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cfta streptococci, codecov.yml

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dr. M.S. (Matthijs) Berends
2019-04-09 14:59:17 +02:00
parent cffb7787d8
commit 461eec9bac
18 changed files with 203 additions and 114 deletions
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6
man/mdro.Rd
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@@ -37,7 +37,7 @@ mdro(tbl, country = NULL, col_mo = NULL, info = TRUE,
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())
trsu = guess_ab_col(), vanc = guess_ab_col(), verbose = FALSE)
brmo(..., country = "nl")
@@ -174,6 +174,8 @@ eucast_exceptional_phenotypes(tbl, country = "EUCAST", ...)
\item{vanc}{column name of an antibiotic, see Antibiotics}
\item{verbose}{print additional info: missing antibiotic columns per parameter}
\item{...}{parameters that are passed on to methods}
}
\value{
@@ -183,7 +185,7 @@ Ordered factor with levels \code{Negative < Positive, unconfirmed < Positive}.
Determine which isolates are multidrug-resistant organisms (MDRO) according to country-specific guidelines.
}
\details{
When \code{country} will be left blank, guidelines will be taken from EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (\url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}).
When \code{country} will be left blank, guidelines will be taken from EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (\href{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}{link}).
}
\section{Antibiotics}{