(v2.1.1.9080) fix rescale_mic() for an outside MIC range

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 2.1.1.9078
+Version: 2.1.1.9080
-Date: 2024-09-22
+Date: 2024-09-24
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
   data analysis and to work with microbial and antimicrobial properties by

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 2.1.1.9078
+# AMR 2.1.1.9080
 
 *(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://msberends.github.io/AMR/#latest-development-version).)*
 
@@ -70,20 +70,7 @@ This package now supports not only tools for AMR data analysis in clinical setti
 * Added Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input
 
 
-# AMR 2.1.1
+# Older Versions
-
-* Fix for selecting first isolates using the phenotype-based method
-  * This included too many isolates when patients had altering antibiograms within the same bacterial species
-  * See for more info [our issue #122](https://github.com/msberends/AMR/issues/122)
-* Added 1,366 LOINC codes to the `antibiotics` data set and updated to the latest version (LOINC v2.76)
-* MICs can now be used in complex number calculations and allow scientific number format as input (e.g., `as.mic("1.28e-2")`)
-* Fix rounding MICs on latest R beta ('R-devel')
-* Removed unneeded note about the used language when option `AMR_locale` is set
-* Fixed non-ASCII characters in documentation, according to CRAN maintainers
-
-----
-
-# Older versions
 
 This changelog only contains changes from AMR v3.0 (October 2024) and later.
 

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 - the default is the current system language (see [get_AMR_locale()]) and can also be set with the [package option][AMR-options] [`AMR_locale`][AMR-options]. Use `language = NULL` or `language = ""` to prevent translation.
+#' @param language language of the returned text - the default is the current system language (see [get_AMR_locale()]) and can also be set with the package 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/antibiogram.R

@@ -33,7 +33,7 @@
 #' @param x a [data.frame] containing at least a column with microorganisms and columns with antibiotic results (class 'sir', see [as.sir()])
 #' @param antibiotics vector of any antibiotic name or code (will be evaluated with [as.ab()], column name of `x`, or (any combinations of) [antibiotic selectors][antibiotic_class_selectors] such as [aminoglycosides()] or [carbapenems()]. For combination antibiograms, this can also be set to values separated with `"+"`, such as "TZP+TOB" or "cipro + genta", given that columns resembling such antibiotics exist in `x`. See *Examples*.
 #' @param mo_transform a character to transform microorganism input - must be `"name"`, `"shortname"` (default), `"gramstain"`, or one of the column names of the [microorganisms] data set: `r vector_or(colnames(microorganisms), sort = FALSE, quotes = TRUE)`. Can also be `NULL` to not transform the input.
-#' @param ab_transform a character to transform antibiotic input - must be one of the column names of the [antibiotics] data set (defaults to "name"): `r vector_or(colnames(antibiotics), sort = FALSE, quotes = TRUE)`. Can also be `NULL` to not transform the input.
+#' @param ab_transform a character to transform antibiotic input - must be one of the column names of the [antibiotics] data set (defaults to `"name"`): `r vector_or(colnames(antibiotics), sort = FALSE, quotes = TRUE)`. Can also be `NULL` to not transform the input.
 #' @param syndromic_group a column name of `x`, or values calculated to split rows of `x`, e.g. by using [ifelse()] or [`case_when()`][dplyr::case_when()]. See *Examples*.
 #' @param add_total_n a [logical] to indicate whether total available numbers per pathogen should be added to the table (default is `TRUE`). This will add the lowest and highest number of available isolate per antibiotic (e.g, if for *E. coli* 200 isolates are available for ciprofloxacin and 150 for amoxicillin, the returned number will be "150-200").
 #' @param only_all_tested (for combination antibiograms): a [logical] to indicate that isolates must be tested for all antibiotics, see *Details*
@@ -68,7 +68,7 @@
 #' 11. 5 (N=15/300)
 #' 12. 5% (N=15/300)
 #' 
-#' The default is `10`, which can be set globally with the [package option][AMR-options] [`AMR_antibiogram_formatting_type`][AMR-options], e.g. `options(AMR_antibiogram_formatting_type = 5)`.
+#' The default is `10`, which can be set globally with the package option [`AMR_antibiogram_formatting_type`][AMR-options], e.g. `options(AMR_antibiogram_formatting_type = 5)`.
 #' 
 #' Set `digits` (defaults to `0`) to alter the rounding of the susceptibility percentage.
 #'

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 - the default is system language (see [get_AMR_locale()]) and can also be set with the [package option][AMR-options] [`AMR_locale`][AMR-options]. Use `language = NULL` or `language = ""` to prevent translation.
+#' @param language language of the returned text - the default is system language (see [get_AMR_locale()]) and can also be set with the package 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

@@ -35,11 +35,11 @@
 #'
 #' There are two ways to circumvent this and automate the process of adding antimicrobials:
 #'
-#' **Method 1:** Using the [package option][AMR-options] [`AMR_custom_ab`][AMR-options], which is the preferred method. To use this method:
+#' **Method 1:** Using the package 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 [package option][AMR-options] [`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:
+#'    2. Set the file location to the package 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 antimicrobial codes:

R/custom_microorganisms.R

@@ -37,11 +37,11 @@
 #'
 #' There are two ways to circumvent this and automate the process of adding microorganisms:
 #'
-#' **Method 1:** Using the [package option][AMR-options] [`AMR_custom_mo`][AMR-options], which is the preferred method. To use this method:
+#' **Method 1:** Using the package option [`AMR_custom_mo`][AMR-options], which is the preferred method. To use this method:
 #'
 #'    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 [package option][AMR-options] [`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:
+#'    2. Set the file location to the package 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/data.R

