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breakpoints UTI interpretation fix

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dr. M.S. (Matthijs) Berends
2023-07-10 13:41:52 +02:00
parent 3829311dd3
commit 70c601ca11
28 changed files with 605 additions and 150 deletions
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4
man/as.mo.Rd
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@ -201,6 +201,10 @@ as.mo(c(
"Ureaplazma urealitycium"
))
# input will get cleaned up with the input given in the `cleaning_regex` argument,
# which defaults to `mo_cleaning_regex()`:
cat(mo_cleaning_regex(), "\n")
as.mo("Streptococcus group A")
as.mo("S. epidermidis") # will remain species: B_STPHY_EPDR

4
man/as.sir.Rd
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@ -171,7 +171,7 @@ After using \code{\link[=as.sir]{as.sir()}}, you can use the \code{\link[=eucast
\subsection{Machine-Readable Clinical Breakpoints}{
The repository of this package \href{https://github.com/msberends/AMR/blob/main/data-raw/clinical_breakpoints.txt}{contains a machine-readable version} of all guidelines. This is a CSV file consisting of 28 454 rows and 12 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 drug 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/main/data-raw/clinical_breakpoints.txt}{contains a machine-readable version} of all guidelines. This is a CSV file consisting of 28 885 rows and 12 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 drug 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}{
@ -185,7 +185,7 @@ The function \code{\link[=is_sir_eligible]{is_sir_eligible()}} returns \code{TRU
}
\section{Interpretation of SIR}{
In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R as shown below (\url{https://www.eucast.org/newsiandr/}):
In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R as shown below (\url{https://www.eucast.org/newsiandr}):
\itemize{
\item \strong{S - Susceptible, standard dosing regimen}\cr
A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.

2
man/clinical_breakpoints.Rd
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@ -5,7 +5,7 @@
\alias{clinical_breakpoints}
\title{Data Set with Clinical Breakpoints for SIR Interpretation}
\format{
A \link[tibble:tibble]{tibble} with 28 454 observations and 12 variables:
A \link[tibble:tibble]{tibble} with 28 885 observations and 12 variables:
\itemize{
\item \code{guideline}\cr Name of the guideline
\item \code{type}\cr Breakpoint type, either "ECOFF", "animal", or "human"

2
man/count.Rd
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@ -71,7 +71,7 @@ The function \code{\link[=count_df]{count_df()}} takes any variable from \code{d
}
\section{Interpretation of SIR}{
In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R as shown below (\url{https://www.eucast.org/newsiandr/}):
In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R as shown below (\url{https://www.eucast.org/newsiandr}):
\itemize{
\item \strong{S - Susceptible, standard dosing regimen}\cr
A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.

2
man/mdro.Rd
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@ -174,7 +174,7 @@ Amikacin (\code{AMK}, \href{https://www.whocc.no/atc_ddd_index/?code=J01GB06&sho
\section{Interpretation of SIR}{
In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R as shown below (\url{https://www.eucast.org/newsiandr/}):
In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R as shown below (\url{https://www.eucast.org/newsiandr}):
\itemize{
\item \strong{S - Susceptible, standard dosing regimen}\cr
A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.

2
man/microorganisms.groups.Rd
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@ -17,7 +17,7 @@ A \link[tibble:tibble]{tibble} with 444 observations and 4 variables:
microorganisms.groups
}
\description{
A data set containing species groups and microbiological complexes, which are used in \link[=clinial_breakpoints]{the clinical breakpoints table}.
A data set containing species groups and microbiological complexes, which are used in \link[=clinical_breakpoints]{the clinical breakpoints table}.
}
\details{
Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for the download links}. The actual files are of course available on \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.

2
man/proportion.Rd
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@ -146,7 +146,7 @@ Using \code{only_all_tested} has no impact when only using one antibiotic as inp
\section{Interpretation of SIR}{
In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R as shown below (\url{https://www.eucast.org/newsiandr/}):
In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R as shown below (\url{https://www.eucast.org/newsiandr}):
\itemize{
\item \strong{S - Susceptible, standard dosing regimen}\cr
A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.

2
man/resistance_predict.Rd
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@ -112,7 +112,7 @@ Valid options for the statistical model (argument \code{model}) are:
}
\section{Interpretation of SIR}{
In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R as shown below (\url{https://www.eucast.org/newsiandr/}):
In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R as shown below (\url{https://www.eucast.org/newsiandr}):
\itemize{
\item \strong{S - Susceptible, standard dosing regimen}\cr
A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.