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(v2.1.1.9272) mo codes sensititre

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dr. M.S. (Matthijs) Berends 2025-05-04 18:50:25 +02:00
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NEWS.md
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@ -136,6 +136,7 @@ This package now supports not only tools for AMR data analysis in clinical setti
* Updated all antimicrobial DDDs from WHOCC * Updated all antimicrobial DDDs from WHOCC
* Fix for using a manual value for `mo_transform` in `antibiogram()` * Fix for using a manual value for `mo_transform` in `antibiogram()`
* Fixed a bug for when `antibiogram()` returns an empty data set * Fixed a bug for when `antibiogram()` returns an empty data set
* Added Sensititre codes for animals, antimicrobials and microorganisms
* Fix for mapping 'high level' antimicrobials in `as.ab()` (amphotericin B-high, gentamicin-high, kanamycin-high, streptomycin-high, tobramycin-high) * Fix for mapping 'high level' antimicrobials in `as.ab()` (amphotericin B-high, gentamicin-high, kanamycin-high, streptomycin-high, tobramycin-high)
* Improved overall algorithm of `as.ab()` for better performance and accuracy, including the new function `as_reset_session()` to remove earlier coercions. * Improved overall algorithm of `as.ab()` for better performance and accuracy, including the new function `as_reset_session()` to remove earlier coercions.
* Improved overall algorithm of `as.mo()` for better performance and accuracy, specifically: * Improved overall algorithm of `as.mo()` for better performance and accuracy, specifically:

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data-raw/datasets/microorganisms.codes.txt
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data-raw/microorganisms.codes.md5
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85b172c713e3e5aed32dc760c337ec34 986d5110a46bbf297ebaeb4dd5179fff

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data-raw/sensititre_mo.R Normal file
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man/microorganisms.codes.Rd
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\docType{data} \docType{data}
\name{microorganisms.codes} \name{microorganisms.codes}
\alias{microorganisms.codes} \alias{microorganisms.codes}
\title{Data Set with 5 063 Common Microorganism Codes} \title{Data Set with 6 036 Common Microorganism Codes}
\format{ \format{
A \link[tibble:tibble]{tibble} with 5 063 observations and 2 variables: A \link[tibble:tibble]{tibble} with 6 036 observations and 2 variables:
\itemize{ \itemize{
\item \code{code}\cr Commonly used code of a microorganism. \emph{\strong{This is a unique identifier.}} \item \code{code}\cr Commonly used code of a microorganism. \emph{\strong{This is a unique identifier.}}
\item \code{mo}\cr ID of the microorganism in the \link{microorganisms} data set \item \code{mo}\cr ID of the microorganism in the \link{microorganisms} data set