add all options to documentation

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.8.2.9098
+Version: 1.8.2.9099
 Date: 2023-01-23
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 1.8.2.9098
+# AMR 1.8.2.9099
 
 *(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*
 

R/aa_options.R

@@ -0,0 +1,70 @@
+# ==================================================================== #
+# TITLE                                                                #
+# AMR: An R Package for Working with Antimicrobial Resistance Data     #
+#                                                                      #
+# SOURCE                                                               #
+# https://github.com/msberends/AMR                                     #
+#                                                                      #
+# CITE AS                                                              #
+# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C    #
+# (2022). AMR: An R Package for Working with Antimicrobial Resistance  #
+# Data. Journal of Statistical Software, 104(3), 1-31.                 #
+# doi:10.18637/jss.v104.i03                                            #
+#                                                                      #
+# Developed at the University of Groningen and the University Medical  #
+# Center Groningen in The Netherlands, in collaboration with many      #
+# colleagues from around the world, see our website.                   #
+#                                                                      #
+# This R package is free software; you can freely use and distribute   #
+# it for both personal and commercial purposes under the terms of the  #
+# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
+# the Free Software Foundation.                                        #
+# We created this package for both routine data analysis and academic  #
+# research and it was publicly released in the hope that it will be    #
+# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
+#                                                                      #
+# Visit our website for the full manual and a complete tutorial about  #
+# how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
+# ==================================================================== #
+
+#' Options for the AMR package
+#'
+#' This is an overview of all the package-specific [options()] you can set in the `AMR` package. 
+#' @section Options:
+#' * `AMR_custom_ab` \cr Allows to use custom antimicrobial drugs with this package. This is explained in [add_custom_antimicrobials()].
+#' * `AMR_custom_mo` \cr Allows to use custom microorganisms with this package. This is explained in [add_custom_microorganisms()].
+#' * `AMR_eucastrules` \cr Used for setting the default types of rules for [eucast_rules()] function, must be one or more of: `"breakpoints"`, `"expert"`, `"other"`, `"custom"`, `"all"`, and defaults to `c("breakpoints", "expert")`.
+#' * `AMR_guideline` \cr Used for setting the default guideline for interpreting MIC values and disk diffusion diameters with [as.sir()]. Can be only the guideline name (e.g., `"CLSI"`) or the name with a year (e.g. `"CLSI 2019"`). The default is \code{"`r clinical_breakpoints$guideline[1]`"}. Supported guideline are currently EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`).
+#' * `AMR_ignore_pattern` \cr A [regular expression][base::regex] to define input that must be ignored in [as.mo()] and all [`mo_*`][mo_property()] functions.
+#' * `AMR_include_PKPD` \cr A [logical] to use in [as.sir()], to indicate that PK/PD clinical breakpoints must be applied as a last resort, defaults to `TRUE`.
+#' * `AMR_keep_synonyms` \cr A [logical] to use in [as.mo()] and all [`mo_*`][mo_property()] functions, to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names.
+#' * `AMR_locale` \cr A language to use for the `AMR` package, can be one of these supported language names or ISO-639-1 codes: `r vector_or(paste0(sapply(LANGUAGES_SUPPORTED_NAMES, function(x) x[[1]]), " (" , LANGUAGES_SUPPORTED, ")"), quotes = FALSE, sort = FALSE)`.
+#' * `AMR_mo_source` \cr A file location for a manual code list to be used in [as.mo()] and all [`mo_*`][mo_property()] functions. This is explained in [set_mo_source()].
+#' 
+#' @section Saving Settings Between Sessions:
+#' Settings in \R are not saved globally and are thus lost when \R is exited. You can save your options to your own `.Rprofile` file, which is a user-specific file. You can edit it using:
+#' 
+#' ```r
+#'   utils::file.edit("~/.Rprofile")
+#' ```
+#' 
+#' In this file, you can set options such as `options(AMR_locale = "pt")` for Portuguese language support of antibiotics.
+#' 
+#' ### Share Options Within Team
+#' 
+#' For a more global approach, e.g. within a data team, save an options file to a remote file location, such as a shared network drive. This would work in this way:
+#' 
+#' 1. Save a plain text file to e.g. "X:/team_folder/R_options.R" and fill it with preferred settings.
+#' 
+#' 2. For each user, open the `.Rprofile` file using `utils::file.edit("~/.Rprofile")` and put in there:
+#' 
+#'    ```r
+#'      source("X:/team_folder/R_options.R")
+#'    ```
+#'    
+#' 3. Reload R/RStudio and check the settings with [getOption()], e.g. `getOption("AMR_locale")` if you have set that value.
+#' 
+#' Now the team settings are configured in only one place, and can be maintained there.
+#' @keywords internal
+#' @name AMR-options
+NULL

R/ab_property.R

@@ -33,7 +33,7 @@
 #' @param x any (vector of) text that can be coerced to a valid antibiotic drug code with [as.ab()]
 #' @param tolower a [logical] to indicate whether the first [character] of every output should be transformed to a lower case [character]. This will lead to e.g. "polymyxin B" and not "polymyxin b".
 #' @param property one of the column names of one of the [antibiotics] data set: `vector_or(colnames(antibiotics), sort = FALSE)`.
-#' @param language language of the returned text, defaults to system language (see [get_AMR_locale()]) and can also be set with `getOption("AMR_locale")`. Use `language = NULL` or `language = ""` to prevent translation.
+#' @param language language of the returned text, defaults to system language (see [get_AMR_locale()]) and can also be set with the option [`AMR_locale`][AMR-options]. Use `language = NULL` or `language = ""` to prevent translation.
 #' @param administration way of administration, either `"oral"` or `"iv"`
 #' @param open browse the URL using [utils::browseURL()]
 #' @param ... in case of [set_ab_names()] and `data` is a [data.frame]: columns to select (supports tidy selection such as `column1:column4`), otherwise other arguments passed on to [as.ab()]

R/av_property.R

@@ -33,7 +33,7 @@
 #' @param x any (vector of) text that can be coerced to a valid antiviral drug code with [as.av()]
 #' @param tolower a [logical] to indicate whether the first [character] of every output should be transformed to a lower case [character].
 #' @param property one of the column names of one of the [antivirals] data set: `vector_or(colnames(antivirals), sort = FALSE)`.
-#' @param language language of the returned text, defaults to system language (see [get_AMR_locale()]) and can also be set with `getOption("AMR_locale")`. Use `language = NULL` or `language = ""` to prevent translation.
+#' @param language language of the returned text, defaults to system language (see [get_AMR_locale()]) and can also be set with the option [`AMR_locale`][AMR-options]. Use `language = NULL` or `language = ""` to prevent translation.
 #' @param administration way of administration, either `"oral"` or `"iv"`
 #' @param open browse the URL using [utils::browseURL()]
 #' @param ... other arguments passed on to [as.av()]

