P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-10 00:23:03 +02:00
Code Releases Activity

(v2.1.1.9203) unit tests

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2025-03-15 13:25:23 +01:00
parent f758ab60f3
commit 7f1ae1f474
12 changed files with 105 additions and 55 deletions
Download Patch File Download Diff File Expand all files Collapse all files

38
man/as.sir.Rd
View File

@ -44,7 +44,7 @@ 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, ...)
verbose = FALSE, conserve_capped_values = NULL, ...)
\method{as.sir}{disk}(x, mo = NULL, ab = deparse(substitute(x)),
guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
@ -65,7 +65,7 @@ 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)
verbose = FALSE, conserve_capped_values = NULL)
sir_interpretation_history(clean = FALSE)
}
@ -87,15 +87,29 @@ sir_interpretation_history(clean = FALSE)
\item{uti}{(Urinary Tract Infection) a vector (or column name) with \link{logical}s (\code{TRUE} or \code{FALSE}) to specify whether a UTI specific interpretation from the guideline should be chosen. For using \code{\link[=as.sir]{as.sir()}} on a \link{data.frame}, this can also be a column containing \link{logical}s or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See \emph{Examples}.}
\item{capped_mic_handling}{A \link{character} string that controls how MIC values with a cap (i.e., starting with \code{<}, \code{<=}, \code{>}, or \code{>=}) are interpreted. Supports the following options:
\code{"none"}
\itemize{
\item \code{"standard"} (default)\cr
\code{<=} and \code{>=} return \code{"NI"} if the value is \strong{within} the breakpoint guideline range, while \code{<} and \code{>} are interpreted normally.
\item \code{"strict"}\cr
Enforces conservative handling; \code{<} always returns \code{"S"}, \code{>} always returns \code{"R"}, and \code{<=}/\code{>=} return \code{"NI"} when within breakpoint guideline range.
\item \code{"relaxed"}\cr
Ignores all signs, treating values as their numeric equivalents (e.g., \verb{>0.5} is regarded \code{0.5}).
\item \code{"inverse"}\cr
Opposite of \code{"standard"}; \code{<} always returns \code{"S"}, \code{>} always returns \code{"R"}, and \code{<=}/\code{>=} are treated as their numeric equivalents
\item \code{<=} and \code{>=} are treated as-is.
\item \code{<} and \code{>} are treated as-is.
}
\code{"conservative"}
\itemize{
\item \code{<=} and \code{>=} return \code{"NI"} (non-interpretable) if the MIC is within the breakpoint guideline range.
\item \code{<} always returns \code{"S"}, and \code{>} always returns \code{"R"}.
}
\code{"standard"} (default)
\itemize{
\item \code{<=} and \code{>=} return \code{"NI"} (non-interpretable) if the MIC is within the breakpoint guideline range.
\item \code{<} and \code{>} are treated as-is.
}
\code{"inverse"}
\itemize{
\item \code{<=} and \code{>=} are treated as-is.
\item \code{<} always returns \code{"S"}, and \code{>} always returns \code{"R"}.
}
The default \code{"standard"} setting ensures cautious handling of uncertain values while preserving interpretability. This option can also be set with the package option \code{\link[=AMR-options]{AMR_capped_mic_handling}}.}
@ -116,6 +130,8 @@ The default \code{"standard"} setting ensures cautious handling of uncertain val
\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}
\item{col_mo}{column name of the names or codes of the microorganisms (see \code{\link[=as.mo]{as.mo()}}) - the default is the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
\item{clean}{a \link{logical} to indicate whether previously stored results should be forgotten after returning the 'logbook' with results}
@ -154,7 +170,7 @@ your_data \%>\% mutate_if(is.mic, as.sir, ab = c("cipro", "ampicillin", ...), mo
# for veterinary breakpoints, also set `host`:
your_data \%>\% mutate_if(is.mic, as.sir, host = "column_with_animal_species", guideline = "CLSI")
}\if{html}{\out{</div>}}
\item Operators like "<=" will be stripped before interpretation. When using \code{capped_mic_handling = "strict"}, an MIC value of e.g. ">2" will always return "R", even if the breakpoint according to the chosen guideline is ">=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (\code{capped_mic_handling = "standard"}) considers ">2" to be lower than ">=4" and might in this case return "S" or "I".
\item Operators like "<=" will be stripped before interpretation. When using \code{capped_mic_handling = "conservative"}, an MIC value of e.g. ">2" will always return "R", even if the breakpoint according to the chosen guideline is ">=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (\code{capped_mic_handling = "standard"}) considers ">2" to be lower than ">=4" and might in this case return "S" or "I".
}
\item For \strong{interpreting disk diffusion diameters} according to EUCAST or CLSI. You must clean your disk zones first using \code{\link[=as.disk]{as.disk()}}, that also gives your columns the new data class \code{\link{disk}}. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the \code{mo} argument.
\itemize{