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(v2.1.1.9126) implemented WISCA! Also added top_n_microorganisms() and fixed Python wrapper

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dr. M.S. (Matthijs) Berends
2025-01-26 23:01:17 +01:00
parent 92c4fc0f94
commit 66833b4f5a
46 changed files with 1786 additions and 1842 deletions
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58
man/proportion.Rd
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@ -18,50 +18,38 @@
\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/}.
}
\usage{
resistance(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)
resistance(..., minimum = 30, as_percent = FALSE,
only_all_tested = FALSE)
susceptibility(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)
susceptibility(..., minimum = 30, as_percent = FALSE,
only_all_tested = FALSE)
sir_confidence_interval(
...,
ab_result = "R",
minimum = 30,
as_percent = FALSE,
only_all_tested = FALSE,
confidence_level = 0.95,
side = "both",
collapse = FALSE
)
sir_confidence_interval(..., ab_result = "R", minimum = 30,
as_percent = FALSE, only_all_tested = FALSE, confidence_level = 0.95,
side = "both", collapse = FALSE)
proportion_R(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)
proportion_R(..., minimum = 30, as_percent = FALSE,
only_all_tested = FALSE)
proportion_IR(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)
proportion_IR(..., minimum = 30, as_percent = FALSE,
only_all_tested = FALSE)
proportion_I(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)
proportion_I(..., minimum = 30, as_percent = FALSE,
only_all_tested = FALSE)
proportion_SI(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)
proportion_SI(..., minimum = 30, as_percent = FALSE,
only_all_tested = FALSE)
proportion_S(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)
proportion_S(..., minimum = 30, as_percent = FALSE,
only_all_tested = FALSE)
proportion_df(
data,
translate_ab = "name",
language = get_AMR_locale(),
minimum = 30,
as_percent = FALSE,
combine_SI = TRUE,
confidence_level = 0.95
)
proportion_df(data, translate_ab = "name", language = get_AMR_locale(),
minimum = 30, as_percent = FALSE, combine_SI = TRUE,
confidence_level = 0.95)
sir_df(
data,
translate_ab = "name",
language = get_AMR_locale(),
minimum = 30,
as_percent = FALSE,
combine_SI = TRUE,
confidence_level = 0.95
)
sir_df(data, translate_ab = "name", language = get_AMR_locale(),
minimum = 30, as_percent = FALSE, combine_SI = TRUE,
confidence_level = 0.95)
}
\arguments{
\item{...}{one or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with \code{\link[=as.sir]{as.sir()}} if needed. Use multiple columns to calculate (the lack of) co-resistance: the probability where one of two drugs have a resistant or susceptible result. See \emph{Examples}.}