R/custom_antimicrobials.R

@@ -35,20 +35,20 @@
 #'
 #' There are two ways to automate this process:
 #'
-#' **Method 1:** Save the antimicrobials to a local or remote file (can even be the internet). To use this method:
+#' **Method 1:** Using the option [`AMR_custom_ab`][AMR-options], which is the preferred method. To use this method:
 #'
 #'    1. Create a data set in the structure of the [antibiotics] data set (containing at the very least columns "ab" and "name") and save it with [saveRDS()] to a location of choice, e.g. `"~/my_custom_ab.rds"`, or any remote location.
 #'
-#'    2. Set the file location to the `AMR_custom_ab` \R option: `options(AMR_custom_ab = "~/my_custom_ab.rds")`. This can even be a remote file location, such as an https URL. Since options are not saved between \R sessions, it is best to save this option to the `.Rprofile` file so that it will loaded on start-up of \R. To do this, open the `.Rprofile` file using e.g. `utils::file.edit("~/.Rprofile")`, add this text and save the file:
+#'    2. Set the file location to the option [`AMR_custom_ab`][AMR-options]: `options(AMR_custom_ab = "~/my_custom_ab.rds")`. This can even be a remote file location, such as an https URL. Since options are not saved between \R sessions, it is best to save this option to the `.Rprofile` file so that it will be loaded on start-up of \R. To do this, open the `.Rprofile` file using e.g. `utils::file.edit("~/.Rprofile")`, add this text and save the file:
 #'
 #'       ```r
-#'       # Add custom antibiotic drug codes:
+#'       # Add custom antimicrobial codes:
 #'       options(AMR_custom_ab = "~/my_custom_ab.rds")
 #'       ```
 #'
 #'       Upon package load, this file will be loaded and run through the [add_custom_antimicrobials()] function.
 #'
-#' **Method 2:** Save the antimicrobial additions directly to your `.Rprofile` file. An important downside is that this requires to load the `AMR` package at every start-up. To use this method:
+#' **Method 2:** Loading the antimicrobial additions directly from your `.Rprofile` file. An important downside is that this requires the `AMR` package to be installed or else this method will fail. To use this method:
 #'
 #'    1. Edit the `.Rprofile` file using e.g. `utils::file.edit("~/.Rprofile")`.
 #'
@@ -56,8 +56,7 @@
 #'
 #'       ```r
 #'        # Add custom antibiotic drug codes:
-#'        library(AMR)
+#'        AMR::add_custom_antimicrobials(
-#'        add_custom_antimicrobials(
 #'          data.frame(ab = "TESTAB",
 #'                     name = "Test Antibiotic",
 #'                     group = "Test Group")

R/custom_microorganisms.R

@@ -41,7 +41,7 @@
 #'
 #'    1. Create a data set in the structure of the [microorganisms] data set (containing at the very least column "genus") and save it with [saveRDS()] to a location of choice, e.g. `"~/my_custom_mo.rds"`, or any remote location.
 #'
-#'    2. Set the file location to the `AMR_custom_mo` \R option: `options(AMR_custom_mo = "~/my_custom_mo.rds")`. This can even be a remote file location, such as an https URL. Since options are not saved between \R sessions, it is best to save this option to the `.Rprofile` file so that it will be loaded on start-up of \R. To do this, open the `.Rprofile` file using e.g. `utils::file.edit("~/.Rprofile")`, add this text and save the file:
+#'    2. Set the file location to the option [`AMR_custom_mo`][AMR-options]: `options(AMR_custom_mo = "~/my_custom_mo.rds")`. This can even be a remote file location, such as an https URL. Since options are not saved between \R sessions, it is best to save this option to the `.Rprofile` file so that it will be loaded on start-up of \R. To do this, open the `.Rprofile` file using e.g. `utils::file.edit("~/.Rprofile")`, add this text and save the file:
 #'
 #'       ```r
 #'       # Add custom microorganism codes:

R/eucast_rules.R

@@ -61,7 +61,7 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
 #' To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see *Details*.
 #' @param x a data set with antibiotic columns, such as `amox`, `AMX` and `AMC`
 #' @param info a [logical] to indicate whether progress should be printed to the console, defaults to only print while in interactive sessions
-#' @param rules a [character] vector that specifies which rules should be applied. Must be one or more of `"breakpoints"`, `"expert"`, `"other"`, `"custom"`, `"all"`, and defaults to `c("breakpoints", "expert")`. The default value can be set to another value, e.g. using `options(AMR_eucastrules = "all")`. If using `"custom"`, be sure to fill in argument `custom_rules` too. Custom rules can be created with [custom_eucast_rules()].
+#' @param rules a [character] vector that specifies which rules should be applied. Must be one or more of `"breakpoints"`, `"expert"`, `"other"`, `"custom"`, `"all"`, and defaults to `c("breakpoints", "expert")`. The default value can be set to another value using the option [`AMR_eucastrules`][AMR-options]: `options(AMR_eucastrules = "all")`. If using `"custom"`, be sure to fill in argument `custom_rules` too. Custom rules can be created with [custom_eucast_rules()].
 #' @param verbose a [logical] to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way. Using Verbose mode takes a lot more time.
 #' @param version_breakpoints the version number to use for the EUCAST Clinical Breakpoints guideline. Can be either `r vector_or(names(EUCAST_VERSION_BREAKPOINTS), reverse = TRUE)`.
 #' @param version_expertrules the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either `r vector_or(names(EUCAST_VERSION_EXPERT_RULES), reverse = TRUE)`.
@@ -98,7 +98,7 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
 #'
 #' Important examples include amoxicillin and amoxicillin/clavulanic acid, and trimethoprim and trimethoprim/sulfamethoxazole. Needless to say, for these rules to work, both drugs must be available in the data set.
 #'
-#' Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include `"other"` to the `rules` argument, or use `eucast_rules(..., rules = "all")`. You can also set the option `AMR_eucastrules`, i.e. run `options(AMR_eucastrules = "all")`.
+#' Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include `"other"` to the `rules` argument, or use `eucast_rules(..., rules = "all")`. You can also set the option [`AMR_eucastrules`][AMR-options], i.e. run `options(AMR_eucastrules = "all")`.
 #' @section Antibiotics:
 #' To define antibiotics column names, leave as it is to determine it automatically with [guess_ab_col()] or input a text (case-insensitive), or use `NULL` to skip a column (e.g. `TIC = NULL` to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.
 #'

R/mo.R

@@ -38,9 +38,9 @@
 #'
 #' This excludes enterococci at default (who are in group D), use `Lancefield = "all"` to also categorise all enterococci as group D.
 #' @param minimum_matching_score a numeric value to set as the lower limit for the [MO matching score][mo_matching_score()]. When left blank, this will be determined automatically based on the character length of `x`, its [taxonomic kingdom][microorganisms] and [human pathogenicity][mo_matching_score()].
-#' @param keep_synonyms a [logical] to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is `FALSE`, which will return a note if old taxonomic names were processed. The default can be set with `options(AMR_keep_synonyms = TRUE)` or `options(AMR_keep_synonyms = FALSE)`.
+#' @param keep_synonyms a [logical] to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is `FALSE`, which will return a note if old taxonomic names were processed. The default can be set with the option [`AMR_keep_synonyms`][AMR-options], i.e. `options(AMR_keep_synonyms = TRUE)` or `options(AMR_keep_synonyms = FALSE)`.
 #' @param reference_df a [data.frame] to be used for extra reference when translating `x` to a valid [`mo`]. See [set_mo_source()] and [get_mo_source()] to automate the usage of your own codes (e.g. used in your analysis or organisation).
-#' @param ignore_pattern a [regular expression][base::regex] (case-insensitive) of which all matches in `x` must return `NA`. This can be convenient to exclude known non-relevant input and can also be set with the option `AMR_ignore_pattern`, e.g. `options(AMR_ignore_pattern = "(not reported|contaminated flora)")`.
+#' @param ignore_pattern a [regular expression][base::regex] (case-insensitive) of which all matches in `x` must return `NA`. This can be convenient to exclude known non-relevant input and can also be set with the option [`AMR_ignore_pattern`][AMR-options], e.g. `options(AMR_ignore_pattern = "(not reported|contaminated flora)")`.
 #' @param remove_from_input a [regular expression][base::regex] (case-insensitive) to clean the input of `x`. Everything matched in `x` will be removed. At default, this is the outcome of [mo_cleaning_regex()], which removes texts between brackets and texts such as "species" and "serovar".
 #' @param language language to translate text like "no growth", which defaults to the system language (see [get_AMR_locale()])
 #' @param info a [logical] to indicate if a progress bar should be printed if more than 25 items are to be coerced, defaults to `TRUE` only in interactive mode

