* Function `is_new_episode()` to determine patient episodes which are not necessarily based on microorganisms. It also supports grouped variables with e.g. `mutate()`, `filter()` and `summarise()` of the `dplyr` package:
@ -45,12 +45,14 @@
@@ -45,12 +45,14 @@
* Fix for plotting MIC values with `plot()`
* Added `plot()` generic to class `<disk>`
* LA-MRSA and CA-MRSA are now recognised as an abbreviation for *Staphylococcus aureus*, meaning that e.g. `mo_genus("LA-MRSA")` will return `"Staphylococcus"` and `mo_is_gram_positive("LA-MRSA")` will return `TRUE`.
* Fix for printing class <mo> in tibbles when all values are `NA`
* Fix for `mo_shortname()` when the input contains `NA`
* If `as.mo()` takes more than 30 seconds, some suggestions will be done to improve speed
### Other
* All messages and warnings thrown by this package now break sentences on whole words
* More extensive unit tests
* Internal calls to `options()` were all removed in favour of a new internal environment `mo_env`
* Our website now also has a dark theme, that switches on automatically based on system settings (such as Night Mode in macOS)
#' The following antibiotics are used for the functions [eucast_rules()] and [mdro()]. These are shown below in the format 'name (`antimicrobial ID`, [ATC code](https://www.whocc.no/atc/structure_and_principles/))', sorted alphabetically:
guideline$name<-"Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance."
guideline$author<-"Magiorakos AP, Srinivasan A, Carey RB, ..., Vatopoulos A, Weber JT, Monnet DL"
guideline$version<-"N/A"
guideline$version<-NA
guideline$source<-"Clinical Microbiology and Infection 18:3, 2012. DOI: 10.1111/j.1469-0691.2011.03570.x"
message_("Using `as.mo()` took ",delta_time," seconds, which is a long time. Some suggestions to improve speed include:")
message_(word_wrap("- Try to use as many valid taxonomic names as possible for your input.",
extra_indent=2),
as_note=FALSE)
message_(word_wrap("- Save the output and use it as input for future calculations, e.g. create a new variable to your data using `as.mo()`. All functions in this package that rely on microorganism codes will automatically use that new column where possible. All `mo_*()` functions also do not require you to set their `x` argument as long as you have the dplyr package installed and you have a column of class <mo>.",
extra_indent=2),
as_note=FALSE)
message_(word_wrap("- Use `set_mo_source()` to continually transform your organisation codes to microorganisms codes used by this package, please see `?mo_source`.",
#' Use these functions to return a specific property of a microorganism based on the latest accepted taxonomy. All input values will be evaluated internally with [as.mo()], which makes it possible to use microbial abbreviations, codes and names as input. Please see *Examples*.
#' @inheritSection lifecycle Stable lifecycle
#' @param x any character (vector) that can be coerced to a valid microorganism code with [as.mo()]. Can be omitted for auto-guessing in `mo_is_*()` functions when used inside `dplyr` verbs, such as [`filter()`][dplyr::filter()], [`mutate()`][dplyr::mutate()] and [`summarise()`][dplyr::summarise()], please see *Examples*.
#' @param x any character (vector) that can be coerced to a valid microorganism code with [as.mo()]. Can be omitted for auto-guessing the column containing microorganism codes when used inside `dplyr` verbs, such as [`filter()`][dplyr::filter()], [`mutate()`][dplyr::mutate()] and [`summarise()`][dplyr::summarise()], please see *Examples*.
#' @param property one of the column names of the [microorganisms] data set: `r paste0('"``', colnames(microorganisms), '\``"', collapse = ", ")`, or must be `"shortname"`
#' @param language language of the returned text, defaults to system language (see [get_locale()]) and can be overwritten by setting the option `AMR_locale`, e.g. `options(AMR_locale = "de")`, see [translate]. Also used to translate text like "no growth". Use `language = NULL` or `language = ""` to prevent translation.
