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mo codes for WHONET

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dr. M.S. (Matthijs) Berends
2019-02-08 16:06:54 +01:00
parent 3d3366faf7
commit ed30312048
60 changed files with 1103 additions and 615 deletions
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13
man/eucast_rules.Rd
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@@ -71,14 +71,14 @@ 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{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}
\item{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. It runs all EUCAST rules, but will not be applied to an output - only an informative \code{data.frame} with changes will be returned as output.}
\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 Antibiotics}
\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 verbose info.
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.
@@ -184,7 +184,9 @@ a
# 4 Klebsiella pneumoniae - - - - - S S
# 5 Pseudomonas aeruginosa - - - - - S S
b <- eucast_rules(a, "mo") # 18 results are forced as R or S
# apply EUCAST rules: 18 results are forced as R or S
b <- eucast_rules(a)
b
# mo vanc amox coli cfta cfur peni cfox
@@ -193,6 +195,11 @@ b
# 3 Escherichia coli R - - - - R S
# 4 Klebsiella pneumoniae R R - - - R S
# 5 Pseudomonas aeruginosa R R - - R R R
# do not apply EUCAST rules, but rather get a a data.frame
# with 18 rows, containing all details about the transformations:
c <- eucast_rules(a, verbose = TRUE)
}
\keyword{eucast}
\keyword{interpretive}