mirror of https://github.com/msberends/AMR.git
(v0.6.1.9050) support staged install
This commit is contained in:
parent
a665612cb8
commit
2667fff8a7
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@ -20,4 +20,4 @@
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^Meta$
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^pkgdown$
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^public$
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^reproduction.*R$
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^data-raw$
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 0.6.1.9049
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Date: 2019-05-31
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Version: 0.6.1.9050
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Date: 2019-06-01
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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person(
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@ -70,5 +70,4 @@ BugReports: https://gitlab.com/msberends/AMR/issues
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License: GPL-2 | file LICENSE
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Encoding: UTF-8
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LazyData: true
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StagedInstall: false
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RoxygenNote: 6.1.1
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@ -92,7 +92,6 @@ export(count_all)
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export(count_df)
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export(eucast_exceptional_phenotypes)
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export(eucast_rules)
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export(eucast_rules_file)
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export(facet_rsi)
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export(filter_1st_cephalosporins)
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export(filter_2nd_cephalosporins)
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13
NEWS.md
13
NEWS.md
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@ -17,11 +17,8 @@
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* All references to antibiotics in our package now use EARS-Net codes, like `AMX` for amoxicillin
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* Functions `atc_certe`, `ab_umcg` and `atc_trivial_nl` have been removed
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* All `atc_*` functions are superceded by `ab_*` functions
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* All output will be translated by using an included, local translation file that can be found after install with:
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```r
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system.file("translations.tsv", package = "AMR")
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```
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Please create an issue in one of our repositories if you want additions in this file.
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* All output will be translated by using an included translation file which [can be viewed here](https://gitlab.com/msberends/AMR/blob/master/data-raw/translations.tsv)
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Please [create an issue in one of our repositories](https://gitlab.com/msberends/AMR/issues/new?issue[title]=Translation%20suggestion) if you want additions in this file.
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* Improvements to plotting AMR results with `ggplot_rsi()`:
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* New parameter `colours` to set the bar colours
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* New parameters `title`, `subtitle`, `caption`, `x.title` and `y.title` to set titles and axis descriptions
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@ -44,7 +41,8 @@
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freq(age) %>%
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boxplot()
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```
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* Removed all hardcoded EUCAST rules and replaced them with a new reference file: `./inst/eucast/eucast.tsv`
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* Removed all hardcoded EUCAST rules and replaced them with a new reference file which [can be viewed here](https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv)
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Please [create an issue in one of our repositories](https://gitlab.com/msberends/AMR/issues/new?issue[title]=EUCAST%20edit) if you want changes in this file.
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* Added ceftazidim intrinsic resistance to *Streptococci*
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* Changed default settings for `age_groups()`, to let groups of fives and tens end with 100+ instead of 120+
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* Fix for `freq()` for when all values are `NA`
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@ -56,8 +54,7 @@
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* Fix for `mo_shortname()` where species would not be determined correctly
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#### Other
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* Support for R 3.6.0
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* Prevented [staged install](https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html) in R 3.6.0 and later by adding `StagedInstall: false` to the DESCRIPTION file
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* Support for R 3.6.0 and later by providing support for [staged install](https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html)
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# AMR 0.6.1
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@ -20,7 +20,6 @@
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# ==================================================================== #
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# global variables
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EUCAST_RULES_FILE_LOCATION <- system.file("eucast/eucast_rules.tsv", package = "AMR")
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EUCAST_VERSION_BREAKPOINTS <- "9.0, 2019"
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EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
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@ -37,10 +36,7 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
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#' \strong{Note:} This function does not translate MIC values to RSI values. Use \code{\link{as.rsi}} for that. \cr
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#' \strong{Note:} When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance.
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#'
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#' The file used for applying all EUCAST rules can be retrieved with \code{\link{eucast_rules_file}()}. It returns an easily readable data set containing all rules. The original TSV file (tab separated file) that is being read by \code{eucast_rules()} can be found by running this command: \cr
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#' \code{AMR::EUCAST_RULES_FILE_LOCATION} (without brackets).
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#'
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#' In the source code the file containing all rules is located \href{https://gitlab.com/msberends/AMR/blob/master/inst/eucast/eucast_rules.tsv}{here}.
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#' The file containing all EUCAST rules is located here: \url{https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv}.
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#'
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#' @section Antibiotics:
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#' To define antibiotics column names, leave as it is to determine it automatically with \code{\link{guess_ab_col}} or input a text (case-insensitive), or use \code{NULL} to skip a column (e.g. \code{TIC = NULL} to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.
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@ -141,8 +137,6 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016"
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#' \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx}
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#' }
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#' }
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#'
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#' For editing the reference file (which is available with \code{\link{eucast_rules_file}}), these values can all be used for target antibiotics: aminoglycosides, tetracyclines, polymyxins, macrolides, glycopeptides, streptogramins, cephalosporins, cephalosporins_without_cfta, carbapenems, aminopenicillins, ureidopenicillins, fluoroquinolones, all_betalactams, and all separate four letter codes like AMC. They can be separated by comma: \code{"AMC, fluoroquinolones"}. The mo_property can be any column name from the \code{\link{microorganisms}} data set, or \code{genus_species} or \code{gramstain}. This file contains references to the 'Burkholderia cepacia complex'. The species in this group can be found in: LiPuma JJ, 2015 (PMID 16217180).
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#' @inheritSection AMR Read more on our website!
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#' @examples
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#' a <- eucast_rules(septic_patients)
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@ -499,7 +493,7 @@ eucast_rules <- function(x,
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y[y != "" & y %in% colnames(df)]
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}
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eucast_rules_df <- eucast_rules_file()
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eucast_rules_df <- eucast_rules_file # internal data file
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no_of_changes <- 0
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for (i in 1:nrow(eucast_rules_df)) {
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@ -754,16 +748,3 @@ eucast_rules <- function(x,
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}
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}
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#' @rdname eucast_rules
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#' @importFrom dplyr %>% arrange
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#' @export
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eucast_rules_file <- function() {
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utils::read.delim(file = EUCAST_RULES_FILE_LOCATION,
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sep = "\t",
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stringsAsFactors = FALSE,
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header = TRUE,
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strip.white = TRUE,
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na = c(NA, "", NULL)) %>%
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arrange(reference.rule_group,
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reference.rule)
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}
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#' Translate strings from AMR package
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#'
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#' For language-dependent output of AMR functions, like \code{\link{mo_fullname}} and \code{\link{mo_type}}.
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#' @details Strings will be translated to foreign languages if they are defined in a local translation file. This file comes with this package and can be found when running:
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#' @details Strings will be translated to foreign languages if they are defined in a local translation file. Additions to this file can be suggested at our repository. The file can be found here: \url{https://gitlab.com/msberends/AMR/blob/master/data-raw/translations.tsv}.
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#'
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#' \code{system.file("translations.tsv", package = "AMR")}
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#' Please suggest your own translations \href{https://gitlab.com/msberends/AMR/issues/new?issue[title]=Translation\%20suggestion}{by creating a new issue on our repository}.
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#'
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#' This file will be read by all functions where a translated output can be desired, like all \code{\link{mo_property}} functions (\code{\link{mo_fullname}}, \code{\link{mo_type}}, etc.). Please suggest your own translations \href{https://gitlab.com/msberends/AMR/issues/new?issue[title]=Translation\%20suggestion}{by creating a new issue on our repository}.
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#' This file will be read by all functions where a translated output can be desired, like all \code{\link{mo_property}} functions (\code{\link{mo_fullname}}, \code{\link{mo_type}}, etc.).
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#'
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#' The system language will be used at default, if supported, using \code{\link{get_locale}}. The system language can be overwritten with \code{\link{getOption}("AMR_locale")}.
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#' @inheritSection AMR Read more on our website!
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18
R/misc.R
18
R/misc.R
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@ -243,9 +243,10 @@ generate_warning_abs_missing <- function(missing, any = FALSE) {
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stopifnot_installed_package <- function(package) {
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if (!package %in% base::rownames(utils::installed.packages())) {
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stop("this function requires the ", package, " package.", call. = FALSE)
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}
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# no "utils::installed.packages()" since it requires non-staged install since R 3.6.0
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# https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html
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get(".packageName", envir = asNamespace(package))
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return(invisible())
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}
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# translate strings based on inst/translations.tsv
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@ -262,16 +263,7 @@ t <- function(from, language = get_locale()) {
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return(from)
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}
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df_trans <- utils::read.table(file = system.file("translations.tsv", package = "AMR"),
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sep = "\t",
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stringsAsFactors = FALSE,
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header = TRUE,
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blank.lines.skip = TRUE,
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fill = TRUE,
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strip.white = TRUE,
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encoding = "UTF-8",
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fileEncoding = "UTF-8",
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na.strings = c(NA, "", NULL))
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df_trans <- translations_file # internal data file
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if (!language %in% df_trans$lang) {
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stop("Unsupported language: '", language, "' - use one of: ",
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4
R/mo.R
4
R/mo.R
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@ -191,7 +191,7 @@
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#' }
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as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE, reference_df = get_mo_source(), ...) {
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if (!"AMR" %in% base::.packages()) {
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library("AMR")
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require("AMR")
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# check onLoad() in R/zzz.R: data tables are created there.
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}
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@ -295,7 +295,7 @@ exec_as.mo <- function(x,
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debug = FALSE) {
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if (!"AMR" %in% base::.packages()) {
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library("AMR")
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require("AMR")
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# check onLoad() in R/zzz.R: data tables are created there.
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}
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@ -364,7 +364,7 @@ mo_validate <- function(x, property, ...) {
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}
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if (!"AMR" %in% base::.packages()) {
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library("AMR")
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require("AMR")
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# check onLoad() in R/zzz.R: data tables are created there.
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}
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Binary file not shown.
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@ -0,0 +1,40 @@
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# EUCAST rules ----
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# For editing the reference file, these values can all be used for target antibiotics:
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# "aminoglycosides", "tetracyclines", "polymyxins", "macrolides", "glycopeptides",
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# "streptogramins", "cephalosporins", "cephalosporins_without_CAZ", "carbapenems",
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# "minopenicillins", "ureidopenicillins", "fluoroquinolones", "all_betalactams",
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# and all separate EARS-Net letter codes like "AMC". They can be separated by comma: "AMC, fluoroquinolones".
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# The mo_property can be any column name from the AMR::microorganisms data set, or "genus_species" or "gramstain".
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# This file contains references to the 'Burkholderia cepacia complex'. The species in this group can be found in:
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# LiPuma JJ, 2015 (PMID 16217180).
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eucast_rules_file <- dplyr::arrange(
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.data = utils::read.delim(file = "data-raw/eucast_rules.tsv",
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sep = "\t",
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stringsAsFactors = FALSE,
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header = TRUE,
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strip.white = TRUE,
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na = c(NA, "", NULL)),
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reference.rule_group,
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reference.rule)
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# Translations -----
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translations_file <- utils::read.table(file = "data-raw/translations.tsv",
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sep = "\t",
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stringsAsFactors = FALSE,
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header = TRUE,
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blank.lines.skip = TRUE,
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fill = TRUE,
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strip.white = TRUE,
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encoding = "UTF-8",
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fileEncoding = "UTF-8",
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na.strings = c(NA, "", NULL))
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# Export to package as internal data ----
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usethis::use_data(eucast_rules_file, translations_file,
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internal = TRUE,
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overwrite = TRUE,
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version = 2)
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# Remove from global environment ----
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rm(eucast_rules_file)
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rm(translations_file)
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@ -78,7 +78,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9049</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
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</span>
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</div>
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@ -78,7 +78,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9049</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
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</span>
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</div>
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|
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@ -78,7 +78,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
|
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9049</span>
|
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
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</span>
