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(v0.7.1.9065) bug-drug fix

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dr. M.S. (Matthijs) Berends
2019-08-27 22:41:09 +02:00
parent f3276592b7
commit 248638ad91
23 changed files with 62 additions and 45 deletions
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2
man/as.rsi.Rd
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@ -33,7 +33,7 @@ is.rsi.eligible(x, threshold = 0.05)
\item{guideline}{defaults to the latest included EUCAST guideline, run \code{unique(AMR::rsi_translation$guideline)} for all options}
\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}}.}
\item{col_mo}{column name of the IDs of the microorganisms (see \code{\link{as.mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.}
\item{threshold}{maximum fraction of invalid antimicrobial interpretations of \code{x}, see Examples}
}

10
man/bug_drug_combinations.Rd
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@ -2,27 +2,33 @@
% Please edit documentation in R/bug_drug_combinations.R
\name{bug_drug_combinations}
\alias{bug_drug_combinations}
\alias{format.bug_drug_combinations}
\title{Determine bug-drug combinations}
\source{
\strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
}
\usage{
bug_drug_combinations(x, col_mo = NULL, minimum = 30)
\method{format}{bug_drug_combinations}(x, combine_IR = FALSE,
add_ab_group = TRUE)
}
\arguments{
\item{x}{data with antibiotic columns, like e.g. \code{AMX} and \code{AMC}}
\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}}.}
\item{col_mo}{column name of the IDs of the microorganisms (see \code{\link{as.mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.}
\item{minimum}{the minimum allowed number of available (tested) isolates. Any isolate count lower than \code{minimum} will return \code{NA} with a warning. The default number of \code{30} isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see Source.}
\item{combine_IR}{logical to indicate whether values R and I should be summed}
\item{add_ab_group}{logical to indicate where the group of the antimicrobials must be included as a first column}
}
\description{
Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use \code{format} on the result to prettify it to a printable format, see Examples.
}
\details{
The function \code{format} calculated the resistance per bug-drug combination. Use \code{combine_IR = FALSE} (default) to test R vs. S+I and \code{combine_IR = TRUE} to test R+I vs. S.
The function \code{format} calculates the resistance per bug-drug combination. Use \code{combine_IR = FALSE} (default) to test R vs. S+I and \code{combine_IR = TRUE} to test R+I vs. S.
}
\section{Read more on our website!}{

2
man/eucast_rules.Rd
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@ -27,7 +27,7 @@ eucast_rules(x, col_mo = NULL, info = TRUE, rules = c("breakpoints",
\arguments{
\item{x}{data with antibiotic columns, like e.g. \code{AMX} and \code{AMC}}
\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}}.}
\item{col_mo}{column name of the IDs of the microorganisms (see \code{\link{as.mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.}
\item{info}{print progress}

2
man/first_isolate.Rd
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@ -30,7 +30,7 @@ filter_first_weighted_isolate(x, col_date = NULL,
\item{col_patient_id}{column name of the unique IDs of the patients, defaults to the first column that starts with 'patient' or 'patid' (case insensitive)}
\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}}.}
\item{col_mo}{column name of the IDs of the microorganisms (see \code{\link{as.mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.}
\item{col_testcode}{column name of the test codes. Use \code{col_testcode = NULL} to \strong{not} exclude certain test codes (like test codes for screening). In that case \code{testcodes_exclude} will be ignored.}

2
man/key_antibiotics.Rd
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@ -28,7 +28,7 @@ key_antibiotics_equal(y, z, type = c("keyantibiotics", "points"),
\arguments{
\item{x}{table with antibiotics coloms, like \code{AMX} or \code{amox}}
\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}}.}
\item{col_mo}{column name of the IDs of the microorganisms (see \code{\link{as.mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.}
\item{universal_1, universal_2, universal_3, universal_4, universal_5, universal_6}{column names of \strong{broad-spectrum} antibiotics, case-insensitive. At default, the columns containing these antibiotics will be guessed with \code{\link{guess_ab_col}}.}

2
man/mdro.Rd
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@ -31,7 +31,7 @@ eucast_exceptional_phenotypes(x, guideline = "EUCAST", ...)
\item{guideline}{a specific guideline to mention, see Details. EUCAST guidelines will be used when left empty, see Details.}
\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}}.}
\item{col_mo}{column name of the IDs of the microorganisms (see \code{\link{as.mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.}
\item{info}{print progress}