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(v1.5.0.9001) more informative argument errors

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dr. M.S. (Matthijs) Berends
2021-01-14 14:41:44 +01:00
parent d014955ce0
commit bc00470dca
30 changed files with 126 additions and 74 deletions
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8
man/as.ab.Rd
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@ -102,6 +102,14 @@ ab_atc("seephthriaaksone") # and even this works
# they use as.ab() internally:
ab_name("J01FA01") # "Erythromycin"
ab_name("eryt") # "Erythromycin"
if (require("dplyr")) {
# you can quickly rename <rsi> columns using dplyr >= 1.0.0:
example_isolates \%>\%
rename_with(as.ab, where(is.rsi))
}
}
\seealso{
\itemize{

4
man/as.rsi.Rd
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@ -104,7 +104,7 @@ your_data \%>\% mutate(across(where(is.disk), as.rsi)) # since dplyr 1.0.0
\subsection{Supported guidelines}{
For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the \code{guideline} argument are: "CLSI 2010", "CLSI 2011", "CLSI 2012", "CLSI 2013", "CLSI 2014", "CLSI 2015", "CLSI 2016", "CLSI 2017", "CLSI 2018", "CLSI 2019", "EUCAST 2011", "EUCAST 2012", "EUCAST 2013", "EUCAST 2014", "EUCAST 2015", "EUCAST 2016", "EUCAST 2017", "EUCAST 2018", "EUCAST 2019", "EUCAST 2020".
For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the \code{guideline} argument are: "CLSI 2010", "CLSI 2011", "CLSI 2012", "CLSI 2013", "CLSI 2014", "CLSI 2015", "CLSI 2016", "CLSI 2017", "CLSI 2018", "CLSI 2019", "EUCAST 2011", "EUCAST 2012", "EUCAST 2013", "EUCAST 2014", "EUCAST 2015", "EUCAST 2016", "EUCAST 2017", "EUCAST 2018", "EUCAST 2019", "EUCAST 2020", "EUCAST 2021".
Simply using \code{"CLSI"} or \code{"EUCAST"} as input will automatically select the latest version of that guideline. You can set your own data set using the \code{reference_data} argument. The \code{guideline} argument will then be ignored.
}
@ -116,7 +116,7 @@ After using \code{\link[=as.rsi]{as.rsi()}}, you can use the \code{\link[=eucast
\subsection{Machine readable interpretation guidelines}{
The repository of this package \href{https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}{contains a machine readable version} of all guidelines. This is a CSV file consisting of 18,650 rows and 10 columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. \strong{This allows for easy implementation of these rules in laboratory information systems (LIS)}. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
The repository of this package \href{https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}{contains a machine readable version} of all guidelines. This is a CSV file consisting of 20,486 rows and 10 columns. This file is machine readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. \strong{This allows for easy implementation of these rules in laboratory information systems (LIS)}. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
}
\subsection{Other}{

2
man/dosage.Rd
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@ -11,7 +11,7 @@ A \link{data.frame} with 135 observations and 9 variables:
\item \code{name}\cr Official name of the antimicrobial agent as used by WHONET/EARS-Net or the WHO
\item \code{type}\cr Type of the dosage, either "high_dosage", "standard_dosage" or "uncomplicated_uti"
\item \code{dose}\cr Dose, such as "2 g" or "25 mg/kg"
\item \code{dose_times}\cr Dose, such as "2 g" or "25 mg/kg"
\item \code{dose_times}\cr Number of times a dose must be administered
\item \code{administration}\cr Route of administration, either "im", "iv" or "oral"
\item \code{notes}\cr Additional dosage notes
\item \code{original_txt}\cr Original text in the PDF file of EUCAST

8
man/eucast_rules.Rd
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@ -23,7 +23,7 @@ eucast_rules(
info = interactive(),
rules = getOption("AMR_eucastrules", default = c("breakpoints", "expert")),
verbose = FALSE,
version_breakpoints = 10,
version_breakpoints = 11,
version_expertrules = 3.2,
ampc_cephalosporin_resistance = NA,
...
@ -42,9 +42,9 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 11)
\item{verbose}{a \link{logical} to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way. Using Verbose mode takes a lot more time.}
\item{version_breakpoints}{the version number to use for the EUCAST Clinical Breakpoints guideline. Currently supported: 11.0, 10.0.}
\item{version_breakpoints}{the version number to use for the EUCAST Clinical Breakpoints guideline. Can be either "11.0" or "10.0".}
\item{version_expertrules}{the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Currently supported: 3.1, 3.2.}
\item{version_expertrules}{the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either "3.2" or "3.1".}
\item{ampc_cephalosporin_resistance}{a character value that should be applied for AmpC de-repressed cephalosporin-resistant mutants, defaults to \code{NA}. Currently only works when \code{version_expertrules} is \code{3.2}; '\emph{EUCAST Expert Rules v3.2 on Enterobacterales}' states that susceptible (S) results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these agents. A value of \code{NA} for this argument will remove results for these agents, while e.g. a value of \code{"R"} will make the results for these agents resistant. Use \code{NULL} to not alter the results for AmpC de-repressed cephalosporin-resistant mutants. \cr For \emph{EUCAST Expert Rules} v3.2, this rule applies to: \emph{Enterobacter, Klebsiella aerogenes, Citrobacter braakii, freundii, gillenii, murliniae, rodenticum, sedlakii, werkmanii, youngae, Hafnia alvei, Serratia, Morganella morganii, Providencia}.}
@ -58,7 +58,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 11)
The input of \code{x}, possibly with edited values of antibiotics. Or, if \code{verbose = TRUE}, a \link{data.frame} with all original and new values of the affected bug-drug combinations.
}
\description{
Apply rules for clinical breakpoints and intrinsic resistance as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{https://eucast.org}), see \emph{Source}. Use \code{\link[=eucast_dosage]{eucast_dosage()}} to get advised dosages of a certain bug-drug combination, which is based on the \link{dosage} data set.
Apply rules for clinical breakpoints and intrinsic resistance as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{https://eucast.org}), see \emph{Source}. Use \code{\link[=eucast_dosage]{eucast_dosage()}} to get a \link{data.frame} with advised dosages of a certain bug-drug combination, which is based on the \link{dosage} data set.
To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see Details.
}

4
man/rsi_translation.Rd
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@ -5,7 +5,7 @@
\alias{rsi_translation}
\title{Data set for R/SI interpretation}
\format{
A \link{data.frame} with 18,650 observations and 10 variables:
A \link{data.frame} with 20,486 observations and 10 variables:
\itemize{
\item \code{guideline}\cr Name of the guideline
\item \code{method}\cr Either "MIC" or "DISK"
@ -23,7 +23,7 @@ A \link{data.frame} with 18,650 observations and 10 variables:
rsi_translation
}
\description{
Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2010-2019) and EUCAST (2011-2020). Use \code{\link[=as.rsi]{as.rsi()}} to transform MICs or disks measurements to R/SI values.
Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2010-2019) and EUCAST (2011-2021). Use \code{\link[=as.rsi]{as.rsi()}} to transform MICs or disks measurements to R/SI values.
}
\details{
The repository of this \code{AMR} package contains a file comprising this exact data set: \url{https://github.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}. This file \strong{allows for machine reading EUCAST and CLSI guidelines}, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically.