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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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14
man/first_isolate.Rd
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@@ -4,13 +4,6 @@
\alias{first_isolate}
\alias{filter_first_isolate}
\title{Determine First Isolates}
\source{
Methodology of these functions is strictly based on:
\itemize{
\item \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 5th Edition}, 2022, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
\item Hindler JF and Stelling J (2007). \strong{Analysis and Presentation of Cumulative Antibiograms: A New Consensus Guideline from the Clinical and Laboratory Standards Institute.} Clinical Infectious Diseases, 44(6), 867-873. \doi{10.1086/511864}
}
}
\usage{
first_isolate(x = NULL, col_date = NULL, col_patient_id = NULL,
col_mo = NULL, col_testcode = NULL, col_specimen = NULL,
@@ -178,6 +171,13 @@ if (require("dplyr")) {
}
}
}
\references{
Methodology of these functions is strictly based on:
\itemize{
\item \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 5th Edition}, 2022, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
\item Hindler JF and Stelling J (2007). \strong{Analysis and Presentation of Cumulative Antibiograms: A New Consensus Guideline from the Clinical and Laboratory Standards Institute.} Clinical Infectious Diseases, 44(6), 867-873. \doi{10.1086/511864}
}
}
\seealso{
\code{\link[=key_antimicrobials]{key_antimicrobials()}}
}