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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
R/proportion.R
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@ -46,6 +46,8 @@
#' @param collapse a [logical] to indicate whether the output values should be 'collapsed', i.e. be merged together into one value, or a character value to use for collapsing
#' @inheritSection as.sir Interpretation of SIR
#' @details
#' For a more automated and comprehensive analysis, consider using [antibiogram()] or [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.
#'
#' **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 [first_isolate()] to determine them in your data set with one of the four available algorithms.
#'
#' The function [resistance()] is equal to the function [proportion_R()]. The function [susceptibility()] is equal to the function [proportion_SI()]. Since AMR v3.0, [proportion_SI()] and [proportion_I()] include dose-dependent susceptibility ('SDD').
@ -63,18 +65,18 @@
#' --------------------------------------------------------------------
#' 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> - - - -
#' --------------------------------------------------------------------
#' ```
#'