R/mo_source.R

@@ -39,7 +39,7 @@
 #' @aliases set_mo_source get_mo_source
 #' @details The reference file can be a text file separated with commas (CSV) or tabs or pipes, an Excel file (either 'xls' or 'xlsx' format) or an \R object file (extension '.rds'). To use an Excel file, you will need to have the `readxl` package installed.
 #'
-#' [set_mo_source()] will check the file for validity: it must be a [data.frame], must have a column named `"mo"` which contains values from [`microorganisms$mo`][microorganisms] or [`microorganisms$fullname`][microorganisms] and must have a reference column with your own defined values. If all tests pass, [set_mo_source()] will read the file into \R and will ask to export it to `"~/mo_source.rds"`. The CRAN policy disallows packages to write to the file system, although '*exceptions may be allowed in interactive sessions if the package obtains confirmation from the user*'. For this reason, this function only works in interactive sessions so that the user can **specifically confirm and allow** that this file will be created. The destination of this file can be set with the `destination` argument and defaults to the user's home directory. It can also be set as an \R option, using `options(AMR_mo_source = "my/location/file.rds")`.
+#' [set_mo_source()] will check the file for validity: it must be a [data.frame], must have a column named `"mo"` which contains values from [`microorganisms$mo`][microorganisms] or [`microorganisms$fullname`][microorganisms] and must have a reference column with your own defined values. If all tests pass, [set_mo_source()] will read the file into \R and will ask to export it to `"~/mo_source.rds"`. The CRAN policy disallows packages to write to the file system, although '*exceptions may be allowed in interactive sessions if the package obtains confirmation from the user*'. For this reason, this function only works in interactive sessions so that the user can **specifically confirm and allow** that this file will be created. The destination of this file can be set with the `destination` argument and defaults to the user's home directory. It can also be set with the option [`AMR_mo_source`][AMR-options], e.g. `options(AMR_mo_source = "my/location/file.rds")`.
 #'
 #' The created compressed data file `"mo_source.rds"` will be used at default for MO determination (function [as.mo()] and consequently all `mo_*` functions like [mo_genus()] and [mo_gramstain()]). The location and timestamp of the original file will be saved as an [attribute][base::attributes()] to the compressed data file.
 #'

R/options.R

@@ -1,39 +0,0 @@
-# ==================================================================== #
-# TITLE                                                                #
-# AMR: An R Package for Working with Antimicrobial Resistance Data     #
-#                                                                      #
-# SOURCE                                                               #
-# https://github.com/msberends/AMR                                     #
-#                                                                      #
-# CITE AS                                                              #
-# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C    #
-# (2022). AMR: An R Package for Working with Antimicrobial Resistance  #
-# Data. Journal of Statistical Software, 104(3), 1-31.                 #
-# doi:10.18637/jss.v104.i03                                            #
-#                                                                      #
-# Developed at the University of Groningen and the University Medical  #
-# Center Groningen in The Netherlands, in collaboration with many      #
-# colleagues from around the world, see our website.                   #
-#                                                                      #
-# This R package is free software; you can freely use and distribute   #
-# it for both personal and commercial purposes under the terms of the  #
-# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
-# the Free Software Foundation.                                        #
-# We created this package for both routine data analysis and academic  #
-# research and it was publicly released in the hope that it will be    #
-# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
-#                                                                      #
-# Visit our website for the full manual and a complete tutorial about  #
-# how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
-# ==================================================================== #
-
-#' Options for the AMR package
-#'
-#' This is an overview of the package-specific [options()] you can set in the `AMR` package.
-#' @section Options:
-#' * `AMR_custom_ab`: allows to use custom antimicrobial drugs with this package. This is explained in [add_custom_antimicrobials()].
-#' * `AMR_custom_mo`: allows to use custom microorganisms with this package. This is explained in [add_custom_microorganisms()].
-#' @keywords internal
-#' @name AMR-options
-# @export
-NULL

R/plot.R

@@ -38,7 +38,7 @@
 #' @param main,title title of the plot
 #' @param xlab,ylab axis title
 #' @param colours_SIR colours to use for filling in the bars, must be a vector of three values (in the order S, I and R). The default colours are colour-blind friendly.
-#' @param language language to be used to translate 'Susceptible', 'Increased exposure'/'Intermediate' and 'Resistant', defaults to system language (see [get_AMR_locale()]) and can be overwritten by setting the option `AMR_locale`, e.g. `options(AMR_locale = "de")`, see [translate]. Use `language = NULL` or `language = ""` to prevent translation.
+#' @param language language to be used to translate 'Susceptible', 'Increased exposure'/'Intermediate' and 'Resistant', defaults to system language (see [get_AMR_locale()]) and can be overwritten by setting the option [`AMR_locale`][AMR-options], e.g. `options(AMR_locale = "de")`, see [translate]. Use `language = NULL` or `language = ""` to prevent translation.
 #' @param expand a [logical] to indicate whether the range on the x axis should be expanded between the lowest and highest value. For MIC values, intermediate values will be factors of 2 starting from the highest MIC value. For disk diameters, the whole diameter range will be filled.
 #' @details
 #' The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.