@@ -276,9 +276,10 @@
 #'
 #' @description Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. This dataset contain breakpoints for humans, `r length(unique(clinical_breakpoints$host[!clinical_breakpoints$host %in% clinical_breakpoints$type]))` different animal groups, and ECOFFs.
 #' 
-#' Currently available breakpoint guidelines for **clinical microbiology** are EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "human")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "human")$guideline)))` and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "human")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "human")$guideline)))`.
+#' These breakpoints are currently implemented:
-#' 
+#' - For **clinical microbiology**: EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "human")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "human")$guideline)))` and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "human")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "human")$guideline)))`;
-#' Currently available breakpoint guidelines for **veterinary microbiology** are EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "animal")$guideline)))` and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`.
+#' - For **veterinary microbiology**: EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "animal")$guideline)))` and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`;
+#' - For **ECOFFs** (Epidemiological Cut-off Values): EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "ECOFF")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "ECOFF")$guideline)))` and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "ECOFF")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "ECOFF")$guideline)))`.
 #' 
 #' Use [as.sir()] to transform MICs or disks measurements to SIR values.
 #' @format A [tibble][tibble::tibble] with `r format(nrow(clinical_breakpoints), big.mark = " ")` observations and `r ncol(clinical_breakpoints)` variables:
@@ -300,7 +301,7 @@
 #' ### Different types of breakpoints
 #' Supported types of breakpoints are `r vector_and(clinical_breakpoints$type, quote = FALSE)`. ECOFF (Epidemiological cut-off) values are used in antimicrobial susceptibility testing to differentiate between wild-type and non-wild-type strains of bacteria or fungi.
 #' 
-#' The default is `"human"`, which can also be set with the [package option][AMR-options] [`AMR_breakpoint_type`][AMR-options]. Use [`as.sir(..., breakpoint_type = ...)`][as.sir()] to interpret raw data using a specific breakpoint type, e.g. `as.sir(..., breakpoint_type = "ECOFF")` to use ECOFFs.
+#' The default is `"human"`, which can also be set with the package option [`AMR_breakpoint_type`][AMR-options]. Use [`as.sir(..., breakpoint_type = ...)`][as.sir()] to interpret raw data using a specific breakpoint type, e.g. `as.sir(..., breakpoint_type = "ECOFF")` to use ECOFFs.
 #' 
 #' ### Imported from WHONET
 #' Clinical breakpoints in this package were validated through and imported from [WHONET](https://whonet.org), a free desktop Windows application developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance. More can be read on [their website](https://whonet.org). The developers of WHONET and this `AMR` package have been in contact about sharing their work. We highly appreciate their great development on the WHONET software.

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 - the default is 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 using the [package option][AMR-options] [`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 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 package 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 `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 `r vector_or(names(EUCAST_VERSION_EXPERT_RULES), reverse = TRUE)`.
@@ -99,7 +99,7 @@ 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 [package option][AMR-options] [`AMR_eucastrules`][AMR-options], 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 package 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/mic.R

@@ -304,9 +304,9 @@ rescale_mic <- function(x, mic_range, keep_operators = "edges", as.mic = TRUE) {
   
   # create a manual factor with levels only within desired range
   expanded <- plotrange_as_table(x,
-                             expand = TRUE,
+                                 expand = TRUE,
-                             keep_operators = ifelse(keep_operators == "edges", "none", keep_operators),
+                                 keep_operators = ifelse(keep_operators == "edges", "none", keep_operators),
-                             mic_range = mic_range)
+                                 mic_range = mic_range)
   if (keep_operators == "edges") {
     names(expanded)[1] <- paste0("<=", names(expanded)[1])
     names(expanded)[length(expanded)] <- paste0(">=", names(expanded)[length(expanded)])

R/mo.R

@@ -38,11 +38,11 @@
 #'
 #' 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 the [package option][AMR-options] [`AMR_keep_synonyms`][AMR-options], i.e. `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 package 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 Perl-compatible [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 [package option][AMR-options] [`AMR_ignore_pattern`][AMR-options], e.g. `options(AMR_ignore_pattern = "(not reported|contaminated flora)")`.
+#' @param ignore_pattern a Perl-compatible [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 package option [`AMR_ignore_pattern`][AMR-options], e.g. `options(AMR_ignore_pattern = "(not reported|contaminated flora)")`.
-#' @param cleaning_regex a Perl-compatible [regular expression][base::regex] (case-insensitive) to clean the input of `x`. Every matched part 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". The default can be set with the [package option][AMR-options] [`AMR_cleaning_regex`][AMR-options].
+#' @param cleaning_regex a Perl-compatible [regular expression][base::regex] (case-insensitive) to clean the input of `x`. Every matched part 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". The default can be set with the package option [`AMR_cleaning_regex`][AMR-options].
-#' @param only_fungi a [logical] to indicate if only fungi must be found, making sure that e.g. misspellings always return records from the kingdom of Fungi. This can be set globally for [all microorganism functions][mo_property()] with the [package option][AMR-options] [`AMR_only_fungi`][AMR-options], i.e. `options(AMR_only_fungi = TRUE)`.
+#' @param only_fungi a [logical] to indicate if only fungi must be found, making sure that e.g. misspellings always return records from the kingdom of Fungi. This can be set globally for [all microorganism functions][mo_property()] with the package option [`AMR_only_fungi`][AMR-options], i.e. `options(AMR_only_fungi = TRUE)`.
 #' @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 that info must be printed, e.g. a progress bar when more than 25 items are to be coerced, or a list with old taxonomic names. The default is `TRUE` only in interactive mode.
 #' @param ... other arguments passed on to functions