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</div>
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|
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@ -42,7 +42,7 @@
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</button>
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<span class="navbar-brand">
|
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<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9049</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
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</span>
|
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</div>
|
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|
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|
|
|
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|
|
@ -78,7 +78,7 @@
|
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</button>
|
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<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9049</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
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</span>
|
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</div>
|
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@ -272,10 +272,7 @@
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<li>All references to antibiotics in our package now use EARS-Net codes, like <code>AMX</code> for amoxicillin</li>
|
||||
<li>Functions <code>atc_certe</code>, <code>ab_umcg</code> and <code>atc_trivial_nl</code> have been removed</li>
|
||||
<li>All <code>atc_*</code> functions are superceded by <code>ab_*</code> functions</li>
|
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<li>
|
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<p>All output will be translated by using an included, local translation file that can be found after install with:</p>
|
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<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.file">system.file</a></span>(<span class="st">"translations.tsv"</span>, <span class="dt">package =</span> <span class="st">"AMR"</span>)</a></code></pre></div>
|
||||
Please create an issue in one of our repositories if you want additions in this file.</li>
|
||||
<li>All output will be translated by using an included translation file which <a href="https://gitlab.com/msberends/AMR/blob/master/data-raw/translations.tsv">can be viewed here</a> Please <a href="https://gitlab.com/msberends/AMR/issues/new?issue%5Btitle%5D=Translation%20suggestion">create an issue in one of our repositories</a> if you want additions in this file.</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>Improvements to plotting AMR results with <code><a href="../reference/ggplot_rsi.html">ggplot_rsi()</a></code>:
|
||||
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|
@ -297,19 +294,18 @@ Please create an issue in one of our repositories if you want additions in this
|
|||
<li>fixed level names in markdown</li>
|
||||
<li>
|
||||
<p>support for boxplots:</p>
|
||||
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb2-2" title="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb2-3" title="3"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/boxplot">boxplot</a></span>()</a>
|
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<a class="sourceLine" id="cb2-4" title="4"><span class="co"># grouped boxplots:</span></a>
|
||||
<a class="sourceLine" id="cb2-5" title="5">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb2-6" title="6"><span class="st"> </span><span class="kw">group_by</span>(hospital_id) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb2-7" title="7"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age) <span class="op">%>%</span></a>
|
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<a class="sourceLine" id="cb2-8" title="8"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/boxplot">boxplot</a></span>()</a></code></pre></div>
|
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<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb1-2" title="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb1-3" title="3"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/boxplot">boxplot</a></span>()</a>
|
||||
<a class="sourceLine" id="cb1-4" title="4"><span class="co"># grouped boxplots:</span></a>
|
||||
<a class="sourceLine" id="cb1-5" title="5">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb1-6" title="6"><span class="st"> </span><span class="kw">group_by</span>(hospital_id) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb1-7" title="7"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age) <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb1-8" title="8"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/boxplot">boxplot</a></span>()</a></code></pre></div>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>Removed all hardcoded EUCAST rules and replaced them with a new reference file: <code>./inst/eucast/eucast.tsv</code>
|
||||
</li>
|
||||
<li>Removed all hardcoded EUCAST rules and replaced them with a new reference file which <a href="https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv">can be viewed here</a> Please <a href="https://gitlab.com/msberends/AMR/issues/new?issue%5Btitle%5D=EUCAST%20edit">create an issue in one of our repositories</a> if you want changes in this file.</li>
|
||||
<li>Added ceftazidim intrinsic resistance to <em>Streptococci</em>
|
||||
</li>
|
||||
<li>Changed default settings for <code><a href="../reference/age_groups.html">age_groups()</a></code>, to let groups of fives and tens end with 100+ instead of 120+</li>
|
||||
|
|
@ -329,8 +325,8 @@ Please create an issue in one of our repositories if you want additions in this
|
|||
<h4 class="hasAnchor">
|
||||
<a href="#other" class="anchor"></a>Other</h4>
|
||||
<ul>
|
||||
<li>Support for R 3.6.0</li>
|
||||
<li>Prevented <a href="https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html">staged install</a> in R 3.6.0 and later by adding <code>StagedInstall: false</code> to the DESCRIPTION file</li>
|
||||
<li>Support for R 3.6.0 and later by providing support for <a href="https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html">staged install</a>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
|
|
@ -387,32 +383,32 @@ This data is updated annually - check the included version with the new function
|
|||
</li>
|
||||
<li>
|
||||
<p>New filters for antimicrobial classes. Use these functions to filter isolates on results in one of more antibiotics from a specific class:</p>
|
||||
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1"><span class="kw"><a href="../reference/filter_ab_class.html">filter_aminoglycosides</a></span>()</a>
|
||||
<a class="sourceLine" id="cb3-2" title="2"><span class="kw"><a href="../reference/filter_ab_class.html">filter_carbapenems</a></span>()</a>
|
||||
<a class="sourceLine" id="cb3-3" title="3"><span class="kw"><a href="../reference/filter_ab_class.html">filter_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb3-4" title="4"><span class="kw"><a href="../reference/filter_ab_class.html">filter_1st_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb3-5" title="5"><span class="kw"><a href="../reference/filter_ab_class.html">filter_2nd_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb3-6" title="6"><span class="kw"><a href="../reference/filter_ab_class.html">filter_3rd_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb3-7" title="7"><span class="kw"><a href="../reference/filter_ab_class.html">filter_4th_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb3-8" title="8"><span class="kw"><a href="../reference/filter_ab_class.html">filter_fluoroquinolones</a></span>()</a>
|
||||
<a class="sourceLine" id="cb3-9" title="9"><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>()</a>
|
||||
<a class="sourceLine" id="cb3-10" title="10"><span class="kw"><a href="../reference/filter_ab_class.html">filter_macrolides</a></span>()</a>
|
||||
<a class="sourceLine" id="cb3-11" title="11"><span class="kw"><a href="../reference/filter_ab_class.html">filter_tetracyclines</a></span>()</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1"><span class="kw"><a href="../reference/filter_ab_class.html">filter_aminoglycosides</a></span>()</a>
|
||||
<a class="sourceLine" id="cb2-2" title="2"><span class="kw"><a href="../reference/filter_ab_class.html">filter_carbapenems</a></span>()</a>
|
||||
<a class="sourceLine" id="cb2-3" title="3"><span class="kw"><a href="../reference/filter_ab_class.html">filter_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb2-4" title="4"><span class="kw"><a href="../reference/filter_ab_class.html">filter_1st_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb2-5" title="5"><span class="kw"><a href="../reference/filter_ab_class.html">filter_2nd_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb2-6" title="6"><span class="kw"><a href="../reference/filter_ab_class.html">filter_3rd_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb2-7" title="7"><span class="kw"><a href="../reference/filter_ab_class.html">filter_4th_cephalosporins</a></span>()</a>
|
||||
<a class="sourceLine" id="cb2-8" title="8"><span class="kw"><a href="../reference/filter_ab_class.html">filter_fluoroquinolones</a></span>()</a>
|
||||
<a class="sourceLine" id="cb2-9" title="9"><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>()</a>