R/sir.R

@@ -39,6 +39,7 @@
 #' @param guideline defaults to EUCAST `r  max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))` (the latest implemented EUCAST guideline in the [clinical_breakpoints] data set), but can be set with the [option][options()] `AMR_guideline`. Supports EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`), see *Details*.
 #' @param conserve_capped_values a [logical] to indicate that MIC values starting with `">"` (but not `">="`) must always return "R" , and that MIC values starting with `"<"` (but not `"<="`) must always return "S"
 #' @param add_intrinsic_resistance *(only useful when using a EUCAST guideline)* a [logical] to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in *Klebsiella* species. Determination is based on the [intrinsic_resistant] data set, that itself is based on `r format_eucast_version_nr(3.3)`.
+#' @param include_PKPD a [logical] to indicate that PK/PD clinical breakpoints must be applied as a last resort, defaults to `TRUE`. Can also be set with the option [`AMR_include_PKPD`][AMR-options].
 #' @param reference_data a [data.frame] to be used for interpretation, which defaults to the [clinical_breakpoints] data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the [clinical_breakpoints] data set (same column names and column types). Please note that the `guideline` argument will be ignored when `reference_data` is manually set.
 #' @param threshold maximum fraction of invalid antimicrobial interpretations of `x`, see *Examples*
 #' @param ... for using on a [data.frame]: names of columns to apply [as.sir()] on (supports tidy selection such as `column1:column4`). Otherwise: arguments passed on to methods.
@@ -72,7 +73,7 @@
 #'
 #' Thus, the `guideline` argument must be set to e.g., ``r paste0('"', subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline[1], '"')`` or ``r paste0('"', subset(clinical_breakpoints, guideline %like% "CLSI")$guideline[1], '"')``. By simply using `"EUCAST"` (the default) or `"CLSI"` as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the `reference_data` argument. The `guideline` argument will then be ignored.
 #'
-#' You can set the default guideline with the `AMR_guideline` [option][options()] (e.g. in your `.Rprofile` file), such as:
+#' You can set the default guideline with the option [`AMR_guideline`][AMR-options] (e.g. in your `.Rprofile` file), such as:
 #'
 #' ```
 #'   options(AMR_guideline = "CLSI")
@@ -417,6 +418,7 @@ as.sir.mic <- function(x,
                        conserve_capped_values = FALSE,
                        add_intrinsic_resistance = FALSE,
                        reference_data = AMR::clinical_breakpoints,
+                       include_PKPD = getOption("AMR_include_PKPD", TRUE),
                        ...) {
   as_sir_method(
     method_short = "mic",
@@ -429,6 +431,7 @@ as.sir.mic <- function(x,
     conserve_capped_values = conserve_capped_values,
     add_intrinsic_resistance = add_intrinsic_resistance,
     reference_data = reference_data,
+    include_PKPD = include_PKPD,
     ...
   )
 }
@@ -442,6 +445,7 @@ as.sir.disk <- function(x,
                         uti = NULL,
                         add_intrinsic_resistance = FALSE,
                         reference_data = AMR::clinical_breakpoints,
+                        include_PKPD = getOption("AMR_include_PKPD", TRUE),
                         ...) {
   as_sir_method(
     method_short = "disk",
@@ -454,6 +458,7 @@ as.sir.disk <- function(x,
     conserve_capped_values = FALSE,
     add_intrinsic_resistance = add_intrinsic_resistance,
     reference_data = reference_data,
+    include_PKPD = include_PKPD,
     ...
   )
 }
@@ -467,7 +472,8 @@ as.sir.data.frame <- function(x,
                               uti = NULL,
                               conserve_capped_values = FALSE,
                               add_intrinsic_resistance = FALSE,
-                              reference_data = AMR::clinical_breakpoints) {
+                              reference_data = AMR::clinical_breakpoints,
+                              include_PKPD = getOption("AMR_include_PKPD", TRUE)) {
   meet_criteria(x, allow_class = "data.frame") # will also check for dimensions > 0
   meet_criteria(col_mo, allow_class = "character", is_in = colnames(x), allow_NULL = TRUE)
   meet_criteria(guideline, allow_class = "character", has_length = 1)
@@ -604,6 +610,7 @@ as.sir.data.frame <- function(x,
           conserve_capped_values = conserve_capped_values,
           add_intrinsic_resistance = add_intrinsic_resistance,
           reference_data = reference_data,
+          include_PKPD = include_PKPD,
           is_data.frame = TRUE
         )
     } else if (types[i] == "disk") {
@@ -619,6 +626,7 @@ as.sir.data.frame <- function(x,
           uti = uti,
           add_intrinsic_resistance = add_intrinsic_resistance,
           reference_data = reference_data,
+          include_PKPD = include_PKPD,
           is_data.frame = TRUE
         )
     } else if (types[i] == "sir") {
@@ -686,6 +694,7 @@ as_sir_method <- function(method_short,
                           conserve_capped_values,
                           add_intrinsic_resistance,
                           reference_data,
+                          include_PKPD,
                           ...) {
   meet_criteria(x, allow_NA = TRUE, .call_depth = -2)
   meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE, .call_depth = -2)
@@ -695,6 +704,7 @@ as_sir_method <- function(method_short,
   meet_criteria(conserve_capped_values, allow_class = "logical", has_length = 1, .call_depth = -2)
   meet_criteria(add_intrinsic_resistance, allow_class = "logical", has_length = 1, .call_depth = -2)
   meet_criteria(reference_data, allow_class = "data.frame", .call_depth = -2)
+  meet_criteria(include_PKPD, allow_class = "logical", has_length = 1, .call_depth = -2)
   check_reference_data(reference_data)
 
   # for dplyr's across()
@@ -850,6 +860,12 @@ as_sir_method <- function(method_short,
       subset(method == method_coerced & ab == ab_coerced)
   }
 
+  if (isFALSE(include_PKPD)) {
+    # remove PKPD rules from the breakpoints table
+    breakpoints <- breakpoints %pm>%
+      subset(mo != "UNKNOWN" & ref_tbl %unlike% "PK.*PD")
+  }
+
   msgs <- character(0)
   if (nrow(breakpoints) == 0) {
     # apparently no breakpoints found
@@ -910,7 +926,7 @@ as_sir_method <- function(method_short,
         mo_current_other
       ))
 
-    if (any(df[rows, "uti", drop = TRUE], na.rm = TRUE)) {
+    if (any(uti, na.rm = TRUE)) {
       breakpoints_current <- breakpoints_current %pm>%
         # be as specific as possible (i.e. prefer species over genus):
         # the below `pm_desc(uti)` will put `TRUE` on top and FALSE on bottom
@@ -946,10 +962,17 @@ as_sir_method <- function(method_short,
     if (isTRUE(add_intrinsic_resistance) && guideline_coerced %like% "EUCAST" && paste(mo_unique, ab_coerced) %in% AMR_env$intrinsic_resistant) {
       msgs <- c(msgs, paste0("Intrinsic resistance applied for ", ab_formatted, " in ", mo_formatted, ""))
       new_sir <- rep(as.sir("R"), length(rows))
+    } else if (nrow(breakpoints_current) == 0) {
+      # no rules available
+      new_sir <- rep(NA_sir_, length(rows))
     } else {
       # then run the rules
       breakpoints_current <- breakpoints_current[1L, , drop = FALSE]
 
+      if (breakpoints_current$mo == "UNKNOWN" | breakpoints_current$ref_tbl %like% "PK.*PD") {
+        msgs <- c(msgs, "(Some) PK/PD breakpoints were applied - use `include_PKPD = FALSE` to prevent this")
+      }
+
       if (method == "mic") {
         new_sir <- quick_case_when(
           is.na(values) ~ NA_sir_,
@@ -1166,6 +1189,9 @@ summary.sir <- function(object, ...) {
   I <- sum(x == "I", na.rm = TRUE)
   R <- sum(x == "R", na.rm = TRUE)
   pad <- function(x) {
+    if (is.na(x)) {
+      return("??")
+    }
     if (x == "0%") {
       x <- " 0.0%"
     }

R/translate.R

@@ -29,12 +29,12 @@
 
 #' Translate Strings from the AMR Package
 #'
-#' For language-dependent output of AMR functions, like [mo_name()], [mo_gramstain()], [mo_type()] and [ab_name()].
+#' For language-dependent output of `AMR` functions, such as [mo_name()], [mo_gramstain()], [mo_type()] and [ab_name()].
 #' @param x text to translate
 #' @param language language to choose. Use one of these supported language names or ISO-639-1 codes: `r vector_or(paste0(sapply(LANGUAGES_SUPPORTED_NAMES, function(x) x[[1]]), " (" , LANGUAGES_SUPPORTED, ")"), quotes = FALSE, sort = FALSE)`.
 #' @details The currently `r length(LANGUAGES_SUPPORTED)` supported languages are `r vector_and(paste0(sapply(LANGUAGES_SUPPORTED_NAMES, function(x) x[[1]]), " (" , LANGUAGES_SUPPORTED, ")"), quotes = FALSE, sort = FALSE)`. All these languages have translations available for all antimicrobial drugs and colloquial microorganism names.
 #'
-#' To permanently silence the once-per-session language note on a non-English operating system, you can set the option `AMR_locale` in your `.Rprofile` file like this:
+#' To permanently silence the once-per-session language note on a non-English operating system, you can set the option [`AMR_locale`][AMR-options] in your `.Rprofile` file like this:
 #'
 #' ```r
 #' # Open .Rprofile file
@@ -51,12 +51,12 @@
 #' ### Changing the Default Language
 #' The system language will be used at default (as returned by `Sys.getenv("LANG")` or, if `LANG` is not set, [`Sys.getlocale("LC_COLLATE")`][Sys.getlocale()]), if that language is supported. But the language to be used can be overwritten in two ways and will be checked in this order:
 #'
-#'   1. Setting the R option `AMR_locale`, either by using e.g. `set_AMR_locale("German")` or by running e.g. `options(AMR_locale = "German")`.
+#'   1. Setting the option [`AMR_locale`][AMR-options], either by using e.g. `set_AMR_locale("German")` or by running e.g. `options(AMR_locale = "German")`.
 #'
 #'      Note that setting an \R option only works in the same session. Save the command `options(AMR_locale = "(your language)")` to your `.Rprofile` file to apply it for every session. Run `utils::file.edit("~/.Rprofile")` to edit your `.Rprofile` file.
 #'   2. Setting the system variable `LANGUAGE` or `LANG`, e.g. by adding `LANGUAGE="de_DE.utf8"` to your `.Renviron` file in your home directory.
 #'
-#' Thus, if the R option `AMR_locale` is set, the system variables `LANGUAGE` and `LANG` will be ignored.
+#' Thus, if the option [`AMR_locale`][AMR-options] is set, the system variables `LANGUAGE` and `LANG` will be ignored.
 #' @rdname translate
 #' @name translate
 #' @export

