactam)
}
if (!is.na(ampi)) {
@ -576,17 +579,17 @@ EUCAST_rules <- function(tbl,
rule = c(rule_group, rule),
rows = which(tbl$genus == "Enterococcus"
& tbl[, ampi] == 'S'),
cols = c(amox, amcl, pita))
cols = c(amox, amcl, pipe, pita))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Enterococcus"
& tbl[, ampi] == 'I'),
cols = c(amox, amcl, pita))
cols = c(amox, amcl, pipe, pita))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Enterococcus"
& tbl[, ampi] == 'R'),
cols = c(amox, amcl, pita))
cols = c(amox, amcl, pipe, pita))
}
if (!is.na(norf)) {
edit_rsi(to = 'S',
@ -678,24 +681,24 @@ EUCAST_rules <- function(tbl,
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus pneumoniae"
& tbl[, peni] == 'S'),
cols = c(ampi, amox, amcl, pita))
cols = c(ampi, amox, amcl, pipe, pita))
}
if (!is.na(ampi)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus pneumoniae"
& tbl[, ampi] == 'S'),
cols = c(ampi, amox, amcl, pita))
cols = c(amox, amcl, pipe, pita))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus pneumoniae"
& tbl[, ampi] == 'I'),
cols = c(ampi, amox, amcl, pita))
cols = c(amox, amcl, pipe, pita))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Streptococcus pneumoniae"
& tbl[, ampi] == 'R'),
cols = c(ampi, amox, amcl, pita))
cols = c(amox, amcl, pipe, pita))
}
if (!is.na(norf)) {
edit_rsi(to = 'S',
@ -743,22 +746,29 @@ EUCAST_rules <- function(tbl,
"intermedius", "mitis", "mutans", "oligofermentans", "oralis",
"parasanguinis", "peroris", "pseudopneumoniae", "salivarius",
"sanguinis", "sinensis", "sobrinus", "thermophilus", "vestibularis")
if (!is.na(peni)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Streptococcus" & tbl$species %in% viridans_group
& tbl[, peni] == 'S'),
cols = c(ampi, amox, amcl, pipe, pita))
}
if (!is.na(ampi)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Streptococcus" & tbl$species %in% viridans_group
& tbl[, ampi] == 'S'),
cols = c(ampi, amox, amcl, pita))
cols = c(amox, amcl, pipe, pita))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Streptococcus" & tbl$species %in% viridans_group
& tbl[, ampi] == 'I'),
cols = c(ampi, amox, amcl, pita))
cols = c(amox, amcl, pipe, pita))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus == "Streptococcus" & tbl$species %in% viridans_group
& tbl[, ampi] == 'R'),
cols = c(ampi, amox, amcl, pita))
cols = c(amox, amcl, pipe, pita))
}
if (info == TRUE) {
txt_ok()
@ -775,17 +785,24 @@ EUCAST_rules <- function(tbl,
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Haemophilus influenzae"
& tbl[, ampi] == 'S'),
cols = c(amox, pita))
cols = c(amox, pipe))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Haemophilus influenzae"
& tbl[, ampi] == 'I'),
cols = c(amox, pita))
cols = c(amox, pipe))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Haemophilus influenzae"
& tbl[, ampi] == 'R'),
cols = c(amox, pita))
cols = c(amox, pipe))
}
if (!is.na(peni)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Haemophilus influenzae"
& tbl[, peni] == 'S'),
cols = c(ampi, amox, amcl, pipe, pita))
}
if (!is.na(amcl)) {
edit_rsi(to = 'S',
@ -889,28 +906,28 @@ EUCAST_rules <- function(tbl,
if (!is.na(peni)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which((tbl$genus %in% c("Clostridium", "Actinomyces", "Propionibacterium",
"Bifidobacterium", "Eggerthella", "Eubacterium",
"Lactobacillus ", "Actinomyces")
| tbl$fullname %like% "^Propionibacterium acnes")
rows = which(tbl$genus %in% c("Clostridium", "Actinomyces", "Propionibacterium",
"Cutibacterium", # new name of Propionibacterium
"Bifidobacterium", "Eggerthella", "Eubacterium",
"Lactobacillus ", "Actinomyces")
& tbl[, peni] == 'S'),
cols = c(ampi, amox, pita, tica))
cols = c(ampi, amox, pipe, pita, tica))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which((tbl$genus %in% c("Clostridium", "Actinomyces", "Propionibacterium",
"Bifidobacterium", "Eggerthella", "Eubacterium",
"Lactobacillus ", "Actinomyces")
| tbl$fullname %like% "^Propionibacterium acnes")
rows = which(tbl$genus %in% c("Clostridium", "Actinomyces", "Propionibacterium",