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 with the [package option][AMR-options] [`AMR_mo_source`][AMR-options], e.g. `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 package 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/plotting.R

@@ -40,7 +40,7 @@
 #' @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' - the default is system language (see [get_AMR_locale()]) and can be overwritten by setting the [package option][AMR-options] [`AMR_locale`][AMR-options], 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' - the default is system language (see [get_AMR_locale()]) and can be overwritten by setting the package 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.
 #' @inheritParams as.sir
 #' @details
@@ -73,7 +73,7 @@
 #' # Plotting using scale_x_mic()
 #' \donttest{
 #' if (require("ggplot2")) {
-#'   mic_plot <- ggplot(data.frame(mics = as.mic(c(0.125, "<=4", 4, 8, 32, ">=32")),
+#'   mic_plot <- ggplot(data.frame(mics = as.mic(c(0.25, "<=4", 4, 8, 32, ">=32")),
 #'                                 counts = c(1, 1, 2, 2, 3, 3)),
 #'                      aes(mics, counts)) +
 #'     geom_col()
@@ -92,8 +92,13 @@
 #' }
 #' if (require("ggplot2")) {
 #'   mic_plot +
-#'     scale_x_mic(mic_range = c(1, 128)) +
+#'     scale_x_mic(mic_range = c(1, 16)) +
-#'     labs(title = "with scale_x_mic() using a manual range")
+#'     labs(title = "with scale_x_mic() using a manual 'within' range")
+#' }
+#' if (require("ggplot2")) {
+#'   mic_plot +
+#'     scale_x_mic(mic_range = c(0.032, 256)) +
+#'     labs(title = "with scale_x_mic() using a manual 'outside' range")
 #' }
 #' 
 #' if (require("ggplot2")) {
@@ -795,7 +800,14 @@ plotrange_as_table <- function(x, expand, keep_operators = "all", mic_range = NU
     x <- as.mic(x, keep_operators = keep_operators)
     if (expand == TRUE) {
       # expand range for MIC by adding common intermediate factors levels
-      extra_range <- COMMON_MIC_VALUES[COMMON_MIC_VALUES > min(x, na.rm = TRUE) & COMMON_MIC_VALUES < max(x, na.rm = TRUE)]
+      if (!is.null(mic_range) && !all(is.na(mic_range))) {
+        # base on mic_range
+        `%na_or%` <- function(x, y) if (is.na(x)) y else x
+        extra_range <- COMMON_MIC_VALUES[COMMON_MIC_VALUES >= (mic_range[1] %na_or% min(x, na.rm = TRUE)) & COMMON_MIC_VALUES <= (mic_range[2] %na_or% max(x, na.rm = TRUE))]
+      } else {
+        # base on x
+        extra_range <- COMMON_MIC_VALUES[COMMON_MIC_VALUES > min(x, na.rm = TRUE) & COMMON_MIC_VALUES < max(x, na.rm = TRUE)]
+      }
       # remove the ones that are in 25% range of user values
       extra_range <- extra_range[!vapply(FUN.VALUE = logical(1), extra_range, function(r) any(abs(r - x) / x < 0.25, na.rm = TRUE))]
       nms <- extra_range