|
||||
<a class="sourceLine" id="cb2-10" title="10"><span class="kw"><a href="../reference/filter_ab_class.html">filter_macrolides</a></span>()</a>
|
||||
<a class="sourceLine" id="cb2-11" title="11"><span class="kw"><a href="../reference/filter_ab_class.html">filter_tetracyclines</a></span>()</a></code></pre></div>
|
||||
<p>The <code>antibiotics</code> data set will be searched, after which the input data will be checked for column names with a value in any abbreviations, codes or official names found in the <code>antibiotics</code> data set. For example:</p>
|
||||
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="dt">result =</span> <span class="st">"R"</span>)</a>
|
||||
<a class="sourceLine" id="cb4-2" title="2"><span class="co"># Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R</span></a>
|
||||
<a class="sourceLine" id="cb4-3" title="3">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="dt">result =</span> <span class="st">"R"</span>, <span class="dt">scope =</span> <span class="st">"all"</span>)</a>
|
||||
<a class="sourceLine" id="cb4-4" title="4"><span class="co"># Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="dt">result =</span> <span class="st">"R"</span>)</a>
|
||||
<a class="sourceLine" id="cb3-2" title="2"><span class="co"># Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R</span></a>
|
||||
<a class="sourceLine" id="cb3-3" title="3">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="dt">result =</span> <span class="st">"R"</span>, <span class="dt">scope =</span> <span class="st">"all"</span>)</a>
|
||||
<a class="sourceLine" id="cb3-4" title="4"><span class="co"># Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R</span></a></code></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>All <code>ab_*</code> functions are deprecated and replaced by <code>atc_*</code> functions:</p>
|
||||
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1">ab_property -><span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_property</a></span>()</a>
|
||||
<a class="sourceLine" id="cb5-2" title="2">ab_name -><span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_name</a></span>()</a>
|
||||
<a class="sourceLine" id="cb5-3" title="3">ab_official -><span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_official</a></span>()</a>
|
||||
<a class="sourceLine" id="cb5-4" title="4">ab_trivial_nl -><span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_trivial_nl</a></span>()</a>
|
||||
<a class="sourceLine" id="cb5-5" title="5">ab_certe -><span class="st"> </span><span class="kw">atc_certe</span>()</a>
|
||||
<a class="sourceLine" id="cb5-6" title="6">ab_umcg -><span class="st"> </span><span class="kw">atc_umcg</span>()</a>
|
||||
<a class="sourceLine" id="cb5-7" title="7">ab_tradenames -><span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_tradenames</a></span>()</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1">ab_property -><span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_property</a></span>()</a>
|
||||
<a class="sourceLine" id="cb4-2" title="2">ab_name -><span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_name</a></span>()</a>
|
||||
<a class="sourceLine" id="cb4-3" title="3">ab_official -><span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_official</a></span>()</a>
|
||||
<a class="sourceLine" id="cb4-4" title="4">ab_trivial_nl -><span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_trivial_nl</a></span>()</a>
|
||||
<a class="sourceLine" id="cb4-5" title="5">ab_certe -><span class="st"> </span><span class="kw">atc_certe</span>()</a>
|
||||
<a class="sourceLine" id="cb4-6" title="6">ab_umcg -><span class="st"> </span><span class="kw">atc_umcg</span>()</a>
|
||||
<a class="sourceLine" id="cb4-7" title="7">ab_tradenames -><span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_tradenames</a></span>()</a></code></pre></div>
|
||||
These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code> internally. The old <code>atc_property</code> has been renamed <code><a href="../reference/atc_online.html">atc_online_property()</a></code>. This is done for two reasons: firstly, not all ATC codes are of antibiotics (ab) but can also be of antivirals or antifungals. Secondly, the input must have class <code>atc</code> or must be coerable to this class. Properties of these classes should start with the same class name, analogous to <code><a href="../reference/as.mo.html">as.mo()</a></code> and e.g. <code>mo_genus</code>.</li>
|
||||
<li>New functions <code><a href="../reference/mo_source.html">set_mo_source()</a></code> and <code><a href="../reference/mo_source.html">get_mo_source()</a></code> to use your own predefined MO codes as input for <code><a href="../reference/as.mo.html">as.mo()</a></code> and consequently all <code>mo_*</code> functions</li>
|
||||
<li>Support for the upcoming <a href="https://dplyr.tidyverse.org"><code>dplyr</code></a> version 0.8.0</li>
|
||||
|
|
@ -424,20 +420,20 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
|
|||
<li>New function <code><a href="../reference/age_groups.html">age_groups()</a></code> to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic antimicrobial resistance analysis per age group.</li>
|
||||
<li>
|
||||
<p>New function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> as well as the base R <code><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot()</a></code> function can now be used for resistance prediction calculated with <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>:</p>
|
||||
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1">x <-<span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(septic_patients, <span class="dt">col_ab =</span> <span class="st">"amox"</span>)</a>
|
||||
<a class="sourceLine" id="cb6-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(x)</a>
|
||||
<a class="sourceLine" id="cb6-3" title="3"><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(x)</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1">x <-<span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(septic_patients, <span class="dt">col_ab =</span> <span class="st">"amox"</span>)</a>
|
||||
<a class="sourceLine" id="cb5-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(x)</a>
|
||||
<a class="sourceLine" id="cb5-3" title="3"><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(x)</a></code></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Functions <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> and <code><a href="../reference/first_isolate.html">filter_first_weighted_isolate()</a></code> to shorten and fasten filtering on data sets with antimicrobial results, e.g.:</p>
|
||||
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(...)</a>
|
||||
<a class="sourceLine" id="cb7-2" title="2"><span class="co"># or</span></a>
|
||||
<a class="sourceLine" id="cb7-3" title="3"><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(septic_patients, ...)</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(...)</a>
|
||||
<a class="sourceLine" id="cb6-2" title="2"><span class="co"># or</span></a>
|
||||
<a class="sourceLine" id="cb6-3" title="3"><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(septic_patients, ...)</a></code></pre></div>
|
||||
<p>is equal to:</p>
|
||||
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1">septic_patients <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb8-2" title="2"><span class="st"> </span><span class="kw">mutate</span>(<span class="dt">only_firsts =</span> <span class="kw"><a href="../reference/first_isolate.html">first_isolate</a></span>(septic_patients, ...)) <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb8-3" title="3"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/stats/topics/filter">filter</a></span>(only_firsts <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>) <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb8-4" title="4"><span class="st"> </span><span class="kw">select</span>(<span class="op">-</span>only_firsts)</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1">septic_patients <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb7-2" title="2"><span class="st"> </span><span class="kw">mutate</span>(<span class="dt">only_firsts =</span> <span class="kw"><a href="../reference/first_isolate.html">first_isolate</a></span>(septic_patients, ...)) <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb7-3" title="3"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/stats/topics/filter">filter</a></span>(only_firsts <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>) <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb7-4" title="4"><span class="st"> </span><span class="kw">select</span>(<span class="op">-</span>only_firsts)</a></code></pre></div>
|
||||
</li>
|
||||
<li>New function <code><a href="../reference/availability.html">availability()</a></code> to check the number of available (non-empty) results in a <code>data.frame</code>
|
||||
</li>
|
||||
|
|
@ -466,33 +462,33 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
|
|||
<ul>
|
||||
<li>
|
||||
<p>Now handles incorrect spelling, like <code>i</code> instead of <code>y</code> and <code>f</code> instead of <code>ph</code>:</p>
|
||||
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1"><span class="co"># mo_fullname() uses as.mo() internally</span></a>