_pkgdown.yml

@@ -72,37 +72,40 @@ navbar:
     - text: "How to"
       icon: "fa-question-circle"
       menu:
-      - text: "Conduct AMR analysis"
+      - text: "User- Or Team-specific Package Settings"
+        icon: "fa-gear"
+        href: "reference/AMR-options.html"
+      - text: "Conduct AMR Analysis"
         icon: "fa-directions"
         href: "articles/AMR.html"
-      - text: "Predict antimicrobial resistance"
+      - text: "Predict Antimicrobial Resistance"
         icon: "fa-dice"
         href: "articles/resistance_predict.html"
-      - text: "Data sets for download / own use"
+      - text: "Data Sets for Download / Own Use"
         icon: "fa-database"
         href: "articles/datasets.html"
-      - text: "Conduct principal component analysis for AMR"
+      - text: "Conduct Principal Component Analysis for AMR"
         icon: "fa-compress"
         href: "articles/PCA.html"
-      - text: "Determine multi-drug resistance (MDR)"
+      - text: "Determine Multi-Drug Resistance (MDR)"
         icon: "fa-skull-crossbones"
         href: "articles/MDR.html"
-      - text: "Work with WHONET data"
+      - text: "Work with WHONET Data"
         icon: "fa-globe-americas"
         href: "articles/WHONET.html"
-      - text: "Import data from SPSS/SAS/Stata"
+      - text: "Import Data From SPSS/SAS/Stata"
         icon: "fa-file-upload"
         href: "articles/SPSS.html"
-      - text: "Apply EUCAST rules"
+      - text: "Apply Eucast Rules"
         icon: "fa-exchange-alt"
         href: "articles/EUCAST.html"
-      - text: "Get taxonomy of a microorganism"
+      - text: "Get Taxonomy of a Microorganism"
         icon: "fa-bug"
         href: "reference/mo_property.html" # reference instead of an article
-      - text: "Get properties of an antibiotic drug"
+      - text: "Get Properties of an Antibiotic Drug"
         icon: "fa-capsules"
         href: "reference/ab_property.html" # reference instead of an article
-      - text: "Get properties of an antiviral drug"
+      - text: "Get Properties of an Antiviral Drug"
         icon: "fa-capsules"
         href: "reference/av_property.html" # reference instead of an article
     - text: "Manual"
@@ -176,6 +179,15 @@ reference:
     - "`resistance_predict`"
     - "`guess_ab_col`"
     
+  - title: "Other: AMR-specific options"
+    desc: >
+      The AMR package is customisable, by providing settings that can be set per user or per team. For
+      example, the default interpretation guideline can be changed from EUCAST to CLSI, or a supported
+      language can be set for the whole team (system-language independent) for antibiotic names in a
+      foreign language.
+    contents:
+    - "`AMR-options`"
+    
   - title: "Other: antiviral drugs"
     desc: >
       This package also provides extensive support for antiviral agents, even though it is not the primary

man/AMR-options.Rd

@@ -1,16 +1,47 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/options.R
+% Please edit documentation in R/aa_options.R
 \name{AMR-options}
 \alias{AMR-options}
 \title{Options for the AMR package}
 \description{
-This is an overview of the package-specific \code{\link[=options]{options()}} you can set in the \code{AMR} package.
+This is an overview of all the package-specific \code{\link[=options]{options()}} you can set in the \code{AMR} package.
 }
 \section{Options}{
 
 \itemize{
-\item \code{AMR_custom_ab}: allows to use custom antimicrobial drugs with this package. This is explained in \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}}.
+\item \code{AMR_custom_ab} \cr Allows to use custom antimicrobial drugs with this package. This is explained in \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}}.
-\item \code{AMR_custom_mo}: allows to use custom microorganisms with this package. This is explained in \code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}}.
+\item \code{AMR_custom_mo} \cr Allows to use custom microorganisms with this package. This is explained in \code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}}.
+\item \code{AMR_eucastrules} \cr Used for setting the default types of rules for \code{\link[=eucast_rules]{eucast_rules()}} function, must be one or more of: \code{"breakpoints"}, \code{"expert"}, \code{"other"}, \code{"custom"}, \code{"all"}, and defaults to \code{c("breakpoints", "expert")}.
+\item \code{AMR_guideline} \cr Used for setting the default guideline for interpreting MIC values and disk diffusion diameters with \code{\link[=as.sir]{as.sir()}}. Can be only the guideline name (e.g., \code{"CLSI"}) or the name with a year (e.g. \code{"CLSI 2019"}). The default is \code{"EUCAST 2022"}. Supported guideline are currently EUCAST (2013-2022) and CLSI (2013-2022).
+\item \code{AMR_ignore_pattern} \cr A \link[base:regex]{regular expression} to define input that must be ignored in \code{\link[=as.mo]{as.mo()}} and all \code{\link[=mo_property]{mo_*}} functions.
+\item \code{AMR_include_PKPD} \cr A \link{logical} to use in \code{\link[=as.sir]{as.sir()}}, to indicate that PK/PD clinical breakpoints must be applied as a last resort, defaults to \code{TRUE}.
+\item \code{AMR_keep_synonyms} \cr A \link{logical} to use in \code{\link[=as.mo]{as.mo()}} and all \code{\link[=mo_property]{mo_*}} functions, to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names.
+\item \code{AMR_locale} \cr A language to use for the \code{AMR} package, can be one of these supported language names or ISO-639-1 codes: English (en), Chinese (zh), Danish (da), Dutch (nl), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Polish (pl), Portuguese (pt), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr) or Ukrainian (uk).
+\item \code{AMR_mo_source} \cr A file location for a manual code list to be used in \code{\link[=as.mo]{as.mo()}} and all \code{\link[=mo_property]{mo_*}} functions. This is explained in \code{\link[=set_mo_source]{set_mo_source()}}.
+}
+}
+
+\section{Saving Settings Between Sessions}{
+
+Settings in \R are not saved globally and are thus lost when \R is exited. You can save your options to your own \code{.Rprofile} file, which is a user-specific file. You can edit it using:
+
+\if{html}{\out{<div class="sourceCode r">}}\preformatted{  utils::file.edit("~/.Rprofile")
+}\if{html}{\out{</div>}}
+
+In this file, you can set options such as \code{options(AMR_locale = "pt")} for Portuguese language support of antibiotics.
+\subsection{Share Options Within Team}{
+
+For a more global approach, e.g. within a data team, save an options file to a remote file location, such as a shared network drive. This would work in this way:
+\enumerate{
+\item Save a plain text file to e.g. "X:/team_folder/R_options.R" and fill it with preferred settings.
+\item For each user, open the \code{.Rprofile} file using \code{utils::file.edit("~/.Rprofile")} and put in there:
+
+\if{html}{\out{<div class="sourceCode r">}}\preformatted{  source("X:/team_folder/R_options.R")
+}\if{html}{\out{</div>}}
+\item Reload R/RStudio and check the settings with \code{\link[=getOption]{getOption()}}, e.g. \code{getOption("AMR_locale")} if you have set that value.
+}
+
+Now the team settings are configured in only one place, and can be maintained there.
 }
 }
 

man/ab_property.Rd

@@ -58,7 +58,7 @@ set_ab_names(
 \arguments{
 \item{x}{any (vector of) text that can be coerced to a valid antibiotic drug code with \code{\link[=as.ab]{as.ab()}}}
 