R/sir.R

@@ -43,12 +43,12 @@
 #' @param ab a vector (or column name) with [character]s that can be coerced to a valid antimicrobial drug code with [as.ab()]
 #' @param uti (Urinary Tract Infection) a vector (or column name) with [logical]s (`TRUE` or `FALSE`) to specify whether a UTI specific interpretation from the guideline should be chosen. For using [as.sir()] on a [data.frame], this can also be a column containing [logical]s or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See *Examples*.
 #' @inheritParams first_isolate
-#' @param guideline defaults to EUCAST `r  max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))` (the latest implemented EUCAST guideline in the [AMR::clinical_breakpoints] data set), but can be set with the [package option][AMR-options] [`AMR_guideline`][AMR-options]. Currently supports EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$guideline)))`), see *Details*.
+#' @param guideline defaults to EUCAST `r  max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))` (the latest implemented EUCAST guideline in the [AMR::clinical_breakpoints] data set), but can be set with the package option [`AMR_guideline`][AMR-options]. Currently supports EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$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_screening a [logical] to indicate that clinical breakpoints for screening are allowed - the default is `FALSE`. Can also be set with the [package option][AMR-options] [`AMR_include_screening`][AMR-options].
+#' @param include_screening a [logical] to indicate that clinical breakpoints for screening are allowed - the default is `FALSE`. Can also be set with the package option [`AMR_include_screening`][AMR-options].
-#' @param include_PKPD a [logical] to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is `TRUE`. Can also be set with the [package option][AMR-options] [`AMR_include_PKPD`][AMR-options].
+#' @param include_PKPD a [logical] to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is `TRUE`. Can also be set with the package option [`AMR_include_PKPD`][AMR-options].
-#' @param breakpoint_type the type of breakpoints to use, either `r vector_or(clinical_breakpoints$type)`. ECOFF stands for Epidemiological Cut-Off values. The default is `"human"`, which can also be set with the [package option][AMR-options] [`AMR_breakpoint_type`][AMR-options]. If `host` is set to values of veterinary species, this will automatically be set to `"animal"`.
+#' @param breakpoint_type the type of breakpoints to use, either `r vector_or(clinical_breakpoints$type)`. ECOFF stands for Epidemiological Cut-Off values. The default is `"human"`, which can also be set with the package option [`AMR_breakpoint_type`][AMR-options]. If `host` is set to values of veterinary species, this will automatically be set to `"animal"`.
 #' @param host a vector (or column name) with [character]s to indicate the host. Only useful for veterinary breakpoints, as it requires `breakpoint_type = "animal"`. The values can be any text resembling the animal species, even in any of the `r length(LANGUAGES_SUPPORTED)` supported languages of this package. For foreign languages, be sure to set the language with [set_AMR_locale()] (though it will be automatically guessed based on the system language).
 #' @param verbose a [logical] to indicate that all notes should be printed during interpretation of MIC values or disk diffusion values.
 #' @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.
@@ -96,7 +96,7 @@
 #'
 #' Thus, the `guideline` argument must be set to e.g., ``r paste0('"', subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline[1], '"')`` or ``r paste0('"', subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$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 [package option][AMR-options] [`AMR_guideline`][AMR-options] (e.g. in your `.Rprofile` file), such as:
+#' You can set the default guideline with the package option [`AMR_guideline`][AMR-options] (e.g. in your `.Rprofile` file), such as:
 #'
 #' ```
 #'   options(AMR_guideline = "CLSI")
@@ -1078,7 +1078,6 @@ as_sir_method <- function(method_short,
   if (length(uti) == 1) {
     uti <- rep(uti, length(x))
   }
-  uti[is.na(uti)] <- FALSE
   if (isTRUE(add_intrinsic_resistance) && guideline_coerced %unlike% "EUCAST") {
     if (message_not_thrown_before("as.sir", "intrinsic")) {
       warning_("in `as.sir()`: using 'add_intrinsic_resistance' is only useful when using EUCAST guidelines, since the rules for intrinsic resistance are based on EUCAST.")
@@ -1211,7 +1210,7 @@ as_sir_method <- function(method_short,
     host_current <- df_unique[i, "host", drop = TRUE]
     uti_current <- df_unique[i, "uti", drop = TRUE]
     notes_current <- character(0)
-    if (isFALSE(uti_current)) {
+    if (is.na(uti_current)) {
       # no preference, so no filter on UTIs
       rows <- which(df$mo == mo_current & df$ab == ab_current & df$host == host_current)
     } else {
@@ -1354,16 +1353,16 @@ as_sir_method <- function(method_short,
     
     # sort on host and taxonomic rank
     # (this will e.g. prefer 'species' breakpoints over 'order' breakpoints)
-    if (all(uti_current == FALSE, na.rm = TRUE)) {
+    if (is.na(uti_current)) {
       breakpoints_current <- breakpoints_current %pm>%
         #  `uti` is a column in the data set
         # this will put UTI = FALSE first, then UTI = NA, then UTI = TRUE
-        pm_mutate(uti_index = ifelse(is.na(uti) & uti == FALSE, 1, 
+        pm_mutate(uti_index = ifelse(!is.na(uti) & uti == FALSE, 1, 
                                      ifelse(is.na(uti), 2,
                                             3))) %pm>%
         # be as specific as possible (i.e. prefer species over genus):
         pm_arrange(rank_index, uti_index)
-    } else if (all(uti_current == TRUE, na.rm = TRUE)) {
+    } else if (uti_current == TRUE) {
       breakpoints_current <- breakpoints_current %pm>%
         subset(uti == TRUE) %pm>%
         # be as specific as possible (i.e. prefer species over genus):
@@ -1377,7 +1376,7 @@ as_sir_method <- function(method_short,
     } else {
       site <- paste0("body site '", site, "'")
     }
-    if (nrow(breakpoints_current) == 1 && all(breakpoints_current$uti == TRUE) && any(uti_current %in% c(FALSE, NA)) && message_not_thrown_before("as.sir", "uti", ab_current)) {
+    if (nrow(breakpoints_current) == 1 && all(breakpoints_current$uti == TRUE) && is.na(uti_current) && message_not_thrown_before("as.sir", "uti", ab_current)) {
       # only UTI breakpoints available
       notes_current <- c(notes_current, paste0("Breakpoints for ", font_bold(ab_formatted), " in ", mo_formatted, " are only available for (uncomplicated) urinary tract infections (UTI); assuming `uti = TRUE`."))
     } else if (nrow(breakpoints_current) > 1 && length(unique(breakpoints_current$site)) > 1 && any(is.na(uti_current)) && all(c(TRUE, FALSE) %in% breakpoints_current$uti, na.rm = TRUE) && message_not_thrown_before("as.sir", "siteUTI", mo_current, ab_current)) {
@@ -1415,8 +1414,8 @@ as_sir_method <- function(method_short,
           guideline_coerced %like% "EUCAST" & values > breakpoints_current$breakpoint_R ~ as.sir("R"),
           guideline_coerced %like% "CLSI" & values >= breakpoints_current$breakpoint_R ~ as.sir("R"),
           # return "I" or "SDD" when breakpoints are in the middle
-          !is.na(breakpoints_current$breakpoint_S) & !is.na(breakpoints_current$breakpoint_R) & breakpoints_current$is_SDD == FALSE ~ as.sir("I"),
           !is.na(breakpoints_current$breakpoint_S) & !is.na(breakpoints_current$breakpoint_R) & breakpoints_current$is_SDD == TRUE ~ as.sir("SDD"),
+          !is.na(breakpoints_current$breakpoint_S) & !is.na(breakpoints_current$breakpoint_R) & breakpoints_current$is_SDD == FALSE ~ as.sir("I"),
           # and NA otherwise
           TRUE ~ NA_sir_
         )
@@ -1427,8 +1426,8 @@ as_sir_method <- function(method_short,
           guideline_coerced %like% "EUCAST" & as.double(values) < as.double(breakpoints_current$breakpoint_R) ~ as.sir("R"),
           guideline_coerced %like% "CLSI" & as.double(values) <= as.double(breakpoints_current$breakpoint_R) ~ as.sir("R"),
           # return "I" or "SDD" when breakpoints are in the middle
-          !is.na(breakpoints_current$breakpoint_S) & !is.na(breakpoints_current$breakpoint_R) & breakpoints_current$is_SDD == FALSE ~ as.sir("I"),
           !is.na(breakpoints_current$breakpoint_S) & !is.na(breakpoints_current$breakpoint_R) & breakpoints_current$is_SDD == TRUE ~ as.sir("SDD"),
+          !is.na(breakpoints_current$breakpoint_S) & !is.na(breakpoints_current$breakpoint_R) & breakpoints_current$is_SDD == FALSE ~ as.sir("I"),
           # and NA otherwise
           TRUE ~ NA_sir_
         )

