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unit tests

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dr. M.S. (Matthijs) Berends
2023-02-12 17:10:48 +01:00
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R/proportion.R
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@ -56,7 +56,7 @@
#' The function [proportion_df()] takes any variable from `data` that has an [`sir`] class (created with [as.sir()]) and calculates the proportions S, I, and R. It also supports grouped variables. The function [sir_df()] works exactly like [proportion_df()], but adds the number of isolates.
#' @section Combination Therapy:
#' When using more than one variable for `...` (= combination therapy), use `only_all_tested` to only count isolates that are tested for all antibiotics/variables that you test them for. See this example for two antibiotics, Drug A and Drug B, about how [susceptibility()] works to calculate the %SI:
#'
#'
#'
#' ```
#' --------------------------------------------------------------------
@ -78,14 +78,14 @@
#' ```
#'
#' Please note that, in combination therapies, for `only_all_tested = TRUE` applies that:
#'
#'
#' ```
#' count_S() + count_I() + count_R() = count_all()
#' proportion_S() + proportion_I() + proportion_R() = 1
#' ```
#'
#'
#' and that, in combination therapies, for `only_all_tested = FALSE` applies that:
#'
#'
#' ```
#' count_S() + count_I() + count_R() >= count_all()
#' proportion_S() + proportion_I() + proportion_R() >= 1
@ -103,8 +103,8 @@
#' # example_isolates is a data set available in the AMR package.
#' # run ?example_isolates for more info.
#' example_isolates
#'
#'
#'
#'
#' # base R ------------------------------------------------------------
#' # determines %R
#' resistance(example_isolates$AMX)