-\item{language}{language of the returned text, defaults to system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with \code{getOption("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
+\item{language}{language of the returned text, defaults to system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the option \code{\link[=AMR-options]{AMR_locale}}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
 
 \item{tolower}{a \link{logical} to indicate whether the first \link{character} of every output should be transformed to a lower case \link{character}. This will lead to e.g. "polymyxin B" and not "polymyxin b".}
 

man/add_custom_antimicrobials.Rd

@@ -20,26 +20,25 @@ With \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} you c
 
 There are two ways to automate this process:
 
-\strong{Method 1:} Save the antimicrobials to a local or remote file (can even be the internet). To use this method:
+\strong{Method 1:} Using the option \code{\link[=AMR-options]{AMR_custom_ab}}, which is the preferred method. To use this method:
 \enumerate{
 \item Create a data set in the structure of the \link{antibiotics} data set (containing at the very least columns "ab" and "name") and save it with \code{\link[=saveRDS]{saveRDS()}} to a location of choice, e.g. \code{"~/my_custom_ab.rds"}, or any remote location.
-\item Set the file location to the \code{AMR_custom_ab} \R option: \code{options(AMR_custom_ab = "~/my_custom_ab.rds")}. This can even be a remote file location, such as an https URL. Since options are not saved between \R sessions, it is best to save this option to the \code{.Rprofile} file so that it will loaded on start-up of \R. To do this, open the \code{.Rprofile} file using e.g. \code{utils::file.edit("~/.Rprofile")}, add this text and save the file:
+\item Set the file location to the option \code{\link[=AMR-options]{AMR_custom_ab}}: \code{options(AMR_custom_ab = "~/my_custom_ab.rds")}. This can even be a remote file location, such as an https URL. Since options are not saved between \R sessions, it is best to save this option to the \code{.Rprofile} file so that it will be loaded on start-up of \R. To do this, open the \code{.Rprofile} file using e.g. \code{utils::file.edit("~/.Rprofile")}, add this text and save the file:
 
-\if{html}{\out{<div class="sourceCode r">}}\preformatted{# Add custom antibiotic drug codes:
+\if{html}{\out{<div class="sourceCode r">}}\preformatted{# Add custom antimicrobial codes:
 options(AMR_custom_ab = "~/my_custom_ab.rds")
 }\if{html}{\out{</div>}}
 
 Upon package load, this file will be loaded and run through the \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} function.
 }
 
-\strong{Method 2:} Save the antimicrobial additions directly to your \code{.Rprofile} file. An important downside is that this requires to load the \code{AMR} package at every start-up. To use this method:
+\strong{Method 2:} Loading the antimicrobial additions directly from your \code{.Rprofile} file. An important downside is that this requires the \code{AMR} package to be installed or else this method will fail. To use this method:
 \enumerate{
 \item Edit the \code{.Rprofile} file using e.g. \code{utils::file.edit("~/.Rprofile")}.
 \item Add a text like below and save the file:
 
 \if{html}{\out{<div class="sourceCode r">}}\preformatted{ # Add custom antibiotic drug codes:
- library(AMR)
+ AMR::add_custom_antimicrobials(
- add_custom_antimicrobials(
    data.frame(ab = "TESTAB",
               name = "Test Antibiotic",
               group = "Test Group")

man/add_custom_microorganisms.Rd

@@ -25,7 +25,7 @@ There are two ways to automate this process:
 \strong{Method 1:} Using the option \code{\link[=AMR-options]{AMR_custom_mo}}, which is the preferred method. To use this method:
 \enumerate{
 \item Create a data set in the structure of the \link{microorganisms} data set (containing at the very least column "genus") and save it with \code{\link[=saveRDS]{saveRDS()}} to a location of choice, e.g. \code{"~/my_custom_mo.rds"}, or any remote location.
-\item Set the file location to the \code{AMR_custom_mo} \R option: \code{options(AMR_custom_mo = "~/my_custom_mo.rds")}. This can even be a remote file location, such as an https URL. Since options are not saved between \R sessions, it is best to save this option to the \code{.Rprofile} file so that it will be loaded on start-up of \R. To do this, open the \code{.Rprofile} file using e.g. \code{utils::file.edit("~/.Rprofile")}, add this text and save the file:
+\item Set the file location to the option \code{\link[=AMR-options]{AMR_custom_mo}}: \code{options(AMR_custom_mo = "~/my_custom_mo.rds")}. This can even be a remote file location, such as an https URL. Since options are not saved between \R sessions, it is best to save this option to the \code{.Rprofile} file so that it will be loaded on start-up of \R. To do this, open the \code{.Rprofile} file using e.g. \code{utils::file.edit("~/.Rprofile")}, add this text and save the file:
 
 \if{html}{\out{<div class="sourceCode r">}}\preformatted{# Add custom microorganism codes:
 options(AMR_custom_mo = "~/my_custom_mo.rds")

man/as.mo.Rd

@@ -50,11 +50,11 @@ This excludes enterococci at default (who are in group D), use \code{Lancefield
 
 \item{minimum_matching_score}{a numeric value to set as the lower limit for the \link[=mo_matching_score]{MO matching score}. When left blank, this will be determined automatically based on the character length of \code{x}, its \link[=microorganisms]{taxonomic kingdom} and \link[=mo_matching_score]{human pathogenicity}.}
 
-\item{keep_synonyms}{a \link{logical} to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is \code{FALSE}, which will return a note if old taxonomic names were processed. The default can be set with \code{options(AMR_keep_synonyms = TRUE)} or \code{options(AMR_keep_synonyms = FALSE)}.}
+\item{keep_synonyms}{a \link{logical} to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is \code{FALSE}, which will return a note if old taxonomic names were processed. The default can be set with the option \code{\link[=AMR-options]{AMR_keep_synonyms}}, i.e. \code{options(AMR_keep_synonyms = TRUE)} or \code{options(AMR_keep_synonyms = FALSE)}.}
 
 \item{reference_df}{a \link{data.frame} to be used for extra reference when translating \code{x} to a valid \code{\link{mo}}. See \code{\link[=set_mo_source]{set_mo_source()}} and \code{\link[=get_mo_source]{get_mo_source()}} to automate the usage of your own codes (e.g. used in your analysis or organisation).}
 
-\item{ignore_pattern}{a \link[base:regex]{regular expression} (case-insensitive) of which all matches in \code{x} must return \code{NA}. This can be convenient to exclude known non-relevant input and can also be set with the option \code{AMR_ignore_pattern}, e.g. \code{options(AMR_ignore_pattern = "(not reported|contaminated flora)")}.}
+\item{ignore_pattern}{a \link[base:regex]{regular expression} (case-insensitive) of which all matches in \code{x} must return \code{NA}. This can be convenient to exclude known non-relevant input and can also be set with the option \code{\link[=AMR-options]{AMR_ignore_pattern}}, e.g. \code{options(AMR_ignore_pattern = "(not reported|contaminated flora)")}.}
 
 \item{remove_from_input}{a \link[base:regex]{regular expression} (case-insensitive) to clean the input of \code{x}. Everything matched in \code{x} will be removed. At default, this is the outcome of \code{\link[=mo_cleaning_regex]{mo_cleaning_regex()}}, which removes texts between brackets and texts such as "species" and "serovar".}
 

man/as.sir.Rd

@@ -41,6 +41,7 @@ is_sir_eligible(x, threshold = 0.05)
   conserve_capped_values = FALSE,
   add_intrinsic_resistance = FALSE,
   reference_data = AMR::clinical_breakpoints,
+  include_PKPD = getOption("AMR_include_PKPD", TRUE),
   ...
 )
 