|
||||
<a class="sourceLine" id="cb9-2" title="2"></a>
|
||||
<a class="sourceLine" id="cb9-3" title="3"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Sthafilokockus aaureuz"</span>)</a>
|
||||
<a class="sourceLine" id="cb9-4" title="4"><span class="co">#> [1] "Staphylococcus aureus"</span></a>
|
||||
<a class="sourceLine" id="cb9-5" title="5"></a>
|
||||
<a class="sourceLine" id="cb9-6" title="6"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. klossi"</span>)</a>
|
||||
<a class="sourceLine" id="cb9-7" title="7"><span class="co">#> [1] "Staphylococcus kloosii"</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1"><span class="co"># mo_fullname() uses as.mo() internally</span></a>
|
||||
<a class="sourceLine" id="cb8-2" title="2"></a>
|
||||
<a class="sourceLine" id="cb8-3" title="3"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Sthafilokockus aaureuz"</span>)</a>
|
||||
<a class="sourceLine" id="cb8-4" title="4"><span class="co">#> [1] "Staphylococcus aureus"</span></a>
|
||||
<a class="sourceLine" id="cb8-5" title="5"></a>
|
||||
<a class="sourceLine" id="cb8-6" title="6"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. klossi"</span>)</a>
|
||||
<a class="sourceLine" id="cb8-7" title="7"><span class="co">#> [1] "Staphylococcus kloosii"</span></a></code></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Uncertainty of the algorithm is now divided into four levels, 0 to 3, where the default <code>allow_uncertain = TRUE</code> is equal to uncertainty level 2. Run <code><a href="../reference/as.mo.html">?as.mo</a></code> for more info about these levels.</p>
|
||||
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1"><span class="co"># equal:</span></a>
|
||||
<a class="sourceLine" id="cb10-2" title="2"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="ot">TRUE</span>)</a>
|
||||
<a class="sourceLine" id="cb10-3" title="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="dv">2</span>)</a>
|
||||
<a class="sourceLine" id="cb10-4" title="4"></a>
|
||||
<a class="sourceLine" id="cb10-5" title="5"><span class="co"># also equal:</span></a>
|
||||
<a class="sourceLine" id="cb10-6" title="6"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="ot">FALSE</span>)</a>
|
||||
<a class="sourceLine" id="cb10-7" title="7"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="dv">0</span>)</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1"><span class="co"># equal:</span></a>
|
||||
<a class="sourceLine" id="cb9-2" title="2"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="ot">TRUE</span>)</a>
|
||||
<a class="sourceLine" id="cb9-3" title="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="dv">2</span>)</a>
|
||||
<a class="sourceLine" id="cb9-4" title="4"></a>
|
||||
<a class="sourceLine" id="cb9-5" title="5"><span class="co"># also equal:</span></a>
|
||||
<a class="sourceLine" id="cb9-6" title="6"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="ot">FALSE</span>)</a>
|
||||
<a class="sourceLine" id="cb9-7" title="7"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="dv">0</span>)</a></code></pre></div>
|
||||
Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a></code> could lead to very unreliable results.</li>
|
||||
<li>Implemented the latest publication of Becker <em>et al.</em> (2019), for categorising coagulase-negative <em>Staphylococci</em>
|
||||
</li>
|
||||
<li>All microbial IDs that found are now saved to a local file <code>~/.Rhistory_mo</code>. Use the new function <code>clean_mo_history()</code> to delete this file, which resets the algorithms.</li>
|
||||
<li>
|
||||
<p>Incoercible results will now be considered ‘unknown’, MO code <code>UNKNOWN</code>. On foreign systems, properties of these will be translated to all languages already previously supported: German, Dutch, French, Italian, Spanish and Portuguese:</p>
|
||||
<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"qwerty"</span>, <span class="dt">language =</span> <span class="st">"es"</span>)</a>
|
||||
<a class="sourceLine" id="cb11-2" title="2"><span class="co"># Warning: </span></a>
|
||||
<a class="sourceLine" id="cb11-3" title="3"><span class="co"># one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it.</span></a>
|
||||
<a class="sourceLine" id="cb11-4" title="4"><span class="co">#> [1] "(género desconocido)"</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"qwerty"</span>, <span class="dt">language =</span> <span class="st">"es"</span>)</a>
|
||||
<a class="sourceLine" id="cb10-2" title="2"><span class="co"># Warning: </span></a>
|
||||
<a class="sourceLine" id="cb10-3" title="3"><span class="co"># one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it.</span></a>
|
||||
<a class="sourceLine" id="cb10-4" title="4"><span class="co">#> [1] "(género desconocido)"</span></a></code></pre></div>
|
||||
</li>
|
||||
<li>Fix for vector containing only empty values</li>
|
||||
<li>Finds better results when input is in other languages</li>
|
||||
|
|
@ -538,19 +534,19 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
|||
<ul>
|
||||
<li>
|
||||
<p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
|
||||
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" title="1"><span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span></a>
|
||||
<a class="sourceLine" id="cb12-2" title="2"><span class="co"># OLD WAY</span></a>
|
||||
<a class="sourceLine" id="cb12-3" title="3">septic_patients <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb12-4" title="4"><span class="st"> </span><span class="kw">mutate</span>(<span class="dt">genus =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo)) <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb12-5" title="5"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(genus)</a>
|
||||
<a class="sourceLine" id="cb12-6" title="6"><span class="co"># NEW WAY</span></a>
|
||||
<a class="sourceLine" id="cb12-7" title="7">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb12-8" title="8"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a>
|
||||
<a class="sourceLine" id="cb12-9" title="9"></a>
|
||||
<a class="sourceLine" id="cb12-10" title="10"><span class="co"># Even supports grouping variables:</span></a>
|
||||
<a class="sourceLine" id="cb12-11" title="11">septic_patients <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb12-12" title="12"><span class="st"> </span><span class="kw">group_by</span>(gender) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb12-13" title="13"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="1"><span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span></a>
|
||||
<a class="sourceLine" id="cb11-2" title="2"><span class="co"># OLD WAY</span></a>
|
||||
<a class="sourceLine" id="cb11-3" title="3">septic_patients <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb11-4" title="4"><span class="st"> </span><span class="kw">mutate</span>(<span class="dt">genus =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo)) <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb11-5" title="5"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(genus)</a>
|
||||
<a class="sourceLine" id="cb11-6" title="6"><span class="co"># NEW WAY</span></a>
|
||||
<a class="sourceLine" id="cb11-7" title="7">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb11-8" title="8"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a>
|
||||
<a class="sourceLine" id="cb11-9" title="9"></a>
|
||||
<a class="sourceLine" id="cb11-10" title="10"><span class="co"># Even supports grouping variables:</span></a>
|
||||
<a class="sourceLine" id="cb11-11" title="11">septic_patients <span class="op">%>%</span></a>
|
||||
<a class="sourceLine" id="cb11-12" title="12"><span class="st"> </span><span class="kw">group_by</span>(gender) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb11-13" title="13"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a></code></pre></div>
|
||||
</li>
|
||||
<li>Header info is now available as a list, with the <code>header</code> function</li>
|
||||
<li>The parameter <code>header</code> is now set to <code>TRUE</code> at default, even for markdown</li>
|
||||
|
|
@ -625,10 +621,10 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
|||
<li>Fewer than 3 characters as input for <code>as.mo</code> will return NA</li>
|
||||
<li>
|
||||
<p>Function <code>as.mo</code> (and all <code>mo_*</code> wrappers) now supports genus abbreviations with “species” attached</p>
|
||||
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" title="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. species"</span>) <span class="co"># B_ESCHR</span></a>
|
||||
<a class="sourceLine" id="cb13-2" title="2"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"E. spp."</span>) <span class="co"># "Escherichia species"</span></a>
|
||||
<a class="sourceLine" id="cb13-3" title="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. spp"</span>) <span class="co"># B_STPHY</span></a>
|
||||
<a class="sourceLine" id="cb13-4" title="4"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. species"</span>) <span class="co"># "Staphylococcus species"</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" title="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. species"</span>) <span class="co"># B_ESCHR</span></a>
|
||||
