P281424/AMR
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(v2.1.1.9272) (v2.1.1.9271) add sensititre AB and animal codes

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dr. M.S. (Matthijs) Berends committed 2025-05-04 16:40:08 +02:00
1 parent dc5559a2c4
commit a778eb9bcf
20 files changed
+841 -309
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man/as.sir.Rd
+8 -5
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@@ -44,8 +44,8 @@ is_sir_eligible(x, threshold = 0.05)
FALSE), include_screening = getOption("AMR_include_screening", FALSE),
include_PKPD = getOption("AMR_include_PKPD", TRUE),
breakpoint_type = getOption("AMR_breakpoint_type", "human"), host = NULL,
verbose = FALSE, info = interactive(), conserve_capped_values = NULL,
...)
language = get_AMR_locale(), verbose = FALSE, info = interactive(),
conserve_capped_values = NULL, ...)
\method{as.sir}{disk}(x, mo = NULL, ab = deparse(substitute(x)),
guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
@@ -55,7 +55,8 @@ is_sir_eligible(x, threshold = 0.05)
FALSE), include_screening = getOption("AMR_include_screening", FALSE),
include_PKPD = getOption("AMR_include_PKPD", TRUE),
breakpoint_type = getOption("AMR_breakpoint_type", "human"), host = NULL,
verbose = FALSE, info = interactive(), ...)
language = get_AMR_locale(), verbose = FALSE, info = interactive(),
...)
\method{as.sir}{data.frame}(x, ..., col_mo = NULL,
guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
@@ -66,8 +67,8 @@ is_sir_eligible(x, threshold = 0.05)
FALSE), include_screening = getOption("AMR_include_screening", FALSE),
include_PKPD = getOption("AMR_include_PKPD", TRUE),
breakpoint_type = getOption("AMR_breakpoint_type", "human"), host = NULL,
verbose = FALSE, info = interactive(), parallel = FALSE,
max_cores = -1, conserve_capped_values = NULL)
language = get_AMR_locale(), verbose = FALSE, info = interactive(),
parallel = FALSE, max_cores = -1, conserve_capped_values = NULL)
sir_interpretation_history(clean = FALSE)
}
@@ -132,6 +133,8 @@ The default \code{"standard"} setting ensures cautious handling of uncertain val
\item{host}{A vector (or column name) with \link{character}s to indicate the host. Only useful for veterinary breakpoints, as it requires \code{breakpoint_type = "animal"}. The values can be any text resembling the animal species, even in any of the 28 supported languages of this package. For foreign languages, be sure to set the language with \code{\link[=set_AMR_locale]{set_AMR_locale()}} (though it will be automatically guessed based on the system language).}
\item{language}{Language to convert values set in \code{host} when using animal breakpoints. Use one of these supported language names or \href{https://en.wikipedia.org/wiki/ISO_639-1}{ISO 639-1 codes}: English (en), Arabic (ar), Bengali (bn), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Hindi (hi), Indonesian (id), Italian (it), Japanese (ja), Korean (ko), Norwegian (no), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swahili (sw), Swedish (sv), Turkish (tr), Ukrainian (uk), Urdu (ur), or Vietnamese (vi).}
\item{verbose}{A \link{logical} to indicate that all notes should be printed during interpretation of MIC values or disk diffusion values.}
\item{conserve_capped_values}{Deprecated, use \code{capped_mic_handling} instead.}