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new EUCAST rules algorithm

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dr. M.S. (Matthijs) Berends
2019-04-05 18:47:39 +02:00
parent 56d4b4719f
commit fbc9191b13
115 changed files with 1340 additions and 2174 deletions
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88
man/eucast_rules.Rd
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@@ -2,8 +2,7 @@
% Please edit documentation in R/eucast_rules.R
\name{eucast_rules}
\alias{eucast_rules}
\alias{EUCAST_rules}
\alias{interpretive_reading}
\alias{eucast_rules_file}
\title{EUCAST rules}
\source{
\itemize{
@@ -21,49 +20,48 @@
\url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx}
}
}
For editing the reference file (which is available with \code{\link{eucast_rules_file}}), these values can all be used for target antibiotics: aminoglycosides, tetracyclines, polymyxins, macrolides, glycopeptides, streptogramins, cephalosporins, cephalosporins_without_cfta, carbapenems, aminopenicillins, ureidopenicillins, fluoroquinolones, all_betalactams, and all separate four letter codes like amcl. They can be separated by comma: \code{"amcl, fluoroquinolones"}. The mo_property can be any column name from the \code{\link{microorganisms}} data set, or \code{genus_species} or \code{gramstain}. This file contains references to the 'Burkholderia cepacia complex'. The species in this group can be found in: LiPuma JJ, 2015 (PMID 16217180).
}
\usage{
eucast_rules(tbl, col_mo = NULL, info = TRUE,
rules = c("breakpoints", "expert", "other", "all"), verbose = FALSE,
amcl = guess_ab_col(), amik = guess_ab_col(),
amox = guess_ab_col(), ampi = guess_ab_col(),
azit = guess_ab_col(), azlo = guess_ab_col(),
aztr = guess_ab_col(), cefa = guess_ab_col(),
cfep = guess_ab_col(), cfot = guess_ab_col(),
cfox = guess_ab_col(), cfra = guess_ab_col(),
cfta = guess_ab_col(), cftr = guess_ab_col(),
cfur = guess_ab_col(), chlo = guess_ab_col(),
cipr = guess_ab_col(), clar = guess_ab_col(),
clin = guess_ab_col(), clox = guess_ab_col(),
coli = guess_ab_col(), czol = guess_ab_col(),
dapt = guess_ab_col(), doxy = guess_ab_col(),
erta = guess_ab_col(), eryt = guess_ab_col(),
fosf = guess_ab_col(), fusi = guess_ab_col(),
gent = guess_ab_col(), imip = guess_ab_col(),
kana = guess_ab_col(), levo = guess_ab_col(),
linc = guess_ab_col(), line = guess_ab_col(),
mero = guess_ab_col(), mezl = guess_ab_col(),
mino = guess_ab_col(), moxi = guess_ab_col(),
nali = guess_ab_col(), neom = guess_ab_col(),
neti = guess_ab_col(), nitr = guess_ab_col(),
norf = guess_ab_col(), novo = guess_ab_col(),
oflo = guess_ab_col(), oxac = guess_ab_col(),
peni = guess_ab_col(), pipe = guess_ab_col(),
pita = guess_ab_col(), poly = guess_ab_col(),
pris = guess_ab_col(), qida = guess_ab_col(),
rifa = guess_ab_col(), roxi = guess_ab_col(),
siso = guess_ab_col(), teic = guess_ab_col(),
tetr = guess_ab_col(), tica = guess_ab_col(),
tige = guess_ab_col(), tobr = guess_ab_col(),
trim = guess_ab_col(), trsu = guess_ab_col(),
vanc = guess_ab_col())
eucast_rules(x, col_mo = NULL, info = TRUE, rules = c("breakpoints",
"expert", "other", "all"), verbose = FALSE, amcl = guess_ab_col(),
amik = guess_ab_col(), amox = guess_ab_col(),
ampi = guess_ab_col(), azit = guess_ab_col(),
azlo = guess_ab_col(), aztr = guess_ab_col(),
cefa = guess_ab_col(), cfep = guess_ab_col(),
cfot = guess_ab_col(), cfox = guess_ab_col(),
cfra = guess_ab_col(), cfta = guess_ab_col(),
cftr = guess_ab_col(), cfur = guess_ab_col(),
chlo = guess_ab_col(), cipr = guess_ab_col(),
clar = guess_ab_col(), clin = guess_ab_col(),
clox = guess_ab_col(), coli = guess_ab_col(),
czol = guess_ab_col(), dapt = guess_ab_col(),
doxy = guess_ab_col(), erta = guess_ab_col(),
eryt = guess_ab_col(), fosf = guess_ab_col(),
fusi = guess_ab_col(), gent = guess_ab_col(),
imip = guess_ab_col(), kana = guess_ab_col(),
levo = guess_ab_col(), linc = guess_ab_col(),
line = guess_ab_col(), mero = guess_ab_col(),
mezl = guess_ab_col(), mino = guess_ab_col(),
moxi = guess_ab_col(), nali = guess_ab_col(),
neom = guess_ab_col(), neti = guess_ab_col(),
nitr = guess_ab_col(), norf = guess_ab_col(),
novo = guess_ab_col(), oflo = guess_ab_col(),
oxac = guess_ab_col(), peni = guess_ab_col(),
pipe = guess_ab_col(), pita = guess_ab_col(),
poly = guess_ab_col(), pris = guess_ab_col(),
qida = guess_ab_col(), rifa = guess_ab_col(),
roxi = guess_ab_col(), siso = guess_ab_col(),
teic = guess_ab_col(), tetr = guess_ab_col(),
tica = guess_ab_col(), tige = guess_ab_col(),
tobr = guess_ab_col(), trim = guess_ab_col(),
trsu = guess_ab_col(), vanc = guess_ab_col(), ...)
EUCAST_rules(...)
interpretive_reading(...)
eucast_rules_file()
}
\arguments{
\item{tbl}{table with antibiotic columns, like e.g. \code{amox} and \code{amcl}}
\item{x}{data with antibiotic columns, like e.g. \code{amox} and \code{amcl}}
\item{col_mo}{column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.}
@@ -78,11 +76,19 @@ interpretive_reading(...)
\item{...}{parameters that are passed on to \code{eucast_rules}}
}
\value{
The input of \code{tbl}, possibly with edited values of antibiotics. Or, if \code{verbose = TRUE}, a \code{data.frame} with all original and new values of the affected bug-drug combinations.
The input of \code{tbl_}, possibly with edited values of antibiotics. Or, if \code{verbose = TRUE}, a \code{data.frame} with all original and new values of the affected bug-drug combinations.
}
\description{
Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{http://eucast.org}), see \emph{Source}. This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables.
}
\details{
The file used for applying all EUCAST rules can be retrieved with \code{\link{eucast_rules_file}()}. It returns an easily readable data set containing all rules. The original TSV file (tab separated file) that is being read by this function can be found when running this command: \cr
\code{AMR::EUCAST_RULES_FILE_LOCATION} (without brackets).
In the source code it is located under \href{https://gitlab.com/msberends/AMR/blob/master/inst/eucast/eucast_rules.tsv}{\code{./inst/eucast/eucast_rules.tsv}}.
\strong{Note:} When ampicillin (J01CA01) is not available but amoxicillin (J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance.
}
\section{Antibiotics}{
To define antibiotics column names, leave as it is to determine it automatically with \code{\link{guess_ab_col}} or input a text (case-insensitive) or use \code{NULL} to skip a column (e.g. \code{tica = NULL}). Non-existing columns will anyway be skipped with a warning.