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(v2.1.1.9157) improved as.ab(), fixed knit_print of antibiogram

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dr. M.S. (Matthijs) Berends
2025-02-26 13:27:20 +01:00
parent b10989f431
commit 195dfb4b91
20 changed files with 107 additions and 42 deletions
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14
R/amr_selectors.R
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@ -47,7 +47,7 @@
#' @details
#' These functions can be used in data set calls for selecting columns and filtering rows. They work with base \R, the Tidyverse, and `data.table`. They are heavily inspired by the [Tidyverse selection helpers][tidyselect::language] such as [`everything()`][tidyselect::everything()], but are not limited to `dplyr` verbs. Nonetheless, they are very convenient to use with `dplyr` functions such as [`select()`][dplyr::select()], [`filter()`][dplyr::filter()] and [`summarise()`][dplyr::summarise()], see *Examples*.
#'
#' All selectors can also be used in `tidymodels` packages such as `recipe` and `parsnip`. See for more info [our tutorial](https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html) on using these AMR functions for predictive modelling.
#' All selectors can also be used in `tidymodels` packages such as `recipe` and `parsnip`. See for more info [our tutorial](https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html) on using antimicrobial selectors for predictive modelling.
#'
#' All columns in the data in which these functions are called will be searched for known antimicrobial names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) according to the [antibiotics] data set. This means that a selector such as [aminoglycosides()] will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.
#'
@ -747,16 +747,8 @@ amr_select_exec <- function(function_name,
if (is.null(vars_df)) {
# no data found, no antimicrobials, so no input. Happens if users run e.g. `aminoglycosides()` as a separate command.
examples <- paste0(
" ", AMR_env$bullet_icon, " your_data %>% select(", function_name, "())\n",
" ", AMR_env$bullet_icon, " your_data %>% select(column_a, column_b, ", function_name, "())\n",
" ", AMR_env$bullet_icon, " your_data %>% filter(any(", function_name, "() == \"R\"))\n",
" ", AMR_env$bullet_icon, " your_data[, ", function_name, "()]\n",
" ", AMR_env$bullet_icon, " your_data[, c(\"column_a\", \"column_b\", ", function_name, "())]")
message_("The function `" , function_name, "()` should be used inside a `dplyr` verb or `data.frame` call, e.g.:\n",
examples,
"\n\nNow returning a vector of all possible antimicrobials that `" , function_name, "()` can select.")
return(sort(abx))
# print.ab will cover the additional printing text
return(structure(sort(abx), amr_selector = function_name))
}
# get the columns with a group names in the chosen ab class