<a class="sourceLine" id="cb12-2" title="2"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"E. spp."</span>) <span class="co"># "Escherichia species"</span></a>
|
||||
<a class="sourceLine" id="cb12-3" title="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. spp"</span>) <span class="co"># B_STPHY</span></a>
|
||||
<a class="sourceLine" id="cb12-4" title="4"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. species"</span>) <span class="co"># "Staphylococcus species"</span></a></code></pre></div>
|
||||
</li>
|
||||
<li>Added parameter <code>combine_IR</code> (TRUE/FALSE) to functions <code>portion_df</code> and <code>count_df</code>, to indicate that all values of I and R must be merged into one, so the output only consists of S vs. IR (susceptible vs. non-susceptible)</li>
|
||||
<li>Fix for <code>portion_*(..., as_percent = TRUE)</code> when minimal number of isolates would not be met</li>
|
||||
|
|
@ -641,15 +637,15 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
|||
<ul>
|
||||
<li>
|
||||
<p>Support for grouping variables, test with:</p>
|
||||
<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb14-2" title="2"><span class="st"> </span><span class="kw">group_by</span>(hospital_id) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb14-3" title="3"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" title="1">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb13-2" title="2"><span class="st"> </span><span class="kw">group_by</span>(hospital_id) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb13-3" title="3"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)</a></code></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Support for (un)selecting columns:</p>
|
||||
<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" title="1">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb15-2" title="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb15-3" title="3"><span class="st"> </span><span class="kw">select</span>(<span class="op">-</span>count, <span class="op">-</span>cum_count) <span class="co"># only get item, percent, cum_percent</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1">septic_patients <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb14-2" title="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb14-3" title="3"><span class="st"> </span><span class="kw">select</span>(<span class="op">-</span>count, <span class="op">-</span>cum_count) <span class="co"># only get item, percent, cum_percent</span></a></code></pre></div>
|
||||
</li>
|
||||
<li>Check for <code><a href="https://www.rdocumentation.org/packages/hms/topics/hms">hms::is.hms</a></code>
|
||||
</li>
|
||||
|
|
@ -729,18 +725,18 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
|||
</li>
|
||||
</ul>
|
||||
<p>They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:</p>
|
||||
<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)</a>
|
||||
<a class="sourceLine" id="cb16-2" title="2"><span class="co"># [1] "Gram negative"</span></a>
|
||||
<a class="sourceLine" id="cb16-3" title="3"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"de"</span>) <span class="co"># German</span></a>
|
||||
<a class="sourceLine" id="cb16-4" title="4"><span class="co"># [1] "Gramnegativ"</span></a>
|
||||
<a class="sourceLine" id="cb16-5" title="5"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"es"</span>) <span class="co"># Spanish</span></a>
|
||||
<a class="sourceLine" id="cb16-6" title="6"><span class="co"># [1] "Gram negativo"</span></a>
|
||||
<a class="sourceLine" id="cb16-7" title="7"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. group A"</span>, <span class="dt">language =</span> <span class="st">"pt"</span>) <span class="co"># Portuguese</span></a>
|
||||
<a class="sourceLine" id="cb16-8" title="8"><span class="co"># [1] "Streptococcus grupo A"</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)</a>
|
||||
<a class="sourceLine" id="cb15-2" title="2"><span class="co"># [1] "Gram negative"</span></a>
|
||||
<a class="sourceLine" id="cb15-3" title="3"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"de"</span>) <span class="co"># German</span></a>
|
||||
<a class="sourceLine" id="cb15-4" title="4"><span class="co"># [1] "Gramnegativ"</span></a>
|
||||
<a class="sourceLine" id="cb15-5" title="5"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"es"</span>) <span class="co"># Spanish</span></a>
|
||||
<a class="sourceLine" id="cb15-6" title="6"><span class="co"># [1] "Gram negativo"</span></a>
|
||||
<a class="sourceLine" id="cb15-7" title="7"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. group A"</span>, <span class="dt">language =</span> <span class="st">"pt"</span>) <span class="co"># Portuguese</span></a>
|
||||
<a class="sourceLine" id="cb15-8" title="8"><span class="co"># [1] "Streptococcus grupo A"</span></a></code></pre></div>
|
||||
<p>Furthermore, former taxonomic names will give a note about the current taxonomic name:</p>
|
||||
<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"Esc blattae"</span>)</a>
|
||||
<a class="sourceLine" id="cb17-2" title="2"><span class="co"># Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)</span></a>
|
||||
<a class="sourceLine" id="cb17-3" title="3"><span class="co"># [1] "Gram negative"</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"Esc blattae"</span>)</a>
|
||||
<a class="sourceLine" id="cb16-2" title="2"><span class="co"># Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)</span></a>
|
||||
<a class="sourceLine" id="cb16-3" title="3"><span class="co"># [1] "Gram negative"</span></a></code></pre></div>
|
||||
</li>
|
||||
<li>Functions <code>count_R</code>, <code>count_IR</code>, <code>count_I</code>, <code>count_SI</code> and <code>count_S</code> to selectively count resistant or susceptible isolates
|
||||
<ul>
|
||||
|
|
@ -751,18 +747,18 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
|||
</li>
|
||||
<li>
|
||||
<p>Functions <code>as.mo</code> and <code>is.mo</code> as replacements for <code>as.bactid</code> and <code>is.bactid</code> (since the <code>microoganisms</code> data set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. The <code>as.mo</code> function determines microbial IDs using intelligent rules:</p>
|
||||
<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb18-1" title="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)</a>
|
||||
<a class="sourceLine" id="cb18-2" title="2"><span class="co"># [1] B_ESCHR_COL</span></a>
|
||||
<a class="sourceLine" id="cb18-3" title="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>)</a>
|
||||
<a class="sourceLine" id="cb18-4" title="4"><span class="co"># [1] B_STPHY_AUR</span></a>
|
||||
<a class="sourceLine" id="cb18-5" title="5"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S group A"</span>)</a>
|
||||
<a class="sourceLine" id="cb18-6" title="6"><span class="co"># [1] B_STRPTC_GRA</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)</a>
|
||||
<a class="sourceLine" id="cb17-2" title="2"><span class="co"># [1] B_ESCHR_COL</span></a>
|
||||
<a class="sourceLine" id="cb17-3" title="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>)</a>
|
||||
<a class="sourceLine" id="cb17-4" title="4"><span class="co"># [1] B_STPHY_AUR</span></a>
|
||||
<a class="sourceLine" id="cb17-5" title="5"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S group A"</span>)</a>
|
||||
<a class="sourceLine" id="cb17-6" title="6"><span class="co"># [1] B_STRPTC_GRA</span></a></code></pre></div>
|
||||
<p>And with great speed too - on a quite regular Linux server from 2007 it takes us less than 0.02 seconds to transform 25,000 items:</p>
|
||||
<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" title="1">thousands_of_E_colis <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/rep">rep</a></span>(<span class="st">"E. coli"</span>, <span class="dv">25000</span>)</a>
|
||||
<a class="sourceLine" id="cb19-2" title="2">microbenchmark<span class="op">::</span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(thousands_of_E_colis), <span class="dt">unit =</span> <span class="st">"s"</span>)</a>
|
||||
<a class="sourceLine" id="cb19-3" title="3"><span class="co"># Unit: seconds</span></a>
|
||||
<a class="sourceLine" id="cb19-4" title="4"><span class="co"># min median max neval</span></a>
|
||||
<a class="sourceLine" id="cb19-5" title="5"><span class="co"># 0.01817717 0.01843957 0.03878077 100</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb18-1" title="1">thousands_of_E_colis <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/rep">rep</a></span>(<span class="st">"E. coli"</span>, <span class="dv">25000</span>)</a>
|
||||
<a class="sourceLine" id="cb18-2" title="2">microbenchmark<span class="op">::</span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(thousands_of_E_colis), <span class="dt">unit =</span> <span class="st">"s"</span>)</a>
|
||||
<a class="sourceLine" id="cb18-3" title="3"><span class="co"># Unit: seconds</span></a>
|
||||
<a class="sourceLine" id="cb18-4" title="4"><span class="co"># min median max neval</span></a>
|
||||
<a class="sourceLine" id="cb18-5" title="5"><span class="co"># 0.01817717 0.01843957 0.03878077 100</span></a></code></pre></div>
|
||||
</li>
|
||||
<li>Added parameter <code>reference_df</code> for <code>as.mo</code>, so users can supply their own microbial IDs, name or codes as a reference table</li>
