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add all options to documentation

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2023-01-23 20:07:57 +01:00
parent 19fd0ef121
commit eef00069fd
31 changed files with 207 additions and 104 deletions
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9
man/as.sir.Rd
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@@ -41,6 +41,7 @@ is_sir_eligible(x, threshold = 0.05)
conserve_capped_values = FALSE,
add_intrinsic_resistance = FALSE,
reference_data = AMR::clinical_breakpoints,
include_PKPD = getOption("AMR_include_PKPD", TRUE),
...
)
@@ -52,6 +53,7 @@ is_sir_eligible(x, threshold = 0.05)
uti = NULL,
add_intrinsic_resistance = FALSE,
reference_data = AMR::clinical_breakpoints,
include_PKPD = getOption("AMR_include_PKPD", TRUE),
...
)
@@ -63,7 +65,8 @@ is_sir_eligible(x, threshold = 0.05)
uti = NULL,
conserve_capped_values = FALSE,
add_intrinsic_resistance = FALSE,
reference_data = AMR::clinical_breakpoints
reference_data = AMR::clinical_breakpoints,
include_PKPD = getOption("AMR_include_PKPD", TRUE)
)
sir_interpretation_history(clean = FALSE)
@@ -89,6 +92,8 @@ sir_interpretation_history(clean = FALSE)
\item{reference_data}{a \link{data.frame} to be used for interpretation, which defaults to the \link{clinical_breakpoints} data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the \link{clinical_breakpoints} data set (same column names and column types). Please note that the \code{guideline} argument will be ignored when \code{reference_data} is manually set.}
\item{include_PKPD}{a \link{logical} to indicate that PK/PD clinical breakpoints must be applied as a last resort, defaults to \code{TRUE}. Can also be set with the option \code{\link[=AMR-options]{AMR_include_PKPD}}.}
\item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to 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}
@@ -134,7 +139,7 @@ For interpreting MIC values as well as disk diffusion diameters, currently imple
Thus, the \code{guideline} argument must be set to e.g., \code{"EUCAST 2022"} or \code{"CLSI 2022"}. By simply using \code{"EUCAST"} (the default) or \code{"CLSI"} as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the \code{reference_data} argument. The \code{guideline} argument will then be ignored.
You can set the default guideline with the \code{AMR_guideline} \link[=options]{option} (e.g. in your \code{.Rprofile} file), such as:
You can set the default guideline with the option \code{\link[=AMR-options]{AMR_guideline}} (e.g. in your \code{.Rprofile} file), such as:
\if{html}{\out{<div class="sourceCode">}}\preformatted{ options(AMR_guideline = "CLSI")
options(AMR_guideline = "CLSI 2018")