* Functions `is_gram_negative()` and `is_gram_positive()` as wrappers around `mo_gramstain()`. They always return `TRUE` or `FALSE`, thus always return `FALSE` for species outside the taxonomic kingdom of Bacteria.
### Changed
* For all function parameters in the code, it is now defined what the exact type of user input should be (inspired by the [`typed`](https://github.com/moodymudskipper/typed) package). If the user input for a certain function does not meet the requirements for a specific parameter (such as the class or length), an informative error will be thrown. This makes the package more robust and the use of it more reproducible and reliable. In total, more than 400 arguments were defined.
* Deprecated function `p_symbol()` that not really fits the scope of this package. It will be removed in a future version. See [here](https://github.com/msberends/AMR/blob/v1.4.0/R/p_symbol.R) for the source code to preserve it.
#' Calculates age in years based on a reference date, which is the sytem date at default.
#' @inheritSection lifecycle Stable lifecycle
#' @param x date(s), will be coerced with [as.POSIXlt()]
#' @param reference reference date(s) (defaults to today), will be coerced with [as.POSIXlt()] and cannot be lower than `x`
#' @param reference reference date(s) (defaults to today), will be coerced with [as.POSIXlt()]
#' @param exact a logical to indicate whether age calculation should be exact, i.e. with decimals. It divides the number of days of [year-to-date](https://en.wikipedia.org/wiki/Year-to-date) (YTD) of `x` by the number of days in the year of `reference` (either 365 or 366).
#' @param na.rm a logical to indicate whether missing values should be removed
#' @param ... parameters passed on to [as.POSIXlt()], such as `origin`
#' @details Ages below 0 will be returned as `NA` with a warning. Ages above 120 will only give a warning.
#' @return An [integer] (no decimals) if `exact = FALSE`, a [double] (with decimals) otherwise
#' @seealso To split ages into groups, use the [age_groups()] function.
#' @param combine_IR logical to indicate whether values R and I should be summed
#' @param add_ab_group logical to indicate where the group of the antimicrobials must be included as a first column
#' @param remove_intrinsic_resistant logical to indicate that rows and columns with 100% resistance for all tested antimicrobials must be removed from the table
#' @param FUN the function to call on the `mo` column to transform the microorganism IDs, defaults to [mo_shortname()]
#' @param translate_ab a character of length 1 containing column names of the [antibiotics] data set
#' @param FUN function to call on the `mo` column to transform the microorganism IDs, defaults to [mo_shortname()]
#' @param translate_ab character of length 1 containing column names of the [antibiotics] data set
#' As per their GPL-2 licence that demands documentation of code changes, the changes made based on the source code were:
#' 1. Rewritten code to remove the dependency on packages `plyr`, `scales` and `grid`
#' 2. Parametrised more options, like arrow and ellipse settings
#' 3. Added total amount of explained variance as a caption in the plot
#' 4. Cleaned all syntax based on the `lintr` package and added integrity checks
#' 5. Updated documentation
#' 3. Hardened all input possibilities by defining the exact type of user input for every parameter
#' 4. Added total amount of explained variance as a caption in the plot
#' 5. Cleaned all syntax based on the `lintr` package, fixed grammatical errors and added integrity checks
#' 6. Updated documentation
#' @details The colours for labels and points can be changed by adding another scale layer for colour, like `scale_colour_viridis_d()` or `scale_colour_brewer()`.