R/translate.R

@@ -34,7 +34,7 @@
 #' @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 [package option][AMR-options] [`AMR_locale`][AMR-options] 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 package 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 [package option][AMR-options] [`AMR_locale`][AMR-options], either by using e.g. `set_AMR_locale("German")` or by running e.g. `options(AMR_locale = "German")`.
+#'   1. Setting the package 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 [package option][AMR-options] [`AMR_locale`][AMR-options] is set, the system variables `LANGUAGE` and `LANG` will be ignored.
+#' Thus, if the package option [`AMR_locale`][AMR-options] is set, the system variables `LANGUAGE` and `LANG` will be ignored.
 #' @rdname translate
 #' @name translate
 #' @export

index.md

@@ -4,7 +4,7 @@
 * Used in over 175 countries, available in 20 languages
 * Generates **antibiograms** - traditional, combined, syndromic, and even WISCA
 * Provides the **full microbiological taxonomy** and extensive info on **all antimicrobial drugs**
-* Applies all recent **CLSI** and **EUCAST** clinical and veterinary breakpoints for MICs and disk zones
+* Applies all recent **CLSI** and **EUCAST** clinical and veterinary breakpoints for MICs, disk zones and ECOFFs
 * Corrects for duplicate isolates, **calculates** and **predicts** AMR per antibiotic class
 * Integrates with **WHONET**, ATC, **EARS-Net**, PubChem, **LOINC**, **SNOMED CT**, and **NCBI**
 * 100% free of costs and dependencies, highly suitable for places with **limited resources**
@@ -98,18 +98,18 @@ antibiogram(example_isolates,
             antibiotics = c(aminoglycosides(), carbapenems()))
 ```
 
-|Pathogen (N min-max)     | AMK| GEN| IPM| KAN| MEM| TOB|
+| Pathogen                | Amikacin         | Gentamicin      | Imipenem         | Kanamycin        | Meropenem        | Tobramycin       |
-|:------------------------|---:|---:|---:|---:|---:|---:|
+|:------------------------|:----------------:|:---------------:|:----------------:|:----------------:|:----------------:|:----------------:|
-|CoNS (43-309)            |   0|  86|  52|   0|  52|  22|
+| CoNS                    | 0% (0/43)        | 86% (267/309)   | 52% (25/48)      | 0% (0/43)        | 52% (25/48)      | 22% (12/55)      |
-|*E. coli* (0-462)        | 100|  98| 100|    | 100|  97|
+| *E. coli*               | 100% (171/171)   | 98% (451/460)   | 100% (422/422)   |                  | 100% (418/418)   | 97% (450/462)    |
-|*E. faecalis* (0-39)     |   0|   0| 100|   0|    |   0|
+| *E. faecalis*           | 0% (0/39)        | 0% (0/39)       | 100% (38/38)     | 0% (0/39)        |                  | 0% (0/39)        |
-|*K. pneumoniae* (0-58)   |    |  90| 100|    | 100|  90|
+| *K. pneumoniae*         |                  | 90% (52/58)     | 100% (51/51)     |                  | 100% (53/53)     | 90% (52/58)      |
-|*P. aeruginosa* (17-30)  |    | 100|    |   0|    | 100|
+| *P. aeruginosa*         |                  | 100% (30/30)    |                  | 0% (0/30)        |                  | 100% (30/30)     |
-|*P. mirabilis* (0-34)    |    |  94|  94|    |    |  94|
+| *P. mirabilis*          |                  | 94% (32/34)     | 94% (30/32)      |                  |                  | 94% (32/34)      |
-|*S. aureus* (2-233)      |    |  99|    |    |    |  98|
+| *S. aureus*             |                  | 99% (231/233)   |                  |                  |                  | 98% (84/86)      |
-|*S. epidermidis* (8-163) |   0|  79|    |   0|    |  51|
+| *S. epidermidis*        | 0% (0/44)        | 79% (128/163)   |                  | 0% (0/44)        |                  | 51% (45/89)      |
-|*S. hominis* (3-80)      |    |  92|    |    |    |  85|
+| *S. hominis*            |                  | 92% (74/80)     |                  |                  |                  | 85% (53/62)      |
-|*S. pneumoniae* (11-117) |   0|   0|    |   0|    |   0|
+| *S. pneumoniae*         | 0% (0/117)       | 0% (0/117)      |                  | 0% (0/117)       |                  | 0% (0/117)       |
 
 In combination antibiograms, it is clear that combined antibiotics yield higher empiric coverage:
 
@@ -119,10 +119,10 @@ antibiogram(example_isolates,
             mo_transform = "gramstain")
 ```
 