@@ -52,6 +53,7 @@ is_sir_eligible(x, threshold = 0.05)
   uti = NULL,
   add_intrinsic_resistance = FALSE,
   reference_data = AMR::clinical_breakpoints,
+  include_PKPD = getOption("AMR_include_PKPD", TRUE),
   ...
 )
 
@@ -63,7 +65,8 @@ is_sir_eligible(x, threshold = 0.05)
   uti = NULL,
   conserve_capped_values = FALSE,
   add_intrinsic_resistance = FALSE,
-  reference_data = AMR::clinical_breakpoints
+  reference_data = AMR::clinical_breakpoints,
+  include_PKPD = getOption("AMR_include_PKPD", TRUE)
 )
 
 sir_interpretation_history(clean = FALSE)
@@ -89,6 +92,8 @@ sir_interpretation_history(clean = FALSE)
 
 \item{reference_data}{a \link{data.frame} to be used for interpretation, which defaults to the \link{clinical_breakpoints} data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the \link{clinical_breakpoints} data set (same column names and column types). Please note that the \code{guideline} argument will be ignored when \code{reference_data} is manually set.}
 
+\item{include_PKPD}{a \link{logical} to indicate that PK/PD clinical breakpoints must be applied as a last resort, defaults to \code{TRUE}. Can also be set with the option \code{\link[=AMR-options]{AMR_include_PKPD}}.}
+
 \item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
 
 \item{clean}{a \link{logical} to indicate whether previously stored results should be forgotten after returning the 'logbook' with results}
@@ -134,7 +139,7 @@ For interpreting MIC values as well as disk diffusion diameters, currently imple
 
 Thus, the \code{guideline} argument must be set to e.g., \code{"EUCAST 2022"} or \code{"CLSI 2022"}. By simply using \code{"EUCAST"} (the default) or \code{"CLSI"} as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the \code{reference_data} argument. The \code{guideline} argument will then be ignored.
 
-You can set the default guideline with the \code{AMR_guideline} \link[=options]{option} (e.g. in your \code{.Rprofile} file), such as:
+You can set the default guideline with the option \code{\link[=AMR-options]{AMR_guideline}} (e.g. in your \code{.Rprofile} file), such as:
 
 \if{html}{\out{<div class="sourceCode">}}\preformatted{  options(AMR_guideline = "CLSI")
   options(AMR_guideline = "CLSI 2018")

man/av_property.Rd

@@ -42,7 +42,7 @@ av_property(x, property = "name", language = get_AMR_locale(), ...)
 \arguments{
 \item{x}{any (vector of) text that can be coerced to a valid antiviral drug code with \code{\link[=as.av]{as.av()}}}
 
-\item{language}{language of the returned text, defaults to system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with \code{getOption("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
+\item{language}{language of the returned text, defaults to system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the option \code{\link[=AMR-options]{AMR_locale}}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
 
 \item{tolower}{a \link{logical} to indicate whether the first \link{character} of every output should be transformed to a lower case \link{character}.}
 

man/bug_drug_combinations.Rd

@@ -31,7 +31,7 @@ bug_drug_combinations(x, col_mo = NULL, FUN = mo_shortname, ...)
 
 \item{translate_ab}{a \link{character} of length 1 containing column names of the \link{antibiotics} data set}
 
-\item{language}{language of the returned text, defaults to system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with \code{getOption("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
+\item{language}{language of the returned text, defaults to system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the option \code{\link[=AMR-options]{AMR_locale}}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
 
 \item{minimum}{the minimum allowed number of available (tested) isolates. Any isolate count lower than \code{minimum} will return \code{NA} with a warning. The default number of \code{30} isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see \emph{Source}.}
 

man/count.Rd

@@ -48,7 +48,7 @@ count_df(
 
 \item{translate_ab}{a column name of the \link{antibiotics} data set to translate the antibiotic abbreviations to, using \code{\link[=ab_property]{ab_property()}}}
 
-\item{language}{language of the returned text, defaults to system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with \code{getOption("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
+\item{language}{language of the returned text, defaults to system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the option \code{\link[=AMR-options]{AMR_locale}}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
 
 \item{combine_SI}{a \link{logical} to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant), defaults to \code{TRUE}}
 }

man/eucast_rules.Rd

@@ -42,7 +42,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 12)
 
 \item{info}{a \link{logical} to indicate whether progress should be printed to the console, defaults to only print while in interactive sessions}
 
-\item{rules}{a \link{character} vector that specifies which rules should be applied. Must be one or more of \code{"breakpoints"}, \code{"expert"}, \code{"other"}, \code{"custom"}, \code{"all"}, and defaults to \code{c("breakpoints", "expert")}. The default value can be set to another value, e.g. using \code{options(AMR_eucastrules = "all")}. If using \code{"custom"}, be sure to fill in argument \code{custom_rules} too. Custom rules can be created with \code{\link[=custom_eucast_rules]{custom_eucast_rules()}}.}
+\item{rules}{a \link{character} vector that specifies which rules should be applied. Must be one or more of \code{"breakpoints"}, \code{"expert"}, \code{"other"}, \code{"custom"}, \code{"all"}, and defaults to \code{c("breakpoints", "expert")}. The default value can be set to another value using the option \code{\link[=AMR-options]{AMR_eucastrules}}: \code{options(AMR_eucastrules = "all")}. If using \code{"custom"}, be sure to fill in argument \code{custom_rules} too. Custom rules can be created with \code{\link[=custom_eucast_rules]{custom_eucast_rules()}}.}
 
 \item{verbose}{a \link{logical} to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way. Using Verbose mode takes a lot more time.}
 
@@ -96,7 +96,7 @@ Before further processing, two non-EUCAST rules about drug combinations can be a
 
 Important examples include amoxicillin and amoxicillin/clavulanic acid, and trimethoprim and trimethoprim/sulfamethoxazole. Needless to say, for these rules to work, both drugs must be available in the data set.
 
-Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include \code{"other"} to the \code{rules} argument, or use \code{eucast_rules(..., rules = "all")}. You can also set the option \code{AMR_eucastrules}, i.e. run \code{options(AMR_eucastrules = "all")}.
+Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include \code{"other"} to the \code{rules} argument, or use \code{eucast_rules(..., rules = "all")}. You can also set the option \code{\link[=AMR-options]{AMR_eucastrules}}, i.e. run \code{options(AMR_eucastrules = "all")}.
 }
 }
 \section{Antibiotics}{

man/ggplot_sir.Rd

@@ -87,7 +87,7 @@ labels_sir_count(
 
 \item{minimum}{the minimum allowed number of available (tested) isolates. Any isolate count lower than \code{minimum} will return \code{NA} with a warning. The default number of \code{30} isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see \emph{Source}.}
 
-\item{language}{language of the returned text, defaults to system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with \code{getOption("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
+\item{language}{language of the returned text, defaults to system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the option \code{\link[=AMR-options]{AMR_locale}}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
 
 \item{nrow}{(when using \code{facet}) number of rows}
 

man/mo_property.Rd

@@ -270,7 +270,7 @@ mo_property(
 
 \item{language}{language to translate text like "no growth", which defaults to the system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}})}
 
-\item{keep_synonyms}{a \link{logical} to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is \code{FALSE}, which will return a note if old taxonomic names were processed. The default can be set with \code{options(AMR_keep_synonyms = TRUE)} or \code{options(AMR_keep_synonyms = FALSE)}.}
+\item{keep_synonyms}{a \link{logical} to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is \code{FALSE}, which will return a note if old taxonomic names were processed. The default can be set with the option \code{\link[=AMR-options]{AMR_keep_synonyms}}, i.e. \code{options(AMR_keep_synonyms = TRUE)} or \code{options(AMR_keep_synonyms = FALSE)}.}
 
 \item{...}{other arguments passed on to \code{\link[=as.mo]{as.mo()}}, such as 'minimum_matching_score', 'ignore_pattern', and 'remove_from_input'}
 

man/mo_source.Rd

@@ -26,7 +26,7 @@ This is \strong{the fastest way} to have your organisation (or analysis) specifi
 \details{
 The reference file can be a text file separated with commas (CSV) or tabs or pipes, an Excel file (either 'xls' or 'xlsx' format) or an \R object file (extension '.rds'). To use an Excel file, you will need to have the \code{readxl} package installed.
 
