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(v2.1.1.9237) clean-up

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dr. M.S. (Matthijs) Berends
2025-04-13 09:59:40 +02:00
parent 40d7a971c3
commit d31371613e
14 changed files with 39 additions and 26 deletions
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4
R/resistance_predict.R
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@ -29,7 +29,9 @@
#' Predict Antimicrobial Resistance
#'
#' Create a prediction model to predict antimicrobial resistance for the next years on statistical solid ground. Standard errors (SE) will be returned as columns `se_min` and `se_max`. See *Examples* for a real live example.
#' @description Create a prediction model to predict antimicrobial resistance for the next years. Standard errors (SE) will be returned as columns `se_min` and `se_max`. See *Examples* for a real live example.
#'
#' **NOTE:** These functions are [deprecated][AMR-deprecated] and will be removed in a future version. Use the AMR package combined with the tidymodels framework instead, for which we have written a [basic and short introduction on our website](https://amr-for-r.org/articles/AMR_with_tidymodels.html).
#' @param object Model data to be plotted.
#' @param col_ab Column name of `x` containing antimicrobial interpretations (`"R"`, `"I"` and `"S"`).
#' @param col_date Column name of the date, will be used to calculate years if this column doesn't consist of years already - the default is the first column of with a date class.

8
R/zz_deprecated.R
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@ -27,7 +27,7 @@
# how to conduct AMR data analysis: https://amr-for-r.org #
# ==================================================================== #
#' Deprecated Functions
#' Deprecated Functions, Arguments, or Datasets
#'
#' These objects are so-called '[Deprecated]'. **They will be removed in a future version of this package.** Using these will give a warning with the name of the alternative object it has been replaced by (if there is one).
#' @keywords internal
@ -40,8 +40,10 @@ NULL
#' @export
"antibiotics"
# REMEMBER to also remove the deprecated `antibiotics` argument in `antibiogram()`
# REMEMBER to also remove the deprecated `converse_capped_values` argument in `as.sir()`
# REMEMBER to search for `deprecation_warning` in the package code to find all instances.
# currently deprecated arguments at least:
# - `antibiotics` in `antibiogram()`
# - `converse_capped_values` in `as.sir()`
#' @rdname AMR-deprecated
#' @export