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(v2.1.1.9279) fix documentation, add foreign S3 exports to functions

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dr. M.S. (Matthijs) Berends
2025-05-16 16:55:29 +02:00
parent 139f79d372
commit 38cebc1541
24 changed files with 292 additions and 239 deletions
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19
R/custom_eucast_rules.R
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@@ -33,7 +33,6 @@
#' @param ... Rules in [formula][base::tilde] notation, see below for instructions, and in *Examples*.
#' @details
#' Some organisations have their own adoption of EUCAST rules. This function can be used to define custom EUCAST rules to be used in the [eucast_rules()] function.
#' @section How it works:
#'
#' ### Basics
#'
@@ -69,7 +68,11 @@
#' #> 1 Escherichia coli R S S
#' #> 2 Klebsiella pneumoniae R S S
#'
#' eucast_rules(df, rules = "custom", custom_rules = x, info = FALSE, overwrite = TRUE)
#' eucast_rules(df,
#' rules = "custom",
#' custom_rules = x,
#' info = FALSE,
#' overwrite = TRUE)
#' #> mo TZP ampi cipro
#' #> 1 Escherichia coli R R S
#' #> 2 Klebsiella pneumoniae R R S
@@ -80,10 +83,16 @@
#' There is one exception in columns used for the rules: all column names of the [microorganisms] data set can also be used, but do not have to exist in the data set. These column names are: `r vector_and(colnames(microorganisms), sort = FALSE)`. Thus, this next example will work as well, despite the fact that the `df` data set does not contain a column `genus`:
#'
#' ```r
#' y <- custom_eucast_rules(TZP == "S" & genus == "Klebsiella" ~ aminopenicillins == "S",
#' TZP == "R" & genus == "Klebsiella" ~ aminopenicillins == "R")
#' y <- custom_eucast_rules(
#' TZP == "S" & genus == "Klebsiella" ~ aminopenicillins == "S",
#' TZP == "R" & genus == "Klebsiella" ~ aminopenicillins == "R"
#' )
#'
#' eucast_rules(df, rules = "custom", custom_rules = y, info = FALSE, overwrite = TRUE)
#' eucast_rules(df,
#' rules = "custom",
#' custom_rules = y,
#' info = FALSE,
#' overwrite = TRUE)
#' #> mo TZP ampi cipro
#' #> 1 Escherichia coli R S S
#' #> 2 Klebsiella pneumoniae R R S