#' @rdname ggplot_pca
#' @export
@ -85,7 +86,7 @@
#' }
ggplot_pca<-function(x,
choices=1:2,
scale=TRUE,
scale=1,
pc.biplot=TRUE,
labels=NULL,
labels_textsize=3,
@ -107,22 +108,27 @@ ggplot_pca <- function(x,
...){
stop_ifnot_installed("ggplot2")
stop_ifnot(length(choices)==2,"`choices` must be of length 2")
stop_ifnot(is.logical(arrows),"`arrows` must be TRUE or FALSE")
stop_ifnot(is.logical(arrows_textangled),"`arrows_textangled` must be TRUE or FALSE")
stop_ifnot(is.logical(ellipse),"`ellipse` must be TRUE or FALSE")
stop_ifnot(is.logical(pc.biplot),"`pc.biplot` must be TRUE or FALSE")
stop_ifnot(is.logical(scale),"`scale` must be TRUE or FALSE")
stop_ifnot(is.numeric(arrows_alpha),"`arrows_alpha` must be numeric")
stop_ifnot(is.numeric(arrows_size),"`arrows_size` must be numeric")
stop_ifnot(is.numeric(arrows_textsize),"`arrows_textsize` must be numeric")
stop_ifnot(is.numeric(base_textsize),"`base_textsize` must be numeric")
stop_ifnot(is.numeric(choices),"`choices` must be numeric")
stop_ifnot(is.numeric(ellipse_alpha),"`ellipse_alpha` must be numeric")
stop_ifnot(is.numeric(ellipse_prob),"`ellipse_prob` must be numeric")
stop_ifnot(is.numeric(ellipse_size),"`ellipse_size` must be numeric")
stop_ifnot(is.numeric(labels_text_placement),"`labels_text_placement` must be numeric")
stop_ifnot(is.numeric(labels_textsize),"`labels_textsize` must be numeric")
#' @param search_string a text to search `x` for, will be checked with [as.ab()] if this value is not a column in `x`
#' @param verbose a logical to indicate whether additional info should be printed
#' @details You can look for an antibiotic (trade) name or abbreviation and it will search `x` and the [antibiotics] data set for any column containing a name or code of that antibiotic. **Longer columns names take precendence over shorter column names.**
#' @details You can look for an antibiotic (trade) name or abbreviation and it will search `x` and the [antibiotics] data set for any column containing a name or code of that antibiotic. **Longer columns names take precedence over shorter column names.**
#' @return A column name of `x`, or `NULL` when no result is found.
#' These function can be used to determine first isolates (see [first_isolate()]). Using key antibiotics to determine first isolates is more reliable than without key antibiotics. These selected isolates will then be called first *weighted* isolates.
#' @inheritSection lifecycle Stable lifecycle
#' @param x table with antibiotics coloms, like `AMX` or `amox`
#' @param y,z characters to compare
#' @param x a data.frame with antibiotics columns, like `AMX` or `amox`
#' @param y,z character vectors to compare
#' @inheritParams first_isolate
#' @param universal_1,universal_2,universal_3,universal_4,universal_5,universal_6 column names of **broad-spectrum** antibiotics, case-insensitive. At default, the columns containing these antibiotics will be guessed with [guess_ab_col()].
#' @param GramPos_1,GramPos_2,GramPos_3,GramPos_4,GramPos_5,GramPos_6 column names of antibiotics for **Gram-positives**, case-insensitive. At default, the columns containing these antibiotics will be guessed with [guess_ab_col()].
#' @param GramNeg_1,GramNeg_2,GramNeg_3,GramNeg_4,GramNeg_5,GramNeg_6 column names of antibiotics for **Gram-negatives**, case-insensitive. At default, the columns containing these antibiotics will be guessed with [guess_ab_col()].
#' @param warnings give warning about missing antibiotic columns, they will anyway be ignored
#' @param ... other parameters passed on to function
#' @param universal_1,universal_2,universal_3,universal_4,universal_5,universal_6 column names of **broad-spectrum** antibiotics, case-insensitive. See details for which antibiotics will be used at default (which are guessed with [guess_ab_col()]).
#' @param GramPos_1,GramPos_2,GramPos_3,GramPos_4,GramPos_5,GramPos_6 column names of antibiotics for **Gram-positives**, case-insensitive. See details for which antibiotics will be used at default (which are guessed with [guess_ab_col()]).