-|Pathogen (N min-max)     | TZP| TZP + GEN| TZP + TOB|
+| Pathogen      | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
-|:------------------------|---:|---------:|---------:|
+|:--------------|:-----------------------:|:-------------------------------------:|:------------------------------------:|
-|Gram-negative (641-693)  |  88|        99|        98|
+| Gram-negative | 88% (565/641)            | 99% (681/691)                        | 98% (679/693)                       |
-|Gram-positive (345-1044) |  86|        98|        95|
+| Gram-positive | 86% (296/345)            | 98% (1018/1044)                      | 95% (524/550)                       |
 
 Like many other functions in this package, `antibiogram()` comes with support for 20 languages that are often detected automatically based on system language:
 
@@ -134,11 +134,10 @@ antibiogram(example_isolates,
             language = "uk") # Ukrainian
 ```
 
-|Збудник (N min-max)      | Гентаміцин| Тобраміцин| Ципрофлоксацин|
+| Збудник        | Гентаміцин           | Тобраміцин          | Ципрофлоксацин     |
-|:------------------------|----------:|----------:|--------------:|
+|:---------------|:--------------------:|:-------------------:|:------------------:|
-|Грамнегативні (684-686)  |         96|         96|             91|
+| Грамнегативні  | 96% (659/684)        | 96% (658/686)       | 91% (621/684)      |
-|Грампозитивні (665-1170) |         63|         34|             77|
+| Грампозитивні  | 63% (740/1170)       | 34% (228/665)       | 77% (560/724)      |
-
 
 #### Calculating resistance per group
 

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 - the default is the current system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_locale}}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
+\item{language}{language of the returned text - the default is the current system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the package 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

@@ -20,10 +20,10 @@ With \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} you c
 
 There are two ways to circumvent this and automate the process of adding antimicrobials:
 
-\strong{Method 1:} Using the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_custom_ab}}, which is the preferred method. To use this method:
+\strong{Method 1:} Using the package 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 \link[=AMR-options]{package 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:
+\item Set the file location to the package 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 antimicrobial codes:
 options(AMR_custom_ab = "~/my_custom_ab.rds")

man/add_custom_microorganisms.Rd

@@ -22,10 +22,10 @@ This function will fill in missing taxonomy for you, if specific taxonomic colum
 
 There are two ways to circumvent this and automate the process of adding microorganisms:
 
-\strong{Method 1:} Using the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_custom_mo}}, which is the preferred method. To use this method:
+\strong{Method 1:} Using the package 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 \link[=AMR-options]{package 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:
+\item Set the file location to the package 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/antibiogram.Rd

@@ -51,7 +51,7 @@ antibiogram(
 
 \item{mo_transform}{a character to transform microorganism input - must be \code{"name"}, \code{"shortname"} (default), \code{"gramstain"}, or one of the column names of the \link{microorganisms} data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "oxygen_tolerance", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "mycobank", "mycobank_parent", "mycobank_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence", or "snomed". Can also be \code{NULL} to not transform the input.}
 
-\item{ab_transform}{a character to transform antibiotic input - must be one of the column names of the \link{antibiotics} data set (defaults to "name"): "ab", "cid", "name", "group", "atc", "atc_group1", "atc_group2", "abbreviations", "synonyms", "oral_ddd", "oral_units", "iv_ddd", "iv_units", or "loinc". Can also be \code{NULL} to not transform the input.}
+\item{ab_transform}{a character to transform antibiotic input - must be one of the column names of the \link{antibiotics} data set (defaults to \code{"name"}): "ab", "cid", "name", "group", "atc", "atc_group1", "atc_group2", "abbreviations", "synonyms", "oral_ddd", "oral_units", "iv_ddd", "iv_units", or "loinc". Can also be \code{NULL} to not transform the input.}
 
 \item{syndromic_group}{a column name of \code{x}, or values calculated to split rows of \code{x}, e.g. by using \code{\link[=ifelse]{ifelse()}} or \code{\link[dplyr:case_when]{case_when()}}. See \emph{Examples}.}
 
@@ -108,7 +108,7 @@ The formatting of the 'cells' of the table can be set with the argument \code{fo
 \item 5\% (N=15/300)
 }
 
-The default is \code{10}, which can be set globally with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_antibiogram_formatting_type}}, e.g. \code{options(AMR_antibiogram_formatting_type = 5)}.
+The default is \code{10}, which can be set globally with the package option \code{\link[=AMR-options]{AMR_antibiogram_formatting_type}}, e.g. \code{options(AMR_antibiogram_formatting_type = 5)}.
 
 Set \code{digits} (defaults to \code{0}) to alter the rounding of the susceptibility percentage.
 }

man/as.mo.Rd

@@ -51,15 +51,15 @@ 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 the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_keep_synonyms}}, i.e. \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 package 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 Perl-compatible \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 \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_ignore_pattern}}, e.g. \code{options(AMR_ignore_pattern = "(not reported|contaminated flora)")}.}
+\item{ignore_pattern}{a Perl-compatible \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 package option \code{\link[=AMR-options]{AMR_ignore_pattern}}, e.g. \code{options(AMR_ignore_pattern = "(not reported|contaminated flora)")}.}
 
-\item{cleaning_regex}{a Perl-compatible \link[base:regex]{regular expression} (case-insensitive) to clean the input of \code{x}. Every matched part 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". The default can be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_cleaning_regex}}.}
+\item{cleaning_regex}{a Perl-compatible \link[base:regex]{regular expression} (case-insensitive) to clean the input of \code{x}. Every matched part 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". The default can be set with the package option \code{\link[=AMR-options]{AMR_cleaning_regex}}.}
 