|
||||
<li>Renamed all previous references to <code>bactid</code> to <code>mo</code>, like:
|
||||
|
|
@ -790,12 +786,12 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
|||
<li>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</li>
|
||||
<li>
|
||||
<p>Added 163 trade names to the <code>antibiotics</code> data set, it now contains 298 different trade names in total, e.g.:</p>
|
||||
<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1"><span class="kw"><a href="../reference/AMR-deprecated.html">ab_official</a></span>(<span class="st">"Bactroban"</span>)</a>
|
||||
<a class="sourceLine" id="cb20-2" title="2"><span class="co"># [1] "Mupirocin"</span></a>
|
||||
<a class="sourceLine" id="cb20-3" title="3"><span class="kw"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
|
||||
<a class="sourceLine" id="cb20-4" title="4"><span class="co"># [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"</span></a>
|
||||
<a class="sourceLine" id="cb20-5" title="5"><span class="kw"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
|
||||
<a class="sourceLine" id="cb20-6" title="6"><span class="co"># [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"</span></a></code></pre></div>
|
||||
<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" title="1"><span class="kw"><a href="../reference/AMR-deprecated.html">ab_official</a></span>(<span class="st">"Bactroban"</span>)</a>
|
||||
<a class="sourceLine" id="cb19-2" title="2"><span class="co"># [1] "Mupirocin"</span></a>
|
||||
<a class="sourceLine" id="cb19-3" title="3"><span class="kw"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
|
||||
<a class="sourceLine" id="cb19-4" title="4"><span class="co"># [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"</span></a>
|
||||
<a class="sourceLine" id="cb19-5" title="5"><span class="kw"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
|
||||
<a class="sourceLine" id="cb19-6" title="6"><span class="co"># [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"</span></a></code></pre></div>
|
||||
</li>
|
||||
<li>For <code>first_isolate</code>, rows will be ignored when there’s no species available</li>
|
||||
<li>Function <code>ratio</code> is now deprecated and will be removed in a future release, as it is not really the scope of this package</li>
|
||||
|
|
@ -806,13 +802,13 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
|||
</li>
|
||||
<li>
|
||||
<p>Support for quasiquotation in the functions series <code>count_*</code> and <code>portions_*</code>, and <code>n_rsi</code>. This allows to check for more than 2 vectors or columns.</p>
|
||||
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" title="1">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw">select</span>(amox, cipr) <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>()</a>
|
||||
<a class="sourceLine" id="cb21-2" title="2"><span class="co"># which is the same as:</span></a>
|
||||
<a class="sourceLine" id="cb21-3" title="3">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>(amox, cipr)</a>
|
||||
<a class="sourceLine" id="cb21-4" title="4"></a>
|
||||
<a class="sourceLine" id="cb21-5" title="5">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl)</a>
|
||||
<a class="sourceLine" id="cb21-6" title="6">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent)</a>
|
||||
<a class="sourceLine" id="cb21-7" title="7">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent, pita)</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw">select</span>(amox, cipr) <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>()</a>
|
||||
<a class="sourceLine" id="cb20-2" title="2"><span class="co"># which is the same as:</span></a>
|
||||
<a class="sourceLine" id="cb20-3" title="3">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>(amox, cipr)</a>
|
||||
<a class="sourceLine" id="cb20-4" title="4"></a>
|
||||
<a class="sourceLine" id="cb20-5" title="5">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl)</a>
|
||||
<a class="sourceLine" id="cb20-6" title="6">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent)</a>
|
||||
<a class="sourceLine" id="cb20-7" title="7">septic_patients <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent, pita)</a></code></pre></div>
|
||||
</li>
|
||||
<li>Edited <code>ggplot_rsi</code> and <code>geom_rsi</code> so they can cope with <code>count_df</code>. The new <code>fun</code> parameter has value <code>portion_df</code> at default, but can be set to <code>count_df</code>.</li>
|
||||
<li>Fix for <code>ggplot_rsi</code> when the <code>ggplot2</code> package was not loaded</li>
|
||||
|
|
@ -826,12 +822,12 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
|||
</li>
|
||||
<li>
|
||||
<p>Support for types (classes) list and matrix for <code>freq</code></p>
|
||||
<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" title="1">my_matrix =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/with">with</a></span>(septic_patients, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/matrix">matrix</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(age, gender), <span class="dt">ncol =</span> <span class="dv">2</span>))</a>
|
||||
<a class="sourceLine" id="cb22-2" title="2"><span class="kw"><a href="../reference/freq.html">freq</a></span>(my_matrix)</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" title="1">my_matrix =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/with">with</a></span>(septic_patients, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/matrix">matrix</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(age, gender), <span class="dt">ncol =</span> <span class="dv">2</span>))</a>
|
||||
<a class="sourceLine" id="cb21-2" title="2"><span class="kw"><a href="../reference/freq.html">freq</a></span>(my_matrix)</a></code></pre></div>
|
||||
<p>For lists, subsetting is possible:</p>
|
||||
<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" title="1">my_list =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="dt">age =</span> septic_patients<span class="op">$</span>age, <span class="dt">gender =</span> septic_patients<span class="op">$</span>gender)</a>
|
||||
<a class="sourceLine" id="cb23-2" title="2">my_list <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age)</a>
|
||||
<a class="sourceLine" id="cb23-3" title="3">my_list <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)</a></code></pre></div>
|
||||
<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" title="1">my_list =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="dt">age =</span> septic_patients<span class="op">$</span>age, <span class="dt">gender =</span> septic_patients<span class="op">$</span>gender)</a>
|
||||
<a class="sourceLine" id="cb22-2" title="2">my_list <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age)</a>
|
||||
<a class="sourceLine" id="cb22-3" title="3">my_list <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)</a></code></pre></div>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -81,7 +81,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -249,9 +249,7 @@
|
|||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>eucast_rules</span>(<span class='no'>x</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>rules</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"breakpoints"</span>,
|
||||
<span class='st'>"expert"</span>, <span class='st'>"other"</span>, <span class='st'>"all"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>eucast_rules_file</span>()</pre>
|
||||
<span class='st'>"expert"</span>, <span class='st'>"other"</span>, <span class='st'>"all"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
|
|
@ -293,7 +291,6 @@
|
|||
<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. <br />
|
||||
<a href='http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx'>http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx</a></p></li>
|
||||
</ul>
|
||||
<p>For editing the reference file (which is available with <code>eucast_rules_file</code>), these values can all be used for target antibiotics: aminoglycosides, tetracyclines, polymyxins, macrolides, glycopeptides, streptogramins, cephalosporins, cephalosporins_without_cfta, carbapenems, aminopenicillins, ureidopenicillins, fluoroquinolones, all_betalactams, and all separate four letter codes like AMC. They can be separated by comma: <code>"AMC, fluoroquinolones"</code>. The mo_property can be any column name from the <code><a href='microorganisms.html'>microorganisms</a></code> data set, or <code>genus_species</code> or <code>gramstain</code>. This file contains references to the 'Burkholderia cepacia complex'. The species in this group can be found in: LiPuma JJ, 2015 (PMID 16217180).</p>
|
||||
|
||||
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
|
||||
|
||||
|
|
@ -303,9 +300,7 @@
|
|||
|
||||
<p><strong>Note:</strong> This function does not translate MIC values to RSI values. Use <code><a href='as.rsi.html'>as.rsi</a></code> for that. <br />
|
||||
<strong>Note:</strong> When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance.</p>
|
||||
<p>The file used for applying all EUCAST rules can be retrieved with <code>eucast_rules_file()</code>. It returns an easily readable data set containing all rules. The original TSV file (tab separated file) that is being read by <code>eucast_rules()</code> can be found by running this command: <br />