"Cutibacterium", # new name of Propionibacterium
"Bifidobacterium", "Eggerthella", "Eubacterium",
"Lactobacillus ", "Actinomyces")
& tbl[, peni] == 'I'),
cols = c(ampi, amox, pita, tica))
cols = c(ampi, amox, pipe, pita, tica))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which((tbl$genus %in% c("Clostridium", "Actinomyces", "Propionibacterium",
"Bifidobacterium", "Eggerthella", "Eubacterium",
"Lactobacillus ", "Actinomyces")
| tbl$fullname %like% "^Propionibacterium acnes")
rows = which(tbl$genus %in% c("Clostridium", "Actinomyces", "Propionibacterium",
"Cutibacterium", # new name of Propionibacterium
"Bifidobacterium", "Eggerthella", "Eubacterium",
"Lactobacillus ", "Actinomyces")
& tbl[, peni] == 'R'),
cols = c(ampi, amox, pita, tica))
cols = c(ampi, amox, pipe, pita, tica))
}
if (info == TRUE) {
txt_ok()
@ -928,19 +945,19 @@ EUCAST_rules <- function(tbl,
rows = which(tbl$genus %in% c("Bacteroides", "Prevotella", "Porphyromonas",
"Fusobacterium", "Bilophila ", "Mobiluncus")
& tbl[, peni] == 'S'),
cols = c(ampi, amox, pita, tica))
cols = c(ampi, amox, pipe, pita, tica))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$genus %in% c("Bacteroides", "Prevotella", "Porphyromonas",
"Fusobacterium", "Bilophila ", "Mobiluncus")
& tbl[, peni] == 'I'),
cols = c(ampi, amox, pita, tica))
cols = c(ampi, amox, pipe, pita, tica))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$genus %in% c("Bacteroides", "Prevotella", "Porphyromonas",
"Fusobacterium", "Bilophila ", "Mobiluncus")
& tbl[, peni] == 'R'),
cols = c(ampi, amox, pita, tica))
cols = c(ampi, amox, pipe, pita, tica))
}
if (info == TRUE) {
txt_ok()
@ -972,8 +989,8 @@ EUCAST_rules <- function(tbl,
if (info == TRUE) {
txt_ok()
}
# Campylobacter jejuni ----
rule <- 'Campylobacter jejuni'
# Campylobacter jejuni and coli ----
rule <- 'Campylobacter jejuni and coli'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
@ -982,34 +999,34 @@ EUCAST_rules <- function(tbl,
if (!is.na(eryt)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Campylobacter jejuni"
rows = which(tbl$fullname %like% "^Campylobacter (jejuni|coli)"
& tbl[, eryt] == 'S'),
cols = c(azit, clar))
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Campylobacter jejuni"
rows = which(tbl$fullname %like% "^Campylobacter (jejuni|coli)"
& tbl[, eryt] == 'I'),
cols = c(azit, clar))
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Campylobacter jejuni"
rows = which(tbl$fullname %like% "^Campylobacter (jejuni|coli)"
& tbl[, eryt] == 'R'),
cols = c(azit, clar))
}
if (!is.na(tetr)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Campylobacter jejuni"
rows = which(tbl$fullname %like% "^Campylobacter (jejuni|coli)"
& tbl[, tetr] == 'S'),
cols = doxy)
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Campylobacter jejuni"
rows = which(tbl$fullname %like% "^Campylobacter (jejuni|coli)"
& tbl[, tetr] == 'I'),
cols = doxy)
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Campylobacter jejuni"
rows = which(tbl$fullname %like% "^Campylobacter (jejuni|coli)"
& tbl[, tetr] == 'R'),
cols = doxy)
}
@ -1023,6 +1040,23 @@ EUCAST_rules <- function(tbl,
changed_results <- 0
cat(rule)
}
if (!is.na(norf)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Aerococcus (sanguinicola|urinae)"
& tbl[, norf] == 'S'),
cols = fluoroquinolones)
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Aerococcus (sanguinicola|urinae)"
& tbl[, norf] == 'I'),
cols = fluoroquinolones)
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Aerococcus (sanguinicola|urinae)"
& tbl[, norf] == 'R'),
cols = fluoroquinolones)
}
if (!is.na(cipr)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
@ -1090,16 +1124,6 @@ EUCAST_rules <- function(tbl,
rows = which(tbl$fullname %like% "^Kingella kingae"
& tbl[, tetr] == 'S'),
cols = doxy)
edit_rsi(to = 'I',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Kingella kingae"
& tbl[, tetr] == 'I'),
cols = doxy)
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% "^Kingella kingae"
& tbl[, tetr] == 'R'),
cols = doxy)
}
if (info == TRUE) {
txt_ok()
@ -1243,9 +1267,9 @@ EUCAST_rules <- function(tbl,
# Burkholderia
edit_rsi(to = 'R',
rule = c(rule_group, rule),
# onder 'Burkholderia cepacia complex' vallen deze species allemaal: PMID 16217180.
# the 'Burkholderia cepacia complex' are all these species: (PMID 16217180)
rows = which(tbl$fullname %like% '^Burkholderia (cepacia|multivorans|cenocepacia|stabilis|vietnamiensis|dolosa|ambifaria|anthina|pyrrocinia|ubonensis)'),
cols = c(aminopenicillins, amcl, tica, pita, czol, cfot, cftr, aztr, erta, cipr, chlo, aminoglycosides, trim, fosf, polymyxins))
cols = c(aminopenicillins, amcl, tica, pipe, pita, czol, cfot, cftr, aztr, erta, cipr, chlo, aminoglycosides, trim, fosf, polymyxins))
# Elizabethkingia
edit_rsi(to = 'R',
rule = c(rule_group, rule),
@ -1255,7 +1279,7 @@ EUCAST_rules <- function(tbl,
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Ochrobactrum anthropi'),
cols = c(aminopenicillins, amcl, tica, pita, czol, cfot, cftr, cfta, cfep, aztr, erta))
cols = c(aminopenicillins, amcl, tica, pipe, pita, czol, cfot, cftr, cfta, cfep, aztr, erta))
# Pseudomonas
edit_rsi(to = 'R',
rule = c(rule_group, rule),
@ -1265,7 +1289,7 @@ EUCAST_rules <- function(tbl,
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$fullname %like% '^Stenotrophomonas maltophilia'),
cols = c(aminopenicillins, amcl, tica, pita, czol, cfot, cftr, cfta, aztr, erta, imip, mero, aminoglycosides, trim, fosf, tetr))
cols = c(aminopenicillins, amcl, tica, pipe, pita, czol, cfot, cftr, cfta, aztr, erta, imip, mero, aminoglycosides, trim, fosf, tetr))
if (info == TRUE) {
txt_ok()
}
@ -1430,13 +1454,13 @@ EUCAST_rules <- function(tbl,
cat(rule)
}
# rule 9.3
if (!is.na(tica) & !is.na(pita)) {
if (!is.na(tica) & !is.na(pipe)) {
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl$family == 'Enterobacteriaceae'
& tbl[, tica] == 'R'
& tbl[, pita] == 'S'),
cols = pita)
& tbl[, pipe] == 'S'),
cols = pipe)
}
if (info == TRUE) {
txt_ok()
@ -1456,7 +1480,7 @@ EUCAST_rules <- function(tbl,
# rule = c(rule_group, rule),
# rows = which(tbl$fullname %like% '^Haemophilus influenza'
# & tbl[, ampi] == 'R'),
# cols = c(ampi, amox, amcl, pita, cfur))
# cols = c(ampi, amox, amcl, pipe, pita, cfur))
# }
if (info == TRUE) {
txt_ok()
@ -1602,6 +1626,21 @@ EUCAST_rules <- function(tbl,
if (info == TRUE) {
txt_ok()
}
rule <- 'Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.na(pita)) {
edit_rsi(to = 'R',
rule = c(rule_group, rule),
rows = which(tbl[, pita] == 'R'),
cols = pipe)
}
if (info == TRUE) {
txt_ok()
}
rule <- 'Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R'
if (info == TRUE) {
warned <- FALSE
@ -1623,7 +1662,7 @@ EUCAST_rules <- function(tbl,
changed_results <- 0
cat(rule)
}
if (!is.na(amcl)) {
if (!is.na(ampi)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl[, ampi] == 'S'),
@ -1632,13 +1671,28 @@ EUCAST_rules <- function(tbl,
if (info == TRUE) {
txt_ok()
}
rule <- 'Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.na(pipe)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl[, pipe] == 'S'),
cols = pita)
}
if (info == TRUE) {
txt_ok()
}
rule <- 'Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S'
if (info == TRUE) {
warned <- FALSE
changed_results <- 0
cat(rule)
}
if (!is.na(trsu)) {
if (!is.na(trim)) {
edit_rsi(to = 'S',
rule = c(rule_group, rule),
rows = which(tbl[, trim] == 'S'),

19
R/freq.R
View File

@ -658,14 +658,27 @@ as_tibble.frequency_tbl <- function(x, validate = TRUE, ..., rownames = NA) {
#' @exportMethod hist.frequency_tbl
#' @export
#' @importFrom graphics hist
hist.frequency_tbl <- function(x, ...) {
hist.frequency_tbl <- function(x, breaks = "Sturges", main = NULL, ...) {
opt <- attr(x, 'opt')
if (!class(x$item) %in% c("numeric", "double", "integer", "Date")) {
stop("'x' must be numeric or Date.", call. = FALSE)
}
if (!is.null(opt$vars)) {
title <- opt$vars
} else if (!is.null(opt$data)) {
title <- opt$data
} else {
title <- ""
title <- "frequency table"
}
hist(as.vector(x), main = paste("Histogram of", title), xlab = title, ...)
if (class(x$item) == "Date") {
x <- as.Date(as.vector(x), origin = "1970-01-01")
} else {
x <- as.vector(x)
}
if (is.null(main)) {
main <- paste("Histogram of", title)
}
hist(x, main = main, xlab = title, ...)
}
#' @noRd

14
man/EUCAST.Rd
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@ -35,11 +35,12 @@ EUCAST_rules(tbl, col_mo = "mo", info = TRUE,
line = "line", mero = "mero", mezl = "mezl", mino = "mino",
moxi = "moxi", nali = "nali", neom = "neom", neti = "neti",
nitr = "nitr", norf = "norf", novo = "novo", oflo = "oflo",
oxac = "oxac", peni = "peni", pita = "pita", poly = "poly",
pris = "pris", qida = "qida", rifa = "rifa", roxi = "roxi",
siso = "siso", teic = "teic", tetr = "tetr", tica = "tica",
tige = "tige", tobr = "tobr", trim = "trim", trsu = "trsu",
vanc = "vanc", col_bactid = "bactid", verbose = FALSE)
oxac = "oxac", peni = "peni", pipe = "pipe", pita = "pita",
poly = "poly", pris = "pris", qida = "qida", rifa = "rifa",
roxi = "roxi", siso = "siso", teic = "teic", tetr = "tetr",
tica = "tica", tige = "tige", tobr = "tobr", trim = "trim",
trsu = "trsu", vanc = "vanc", col_bactid = "bactid",
verbose = FALSE)
interpretive_reading(...)
}
@ -52,7 +53,7 @@ interpretive_reading(...)
\item{rules}{a character vector that specifies which rules should be applied - one or more of \code{c("breakpoints", "expert", "other", "all")}}
\item{amcl, amik, amox, ampi, azit, azlo, aztr, cefa, cfep, cfot, cfox, cfra, cfta, cftr, cfur, chlo, cipr, clar, clin, clox, coli, czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana, levo, linc, line, mero, mezl, mino, moxi, nali, neom, neti, nitr, norf, novo, oflo, oxac, peni, pita, poly, pris, qida, rifa, roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu, vanc}{column name of an antibiotic, see Details}
\item{amcl, amik, amox, ampi, azit, azlo, aztr, cefa, cfep, cfot, cfox, cfra, cfta, cftr, cfur, chlo, cipr, clar, clin, clox, coli, czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana, levo, linc, line, mero, mezl, mino, moxi, nali, neom, neti, nitr, norf, novo, oflo, oxac, peni, pipe, pita, poly, pris, qida, rifa, roxi, siso, teic, tetr, tica, tige, tobr, trim, trsu, vanc}{column name of an antibiotic, see Details}
\item{col_bactid}{Deprecated. Use \code{col_mo} instead.}
@ -119,6 +120,7 @@ Abbrevations of the column containing antibiotics in the form: \strong{abbreviat
\strong{novo}: novobiocin (an ATCvet code: \emph{QJ01XX95}),
\strong{oflo}: ofloxacin (\emph{J01MA01}),
\strong{peni}: penicillin (\emph{J01RA01}),
\strong{pipe}: piperacillin (\emph{J01CA12}),
\strong{pita}: piperacillin+tazobactam (\emph{J01CR05}),
\strong{poly}: polymyxin B (\emph{J01XB02}),
\strong{pris}: pristinamycin (\emph{J01FG01}),

1
man/MDRO.Rd
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@ -220,6 +220,7 @@ Abbrevations of the column containing antibiotics in the form: \strong{abbreviat
\strong{novo}: novobiocin (an ATCvet code: \emph{QJ01XX95}),
\strong{oflo}: ofloxacin (\emph{J01MA01}),
\strong{peni}: penicillin (\emph{J01RA01}),
\strong{pipe}: piperacillin (\emph{J01CA12}),
\strong{pita}: piperacillin+tazobactam (\emph{J01CR05}),
\strong{poly}: polymyxin B (\emph{J01XB02}),
\strong{pris}: pristinamycin (\emph{J01FG01}),