-\item{only_fungi}{a \link{logical} to indicate if only fungi must be found, making sure that e.g. misspellings always return records from the kingdom of Fungi. This can be set globally for \link[=mo_property]{all microorganism functions} with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_only_fungi}}, i.e. \code{options(AMR_only_fungi = TRUE)}.}
+\item{only_fungi}{a \link{logical} to indicate if only fungi must be found, making sure that e.g. misspellings always return records from the kingdom of Fungi. This can be set globally for \link[=mo_property]{all microorganism functions} with the package option \code{\link[=AMR-options]{AMR_only_fungi}}, i.e. \code{options(AMR_only_fungi = TRUE)}.}
 
 \item{language}{language to translate text like "no growth", which defaults to the system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}})}
 

man/as.sir.Rd

@@ -107,7 +107,7 @@ sir_interpretation_history(clean = FALSE)
 
 \item{ab}{a vector (or column name) with \link{character}s that can be coerced to a valid antimicrobial drug code with \code{\link[=as.ab]{as.ab()}}}
 
-\item{guideline}{defaults to EUCAST 2024 (the latest implemented EUCAST guideline in the \link{clinical_breakpoints} data set), but can be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_guideline}}. Currently supports EUCAST (2011-2024) and CLSI (2011-2024), see \emph{Details}.}
+\item{guideline}{defaults to EUCAST 2024 (the latest implemented EUCAST guideline in the \link{clinical_breakpoints} data set), but can be set with the package option \code{\link[=AMR-options]{AMR_guideline}}. Currently supports EUCAST (2011-2024) and CLSI (2011-2024), see \emph{Details}.}
 
 \item{uti}{(Urinary Tract Infection) a vector (or column name) with \link{logical}s (\code{TRUE} or \code{FALSE}) to specify whether a UTI specific interpretation from the guideline should be chosen. For using \code{\link[=as.sir]{as.sir()}} on a \link{data.frame}, this can also be a column containing \link{logical}s or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See \emph{Examples}.}
 
@@ -117,11 +117,11 @@ 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_screening}{a \link{logical} to indicate that clinical breakpoints for screening are allowed - the default is \code{FALSE}. Can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_include_screening}}.}
+\item{include_screening}{a \link{logical} to indicate that clinical breakpoints for screening are allowed - the default is \code{FALSE}. Can also be set with the package option \code{\link[=AMR-options]{AMR_include_screening}}.}
 
-\item{include_PKPD}{a \link{logical} to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is \code{TRUE}. Can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_include_PKPD}}.}
+\item{include_PKPD}{a \link{logical} to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is \code{TRUE}. Can also be set with the package option \code{\link[=AMR-options]{AMR_include_PKPD}}.}
 
-\item{breakpoint_type}{the type of breakpoints to use, either "ECOFF", "animal", or "human". ECOFF stands for Epidemiological Cut-Off values. The default is \code{"human"}, which can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_breakpoint_type}}. If \code{host} is set to values of veterinary species, this will automatically be set to \code{"animal"}.}
+\item{breakpoint_type}{the type of breakpoints to use, either "ECOFF", "animal", or "human". ECOFF stands for Epidemiological Cut-Off values. The default is \code{"human"}, which can also be set with the package option \code{\link[=AMR-options]{AMR_breakpoint_type}}. If \code{host} is set to values of veterinary species, this will automatically be set to \code{"animal"}.}
 
 \item{host}{a vector (or column name) with \link{character}s to indicate the host. Only useful for veterinary breakpoints, as it requires \code{breakpoint_type = "animal"}. The values can be any text resembling the animal species, even in any of the 20 supported languages of this package. For foreign languages, be sure to set the language with \code{\link[=set_AMR_locale]{set_AMR_locale()}} (though it will be automatically guessed based on the system language).}
 
@@ -192,7 +192,7 @@ 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 2024"} or \code{"CLSI 2024"}. 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 \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_guideline}} (e.g. in your \code{.Rprofile} file), such as:
+You can set the default guideline with the package 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 - the default is system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_locale}}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
+\item{language}{language of the returned text - the default is system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the package 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 - the default is the current system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_locale}}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
+\item{language}{language of the returned text - the default is the current system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the package 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/clinical_breakpoints.Rd

@@ -29,9 +29,12 @@ clinical_breakpoints
 \description{
 Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. This dataset contain breakpoints for humans, 7 different animal groups, and ECOFFs.
 
-Currently available breakpoint guidelines for \strong{clinical microbiology} are EUCAST 2011-2024 and CLSI 2011-2024.
+These breakpoints are currently implemented:
-
+\itemize{
-Currently available breakpoint guidelines for \strong{veterinary microbiology} are EUCAST 2021-2024 and CLSI 2019-2024.
+\item For \strong{clinical microbiology}: EUCAST 2011-2024 and CLSI 2011-2024;
+\item For \strong{veterinary microbiology}: EUCAST 2021-2024 and CLSI 2019-2024;
+\item For \strong{ECOFFs} (Epidemiological Cut-off Values): EUCAST 2020-2024 and CLSI 2022-2024.
+}
 
 Use \code{\link[=as.sir]{as.sir()}} to transform MICs or disks measurements to SIR values.
 }
@@ -40,7 +43,7 @@ Use \code{\link[=as.sir]{as.sir()}} to transform MICs or disks measurements to S
 
 Supported types of breakpoints are ECOFF, animal, and human. ECOFF (Epidemiological cut-off) values are used in antimicrobial susceptibility testing to differentiate between wild-type and non-wild-type strains of bacteria or fungi.
 
-The default is \code{"human"}, which can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_breakpoint_type}}. Use \code{\link[=as.sir]{as.sir(..., breakpoint_type = ...)}} to interpret raw data using a specific breakpoint type, e.g. \code{as.sir(..., breakpoint_type = "ECOFF")} to use ECOFFs.