-\code{\link[=set_mo_source]{set_mo_source()}} will check the file for validity: it must be a \link{data.frame}, must have a column named \code{"mo"} which contains values from \code{\link[=microorganisms]{microorganisms$mo}} or \code{\link[=microorganisms]{microorganisms$fullname}} and must have a reference column with your own defined values. If all tests pass, \code{\link[=set_mo_source]{set_mo_source()}} will read the file into \R and will ask to export it to \code{"~/mo_source.rds"}. The CRAN policy disallows packages to write to the file system, although '\emph{exceptions may be allowed in interactive sessions if the package obtains confirmation from the user}'. For this reason, this function only works in interactive sessions so that the user can \strong{specifically confirm and allow} that this file will be created. The destination of this file can be set with the \code{destination} argument and defaults to the user's home directory. It can also be set as an \R option, using \code{options(AMR_mo_source = "my/location/file.rds")}.
+\code{\link[=set_mo_source]{set_mo_source()}} will check the file for validity: it must be a \link{data.frame}, must have a column named \code{"mo"} which contains values from \code{\link[=microorganisms]{microorganisms$mo}} or \code{\link[=microorganisms]{microorganisms$fullname}} and must have a reference column with your own defined values. If all tests pass, \code{\link[=set_mo_source]{set_mo_source()}} will read the file into \R and will ask to export it to \code{"~/mo_source.rds"}. The CRAN policy disallows packages to write to the file system, although '\emph{exceptions may be allowed in interactive sessions if the package obtains confirmation from the user}'. For this reason, this function only works in interactive sessions so that the user can \strong{specifically confirm and allow} that this file will be created. The destination of this file can be set with the \code{destination} argument and defaults to the user's home directory. It can also be set with the option \code{\link[=AMR-options]{AMR_mo_source}}, e.g. \code{options(AMR_mo_source = "my/location/file.rds")}.
 
 The created compressed data file \code{"mo_source.rds"} will be used at default for MO determination (function \code{\link[=as.mo]{as.mo()}} and consequently all \verb{mo_*} functions like \code{\link[=mo_genus]{mo_genus()}} and \code{\link[=mo_gramstain]{mo_gramstain()}}). The location and timestamp of the original file will be saved as an \link[base:attributes]{attribute} to the compressed data file.
 

man/plot.Rd

@@ -109,7 +109,7 @@
 
 \item{colours_SIR}{colours to use for filling in the bars, must be a vector of three values (in the order S, I and R). The default colours are colour-blind friendly.}
 
-\item{language}{language to be used to translate 'Susceptible', 'Increased exposure'/'Intermediate' and 'Resistant', defaults to system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can be overwritten by setting the option \code{AMR_locale}, e.g. \code{options(AMR_locale = "de")}, see \link{translate}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
+\item{language}{language to be used to translate 'Susceptible', 'Increased exposure'/'Intermediate' and 'Resistant', defaults to system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can be overwritten by setting the option \code{\link[=AMR-options]{AMR_locale}}, e.g. \code{options(AMR_locale = "de")}, see \link{translate}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
 
 \item{expand}{a \link{logical} to indicate whether the range on the x axis should be expanded between the lowest and highest value. For MIC values, intermediate values will be factors of 2 starting from the highest MIC value. For disk diameters, the whole diameter range will be filled.}
 

man/proportion.Rd

@@ -81,7 +81,7 @@ sir_df(
 
 \item{translate_ab}{a column name of the \link{antibiotics} data set to translate the antibiotic abbreviations to, using \code{\link[=ab_property]{ab_property()}}}
 
-\item{language}{language of the returned text, defaults to system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with \code{getOption("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
+\item{language}{language of the returned text, defaults to system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the option \code{\link[=AMR-options]{AMR_locale}}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
 
 \item{combine_SI}{a \link{logical} to indicate whether all values of S and I must be merged into one, so the output only consists of S+I vs. R (susceptible vs. resistant), defaults to \code{TRUE}}
 }

man/translate.Rd

@@ -22,12 +22,12 @@ translate_AMR(x, language = get_AMR_locale())
 \item{x}{text to translate}
 }
 \description{
-For language-dependent output of AMR functions, like \code{\link[=mo_name]{mo_name()}}, \code{\link[=mo_gramstain]{mo_gramstain()}}, \code{\link[=mo_type]{mo_type()}} and \code{\link[=ab_name]{ab_name()}}.
+For language-dependent output of \code{AMR} functions, such as \code{\link[=mo_name]{mo_name()}}, \code{\link[=mo_gramstain]{mo_gramstain()}}, \code{\link[=mo_type]{mo_type()}} and \code{\link[=ab_name]{ab_name()}}.
 }
 \details{
 The currently 16 supported languages are English (en), Chinese (zh), Danish (da), Dutch (nl), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Polish (pl), Portuguese (pt), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr) and Ukrainian (uk). All these languages have translations available for all antimicrobial drugs and colloquial microorganism names.
 
-To permanently silence the once-per-session language note on a non-English operating system, you can set the option \code{AMR_locale} in your \code{.Rprofile} file like this:
+To permanently silence the once-per-session language note on a non-English operating system, you can set the option \code{\link[=AMR-options]{AMR_locale}} in your \code{.Rprofile} file like this:
 
 \if{html}{\out{<div class="sourceCode r">}}\preformatted{# Open .Rprofile file
 utils::file.edit("~/.Rprofile")
@@ -43,13 +43,13 @@ Please read about adding or updating a language in \href{https://github.com/msbe
 
 The system language will be used at default (as returned by \code{Sys.getenv("LANG")} or, if \code{LANG} is not set, \code{\link[=Sys.getlocale]{Sys.getlocale("LC_COLLATE")}}), if that language is supported. But the language to be used can be overwritten in two ways and will be checked in this order:
 \enumerate{
-\item Setting the R option \code{AMR_locale}, either by using e.g. \code{set_AMR_locale("German")} or by running e.g. \code{options(AMR_locale = "German")}.
+\item Setting the option \code{\link[=AMR-options]{AMR_locale}}, either by using e.g. \code{set_AMR_locale("German")} or by running e.g. \code{options(AMR_locale = "German")}.
 
 Note that setting an \R option only works in the same session. Save the command \code{options(AMR_locale = "(your language)")} to your \code{.Rprofile} file to apply it for every session. Run \code{utils::file.edit("~/.Rprofile")} to edit your \code{.Rprofile} file.
 \item Setting the system variable \code{LANGUAGE} or \code{LANG}, e.g. by adding \code{LANGUAGE="de_DE.utf8"} to your \code{.Renviron} file in your home directory.
 }
 
-Thus, if the R option \code{AMR_locale} is set, the system variables \code{LANGUAGE} and \code{LANG} will be ignored.
+Thus, if the option \code{\link[=AMR-options]{AMR_locale}} is set, the system variables \code{LANGUAGE} and \code{LANG} will be ignored.
 }
 }
 \examples{