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(v2.1.1.9140) WISCA fix

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dr. M.S. (Matthijs) Berends
2025-02-05 20:48:35 +01:00
parent d84033bbcb
commit baea4323c7
23 changed files with 408 additions and 202 deletions
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26
man/proportion.Rd
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@ -85,6 +85,8 @@ These functions can be used to calculate the (co-)resistance or susceptibility o
\code{\link[=resistance]{resistance()}} should be used to calculate resistance, \code{\link[=susceptibility]{susceptibility()}} should be used to calculate susceptibility.\cr
}
\details{
For a more automated and comprehensive analysis, consider using \code{\link[=antibiogram]{antibiogram()}} or \code{\link[=wisca]{wisca()}}, which streamline many aspects of susceptibility reporting and, importantly, also support WISCA. The functions described here offer a more hands-on, manual approach for greater customisation.
\strong{Remember that you should filter your data to let it contain only first isolates!} This is needed to exclude duplicates and to reduce selection bias. Use \code{\link[=first_isolate]{first_isolate()}} to determine them in your data set with one of the four available algorithms.
The function \code{\link[=resistance]{resistance()}} is equal to the function \code{\link[=proportion_R]{proportion_R()}}. The function \code{\link[=susceptibility]{susceptibility()}} is equal to the function \code{\link[=proportion_SI]{proportion_SI()}}. Since AMR v3.0, \code{\link[=proportion_SI]{proportion_SI()}} and \code{\link[=proportion_I]{proportion_I()}} include dose-dependent susceptibility ('SDD').
@ -102,18 +104,18 @@ When using more than one variable for \code{...} (= combination therapy), use \c
\if{html}{\out{<div class="sourceCode">}}\preformatted{--------------------------------------------------------------------
only_all_tested = FALSE only_all_tested = TRUE
----------------------- -----------------------
Drug A Drug B include as include as include as include as
numerator denominator numerator denominator
-------- -------- ---------- ----------- ---------- -----------
S or I S or I X X X X
R S or I X X X X
<NA> S or I X X - -
S or I R X X X X
R R - X - X
<NA> R - - - -
S or I <NA> X X - -
R <NA> - - - -
<NA> <NA> - - - -
Drug A Drug B considered considered considered considered
susceptible tested susceptible tested
-------- -------- ----------- ---------- ----------- ----------
S or I S or I X X X X
R S or I X X X X
<NA> S or I X X - -
S or I R X X X X
R R - X - X
<NA> R - - - -
S or I <NA> X X - -
R <NA> - - - -
<NA> <NA> - - - -
--------------------------------------------------------------------
}\if{html}{\out{</div>}}