|
||||
<code>AMR::EUCAST_RULES_FILE_LOCATION</code> (without brackets).</p>
|
||||
<p>In the source code the file containing all rules is located <a href='https://gitlab.com/msberends/AMR/blob/master/inst/eucast/eucast_rules.tsv'>here</a>.</p>
|
||||
<p>The file containing all EUCAST rules is located here: <a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv'>https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv</a>.</p>
|
||||
|
||||
<h2 class="hasAnchor" id="antibiotics"><a class="anchor" href="#antibiotics"></a>Antibiotics</h2>
|
||||
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -81,7 +81,7 @@ top_freq can be used to get the top/bottom n items of a frequency table, with co
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9049</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9045</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -78,7 +78,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9049</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -330,7 +330,7 @@
|
|||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="eucast_rules.html">eucast_rules()</a></code> <code><a href="eucast_rules.html">eucast_rules_file()</a></code> </p>
|
||||
<p><code><a href="eucast_rules.html">eucast_rules()</a></code> </p>
|
||||
</td>
|
||||
<td><p>EUCAST rules</p></td>
|
||||
</tr><tr>
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -81,7 +81,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -81,7 +81,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -81,7 +81,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9050</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -252,9 +252,9 @@
|
|||
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p>Strings will be translated to foreign languages if they are defined in a local translation file. This file comes with this package and can be found when running:</p>
|
||||
<p><code><a href='https://www.rdocumentation.org/packages/base/topics/system.file'>system.file("translations.tsv", package = "AMR")</a></code></p>
|
||||
<p>This file will be read by all functions where a translated output can be desired, like all <code><a href='mo_property.html'>mo_property</a></code> functions (<code><a href='mo_property.html'>mo_fullname</a></code>, <code><a href='mo_property.html'>mo_type</a></code>, etc.). Please suggest your own translations <a href='https://gitlab.com/msberends/AMR/issues/new?issue[title]=Translation%20suggestion'>by creating a new issue on our repository</a>.</p>
|
||||
<p>Strings will be translated to foreign languages if they are defined in a local translation file. Additions to this file can be suggested at our repository. The file can be found here: <a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/translations.tsv'>https://gitlab.com/msberends/AMR/blob/master/data-raw/translations.tsv</a>.</p>
|
||||
<p>Please suggest your own translations <a href='https://gitlab.com/msberends/AMR/issues/new?issue[title]=Translation%20suggestion'>by creating a new issue on our repository</a>.</p>
|
||||
<p>This file will be read by all functions where a translated output can be desired, like all <code><a href='mo_property.html'>mo_property</a></code> functions (<code><a href='mo_property.html'>mo_fullname</a></code>, <code><a href='mo_property.html'>mo_type</a></code>, etc.).</p>
|
||||
<p>The system language will be used at default, if supported, using <code>get_locale</code>. The system language can be overwritten with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a>("AMR_locale")</code>.</p>
|
||||
|
||||
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
|
||||
|
|
|
|||
|
|
@ -13,13 +13,15 @@
|
|||
git checkout master --quiet
|
||||
echo "changed branch to master"
|
||||
# import everything from premaster
|
||||
git merge premaster
|
||||
git merge premaster --quiet
|
||||
# and send it to git
|
||||
git push
|
||||
# echo "pushed changes to master"
|
||||
git push --quiet
|
||||
echo "pushed changes to master"
|
||||
# return to premaster
|
||||
git checkout premaster --quiet
|
||||
echo "changed branch back to premaster"
|
||||
git status --short
|
||||
|
||||
|
||||
# and get stashed changes back
|
||||
# git stash apply --quiet
|
||||
|
|
|
|||
|
|
@ -31,17 +31,21 @@ echo "First 3 lines of DESCRIPTION:"
|
|||
head -3 DESCRIPTION
|
||||
echo
|
||||
echo "•••••••••••••••••••••••••••••••••"
|
||||
echo "• Reloading/Documenting package •"
|
||||
echo "• Reloading/documenting package •"
|
||||
echo "•••••••••••••••••••••••••••••••••"
|
||||
Rscript -e "devtools::load_all(quiet = TRUE)"
|
||||
Rscript -e "suppressMessages(devtools::document())"
|
||||
Rscript -e "devtools::install(quiet = TRUE, dependencies = FALSE)"
|
||||
echo
|
||||
echo "••••••••••••••••••••••••••"
|
||||
echo "• Updating internal data •"
|
||||
echo "••••••••••••••••••••••••••"
|
||||
Rscript -e "source('data-raw/internals.R')"
|
||||
echo
|
||||
echo "•••••••••••••••••"
|
||||
echo "• Building site •"
|
||||
echo "•••••••••••••••••"
|
||||
Rscript -e "suppressMessages(pkgdown::build_site(lazy = $lazy, examples = FALSE))"
|
||||
|
||||
echo
|
||||
echo "•••••••••••••••••••••••••"
|
||||
echo "• List of changed files •"
|
||||
|
|
|
|||
|
|
@ -2,7 +2,6 @@
|
|||
% Please edit documentation in R/eucast_rules.R
|
||||
\name{eucast_rules}
|
||||
\alias{eucast_rules}
|
||||
\alias{eucast_rules_file}
|
||||
\title{EUCAST rules}
|
||||
\source{
|
||||
\itemize{
|
||||
|
|
@ -20,14 +19,10 @@
|
|||
\url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx}
|
||||
}
|
||||
}
|
||||
|
||||
For editing the reference file (which is available with \code{\link{eucast_rules_file}}), these values can all be used for target antibiotics: aminoglycosides, tetracyclines, polymyxins, macrolides, glycopeptides, streptogramins, cephalosporins, cephalosporins_without_cfta, carbapenems, aminopenicillins, ureidopenicillins, fluoroquinolones, all_betalactams, and all separate four letter codes like AMC. They can be separated by comma: \code{"AMC, fluoroquinolones"}. The mo_property can be any column name from the \code{\link{microorganisms}} data set, or \code{genus_species} or \code{gramstain}. This file contains references to the 'Burkholderia cepacia complex'. The species in this group can be found in: LiPuma JJ, 2015 (PMID 16217180).
|
||||
}
|
||||
\usage{
|
||||
eucast_rules(x, col_mo = NULL, info = TRUE, rules = c("breakpoints",
|
||||
"expert", "other", "all"), verbose = FALSE, ...)
|
||||
|
||||
eucast_rules_file()
|
||||
}
|
||||
\arguments{
|
||||
\item{x}{data with antibiotic columns, like e.g. \code{AMX} and \code{AMC}}
|
||||
|
|
@ -52,10 +47,7 @@ Apply susceptibility rules as defined by the European Committee on Antimicrobial
|
|||
\strong{Note:} This function does not translate MIC values to RSI values. Use \code{\link{as.rsi}} for that. \cr
|
||||
\strong{Note:} When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance.
|
||||
|
||||
The file used for applying all EUCAST rules can be retrieved with \code{\link{eucast_rules_file}()}. It returns an easily readable data set containing all rules. The original TSV file (tab separated file) that is being read by \code{eucast_rules()} can be found by running this command: \cr
|
||||
\code{AMR::EUCAST_RULES_FILE_LOCATION} (without brackets).
|
||||
|
||||
In the source code the file containing all rules is located \href{https://gitlab.com/msberends/AMR/blob/master/inst/eucast/eucast_rules.tsv}{here}.
|
||||
The file containing all EUCAST rules is located here: \url{https://gitlab.com/msberends/AMR/blob/master/data-raw/eucast_rules.tsv}.
|
||||
}
|
||||
\section{Antibiotics}{
|
||||
|
||||
|
|
|
|||
|
|
@ -11,11 +11,11 @@ get_locale()
|
|||
For language-dependent output of AMR functions, like \code{\link{mo_fullname}} and \code{\link{mo_type}}.
|
||||
}
|
||||
\details{
|
||||
Strings will be translated to foreign languages if they are defined in a local translation file. This file comes with this package and can be found when running:
|
||||
Strings will be translated to foreign languages if they are defined in a local translation file. Additions to this file can be suggested at our repository. The file can be found here: \url{https://gitlab.com/msberends/AMR/blob/master/data-raw/translations.tsv}.
|
||||
|
||||
\code{system.file("translations.tsv", package = "AMR")}
|
||||
Please suggest your own translations \href{https://gitlab.com/msberends/AMR/issues/new?issue[title]=Translation\%20suggestion}{by creating a new issue on our repository}.
|
||||
|
||||
This file will be read by all functions where a translated output can be desired, like all \code{\link{mo_property}} functions (\code{\link{mo_fullname}}, \code{\link{mo_type}}, etc.). Please suggest your own translations \href{https://gitlab.com/msberends/AMR/issues/new?issue[title]=Translation\%20suggestion}{by creating a new issue on our repository}.
|
||||
This file will be read by all functions where a translated output can be desired, like all \code{\link{mo_property}} functions (\code{\link{mo_fullname}}, \code{\link{mo_type}}, etc.).
|
||||
|
||||
The system language will be used at default, if supported, using \code{\link{get_locale}}. The system language can be overwritten with \code{\link{getOption}("AMR_locale")}.
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue