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(v3.0.1.9059) Update taxonomy of microorganisms

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Matthijs Berends
2026-06-23 01:38:13 +02:00
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parent 0af3f84655
commit 3f9f931777
123 changed files with 121928 additions and 94162 deletions
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man/intrinsic_resistant.Rd
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@@ -5,7 +5,7 @@
\alias{intrinsic_resistant}
\title{Data Set Denoting Bacterial Intrinsic Resistance}
\format{
A \link[tibble:tibble]{tibble} with 285 928 observations and 2 variables:
A \link[tibble:tibble]{tibble} with 294 079 observations and 2 variables:
\itemize{
\item \code{mo}\cr Microorganism ID which occurs in \code{\link[=microorganisms]{microorganisms$mo}}. Names can be retrieved using \code{\link[=mo_name]{mo_name()}}.
\item \code{ab}\cr Antimicrobial ID which occurs in \code{\link[=antimicrobials]{antimicrobials$ab}}. Names can be retrieved using \code{\link[=ab_name]{ab_name()}}.
@@ -24,6 +24,7 @@ This data set is internally used by:
\itemize{
\item \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} (an \link[=antimicrobial_selectors]{antimicrobial selector})
\item \code{\link[=mo_is_intrinsic_resistant]{mo_is_intrinsic_resistant()}}
\item \code{\link[=wisca]{wisca()}} to model \eqn{\beta(1, 9999)} for resistant bug-drug combinations, per \doi{10.1093/jac/dkv397}
}
}
\section{Download Our Reference Data}{