+The default is \code{"human"}, which can also be set with the package option \code{\link[=AMR-options]{AMR_breakpoint_type}}. Use \code{\link[=as.sir]{as.sir(..., breakpoint_type = ...)}} to interpret raw data using a specific breakpoint type, e.g. \code{as.sir(..., breakpoint_type = "ECOFF")} to use ECOFFs.
 }
 
 \subsection{Imported from WHONET}{

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 - the default is the current system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_locale}}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
+\item{language}{language of the returned text - the default is the current system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the package 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) - the default is \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 - the default is 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 using the \link[=AMR-options]{package 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{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 package 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 \link[=AMR-options]{package option} \code{\link[=AMR-options]{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 package 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 - the default is the current system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_locale}}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
+\item{language}{language of the returned text - the default is the current system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the package 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

@@ -302,7 +302,7 @@ 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 the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_keep_synonyms}}, i.e. \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 package 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 with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_mo_source}}, e.g. \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 package 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

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/plot.R
+% Please edit documentation in R/plotting.R
 \name{plot}
 \alias{plot}
 \alias{scale_x_mic}
@@ -137,13 +137,13 @@ scale_fill_mic(keep_operators = "edges", mic_range = NULL, drop = FALSE, ...)
 
 \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' - the default is system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can be overwritten by setting the \link[=AMR-options]{package 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{language}{language to be used to translate 'Susceptible', 'Increased exposure'/'Intermediate' and 'Resistant' - the default is system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can be overwritten by setting the package 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.}
 
-\item{include_PKPD}{a \link{logical} to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is \code{TRUE}. Can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_include_PKPD}}.}
+\item{include_PKPD}{a \link{logical} to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is \code{TRUE}. Can also be set with the package option \code{\link[=AMR-options]{AMR_include_PKPD}}.}
 
-\item{breakpoint_type}{the type of breakpoints to use, either "ECOFF", "animal", or "human". ECOFF stands for Epidemiological Cut-Off values. The default is \code{"human"}, which can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_breakpoint_type}}. If \code{host} is set to values of veterinary species, this will automatically be set to \code{"animal"}.}
+\item{breakpoint_type}{the type of breakpoints to use, either "ECOFF", "animal", or "human". ECOFF stands for Epidemiological Cut-Off values. The default is \code{"human"}, which can also be set with the package option \code{\link[=AMR-options]{AMR_breakpoint_type}}. If \code{host} is set to values of veterinary species, this will automatically be set to \code{"animal"}.}
 }
 \value{
 The \code{autoplot()} functions return a \code{\link[ggplot2:ggplot]{ggplot}} model that is extendible with any \code{ggplot2} function.
@@ -180,7 +180,7 @@ plot(some_disk_values, mo = "Escherichia coli", ab = "cipro", language = "nl")
 # Plotting using scale_x_mic()
 \donttest{
 if (require("ggplot2")) {
-  mic_plot <- ggplot(data.frame(mics = as.mic(c(0.125, "<=4", 4, 8, 32, ">=32")),
+  mic_plot <- ggplot(data.frame(mics = as.mic(c(0.25, "<=4", 4, 8, 32, ">=32")),
                                 counts = c(1, 1, 2, 2, 3, 3)),
                      aes(mics, counts)) +
     geom_col()
@@ -199,8 +199,13 @@ if (require("ggplot2")) {
 }
 if (require("ggplot2")) {
   mic_plot +
-    scale_x_mic(mic_range = c(1, 128)) +
+    scale_x_mic(mic_range = c(1, 16)) +
-    labs(title = "with scale_x_mic() using a manual range")
+    labs(title = "with scale_x_mic() using a manual 'within' range")
+}
+if (require("ggplot2")) {
+  mic_plot +
+    scale_x_mic(mic_range = c(0.032, 256)) +
+    labs(title = "with scale_x_mic() using a manual 'outside' range")
 }
 
 if (require("ggplot2")) {

man/proportion.Rd

@@ -84,7 +84,7 @@ 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 - the default is the current system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_locale}}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
+\item{language}{language of the returned text - the default is the current system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the package 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) - the default is \code{TRUE}}
 }

man/translate.Rd

@@ -27,7 +27,7 @@ For language-dependent output of \code{AMR} functions, such as \code{\link[=mo_n
 \details{
 The currently 20 supported languages are English (en), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Norwegian (no), Polish (pl), Portuguese (pt), Romanian (ro), 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 \link[=AMR-options]{package option} \code{\link[=AMR-options]{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 package 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 \link[=AMR-options]{package 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")}.
+\item Setting the package 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 \link[=AMR-options]{package option} \code{\link[=AMR-options]{AMR_locale}} is set, the system variables \code{LANGUAGE} and \code{LANG} will be ignored.
+Thus, if the package option \code{\link[=AMR-options]{AMR_locale}} is set, the system variables \code{LANGUAGE} and \code{LANG} will be ignored.
 }
 }
 \examples{