#' @param ... other arguments passed on to [as.mo()], such as 'allow_uncertain' and 'ignore_pattern'
#' @param ab any (vector of) text that can be coerced to a valid antibiotic code with [as.ab()]
#' @param open browse the URL using [utils::browseURL()]
#' @param open browse the URL using [`browseURL()`][utils::browseURL()]
#' @details All functions will return the most recently known taxonomic property according to the Catalogue of Life, except for [mo_ref()], [mo_authors()] and [mo_year()]. Please refer to this example, knowing that *Escherichia blattae* was renamed to *Shimwellia blattae* in 2010:
#' - `mo_name("Escherichia blattae")` will return `"Shimwellia blattae"` (with a message about the renaming)
#' - `mo_ref("Escherichia blattae")` will return `"Burgess et al., 1973"` (with a message about the renaming)
@ -161,9 +161,13 @@
@@ -161,9 +161,13 @@
#' mo_info("E. coli")
#' }
mo_name<-function(x,language=get_locale(),...){
if (missing(x)){
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
shortnames[shortnames%like%"S. group [ABCDFGHK]"]<-paste0("G",gsub("S. group ([ABCDFGHK])","\\1",shortnames[shortnames%like%"S. group [ABCDFGHK]"]),"S")
#' User-defined reference data set for microorganisms
#'
#' @description These functions can be used to predefine your own reference to be used in [as.mo()] and consequently all `mo_*` functions like [mo_genus()] and [mo_gramstain()].
#' @description These functions can be used to predefine your own reference to be used in [as.mo()] and consequently all [`mo_*`][mo_property()] functions (such as [mo_genus()] and [mo_gramstain()]).
#'
#' This is **the fastest way** to have your organisation (or analysis) specific codes picked up and translated by this package.
#' This is **the fastest way** to have your organisation (or analysis) specific codes picked up and translated by this package, since you don't have to bother about it again after setting it up once.
#' @inheritSection lifecycle Stable lifecycle
#' @param path location of your reference file, see Details. Can be `""`, `NULL` or `FALSE` to delete the reference file.
#' @param destination destination of the compressed data file, default to the user's home directory.
@ -103,7 +103,7 @@
@@ -103,7 +103,7 @@
#' ```
#' as.mo("lab_mo_ecoli")
#' #> NOTE: Updated mo_source file '/Users/me/mo_source.rds' (0.3 kB) from
#' If the original Excel file is moved or deleted, the mo_source file will be removed upon the next use of [as.mo()].
#' If the original file (in the previous case an Excel file) is moved or deleted, the `mo_source.rds` file will be removed upon the next use of [as.mo()] or any [`mo_*`][mo_property()] function.
if (isTRUE(add_intrinsic_resistance)&is_intrinsic_r){
if (!guideline_coerced%like%"EUCAST"){
warning_("Using 'add_intrinsic_resistance' is only useful when using EUCAST guidelines, since the rules for intrinsic resistance are based on EUCAST.",call=FALSE)
if (message_not_thrown_before("as.rsi2")){
warning_("Using 'add_intrinsic_resistance' is only useful when using EUCAST guidelines, since the rules for intrinsic resistance are based on EUCAST.",call=FALSE)
warning_("Found intrinsic resistance in some bug/drug combinations, although it was not applied.\nUse `as.rsi(..., add_intrinsic_resistance = TRUE)` to apply it.",call=FALSE)
if (message_not_thrown_before("as.rsi3")){
warning_("Found intrinsic resistance in some bug/drug combinations, although it was not applied.\nUse `as.rsi(..., add_intrinsic_resistance = TRUE)` to apply it.",call=FALSE)
<spanclass="version label label-default"data-toggle="tooltip"data-placement="bottom"title="Latest development version">1.4.0.9043</span>
<spanclass="version label label-default"data-toggle="tooltip"data-placement="bottom"title="Latest development version">1.4.0.9044</span>
</span>
</div>
@ -235,7 +205,6 @@
@@ -235,7 +205,6 @@
</li>
</ul>
<ulclass="nav navbar-nav navbar-right">
<li>
<ahref="https://github.com/msberends/AMR">
<spanclass="fab fa-github"></span>
@ -286,7 +255,7 @@ Content not found. Please use links in the navbar.
@@ -286,7 +255,7 @@ Content not found. Please use links in the navbar.
</div>
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