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(v0.7.0.9005) ab algorithm update
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 0.7.0.9004
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Date: 2019-06-09
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Version: 0.7.0.9005
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Date: 2019-06-11
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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person(
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@ -142,6 +142,7 @@ export(mo_family)
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export(mo_fullname)
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export(mo_genus)
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export(mo_gramstain)
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export(mo_info)
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export(mo_kingdom)
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export(mo_name)
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export(mo_order)
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6
NEWS.md
6
NEWS.md
@ -1,4 +1,4 @@
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# AMR 0.7.0.9004
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# AMR 0.7.0.9005
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#### New
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* Support for all scientifically published pathotypes of *E. coli* to date. Supported are: AIEC (Adherent-Invasive *E. coli*), ATEC (Atypical Entero-pathogenic *E. coli*), DAEC (Diffusely Adhering *E. coli*), EAEC (Entero-Aggresive *E. coli*), EHEC (Entero-Haemorrhagic *E. coli*), EIEC (Entero-Invasive *E. coli*), EPEC (Entero-Pathogenic *E. coli*), ETEC (Entero-Toxigenic *E. coli*), NMEC (Neonatal Meningitis‐causing *E. coli*), STEC (Shiga-toxin producing *E. coli*) and UPEC (Uropathogenic *E. coli*). All these lead to the microbial ID of *E. coli*:
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@ -8,16 +8,20 @@
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mo_fullname("UPEC")
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# "Escherichia coli"
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```
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* Function `mo_info()` as an analogy to `ab_info()`. The `mo_info()` prints a list with the full taxonomy, authors, and the URL to the online database of a microorganism
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#### Changed
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* Fixed bug in translation of microorganism names
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* Fixed bug in determining taxonomic kingdoms
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* Algorithm improvements for `as.ab()` and `as.mo()` to understand even more severely misspelled input
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* Function `as.ab()` now allows spaces for coercing antibiotics names
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* Added `ggplot2` methods for automatically determining the scale type of classes `mo` and `ab`
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* Added names of object in the header in frequency tables, even when using pipes
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* Prevented `"bacteria"` from getting coerced by `as.ab()` because Bacterial is a brand name of trimethoprim (TMP)
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* Fixed a bug where setting an antibiotic would not work for `eucast_rules()` and `mdro()`
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* Fixed a EUCAST rule for Staphylococci, where amikacin resistance would not be inferred from tobramycin
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* Removed `latest_annual_release` from the `catalogue_of_life_version()` function
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* Removed antibiotic code `PVM1` from the `antibiotics` data set as this was a duplicate of `PME`
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#### Other
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* Fixed a note thrown by CRAN tests
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32
R/ab.R
32
R/ab.R
@ -70,15 +70,15 @@ as.ab <- function(x) {
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x_bak <- x
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# remove suffices
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x_bak_clean <- gsub("_(mic|rsi|disk|disc)$", "", x, ignore.case = TRUE)
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x_bak_clean <- gsub("_(mic|rsi|dis[ck])$", "", x, ignore.case = TRUE)
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# remove disk concentrations, like LVX_NM -> LVX
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x_bak_clean <- gsub("_[A-Z]{2}[0-9_]{0,3}$", "", x_bak_clean, ignore.case = TRUE)
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# clean rest of it
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x_bak_clean <- gsub("[^A-Z0-9/-]", "", x_bak_clean, ignore.case = TRUE)
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# keep only a-z when it's not an ATC code or only numbers
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x_bak_clean[!x_bak_clean %like% "^([A-Z][0-9]{2}[A-Z]{2}[0-9]{2}|[0-9]+)$"] <- gsub("[^a-zA-Z]+",
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"",
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x_bak_clean[!x_bak_clean %like% "^([A-Z][0-9]{2}[A-Z]{2}[0-9]{2}|[0-9]+)$"])
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# remove part between brackets if that's followed by another string
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x_bak_clean <- gsub("(.*)+ [(].*[)]", "\\1", x_bak_clean)
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# keep only a-Z, 0-9, space, slash and dash
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x_bak_clean <- gsub("[^A-Z0-9 /-]", "", x_bak_clean, ignore.case = TRUE)
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# keep only max 1 space
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x_bak_clean <- trimws(gsub(" +", " ", x_bak_clean, ignore.case = TRUE))
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x <- unique(x_bak_clean)
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x_new <- rep(NA_character_, length(x))
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x_unknown <- character(0)
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@ -200,6 +200,24 @@ as.ab <- function(x) {
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next
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}
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# try by removing all spaces
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if (x[i] %like% " ") {
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found <- suppressWarnings(as.ab(gsub(" +", "", x[i])))
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if (length(found) > 0) {
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x_new[i] <- found[1L]
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next
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}
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}
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# try by removing all spaces and numbers
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if (x[i] %like% " " | x[i] %like% "[0-9]") {
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found <- suppressWarnings(as.ab(gsub("[ 0-9]", "", x[i])))
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if (length(found) > 0) {
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x_new[i] <- found[1L]
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next
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}
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}
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# not found
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x_unknown <- c(x_unknown, x_bak[x[i] == x_bak_clean][1])
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}
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@ -73,14 +73,13 @@
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#' ab_name(21319) # "Flucloxacillin" (using CID)
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#' ab_name("J01CF05") # "Flucloxacillin" (using ATC)
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ab_name <- function(x, language = get_locale(), tolower = FALSE, ...) {
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x <- ab_validate(x = x, property = "name", ...)
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res <- t(x, language = language)
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x <- translate_AMR(ab_validate(x = x, property = "name", ...), language = language)
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if (tolower == TRUE) {
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# use perl to only transform the first character
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# as we want "polymyxin B", not "polymyxin b"
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res <- gsub("^([A-Z])", "\\L\\1", res, perl = TRUE)
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x <- gsub("^([A-Z])", "\\L\\1", x, perl = TRUE)
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}
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res
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x
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}
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#' @rdname ab_property
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@ -116,19 +115,19 @@ ab_tradenames <- function(x, ...) {
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#' @rdname ab_property
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#' @export
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ab_group <- function(x, language = get_locale(), ...) {
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t(ab_validate(x = x, property = "group", ...), language = language)
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translate_AMR(ab_validate(x = x, property = "group", ...), language = language)
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}
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#' @rdname ab_property
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#' @export
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ab_atc_group1 <- function(x, language = get_locale(), ...) {
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t(ab_validate(x = x, property = "atc_group1", ...), language = language)
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translate_AMR(ab_validate(x = x, property = "atc_group1", ...), language = language)
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}
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#' @rdname ab_property
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#' @export
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ab_atc_group2 <- function(x, language = get_locale(), ...) {
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t(ab_validate(x = x, property = "atc_group2", ...), language = language)
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translate_AMR(ab_validate(x = x, property = "atc_group2", ...), language = language)
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}
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#' @rdname ab_property
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@ -150,8 +149,8 @@ ab_ddd <- function(x, administration = "oral", units = FALSE, ...) {
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#' @export
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ab_info <- function(x, language = get_locale(), ...) {
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x <- AMR::as.ab(x, ...)
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base::list(ab = x,
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atc = ab_atc(x),
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base::list(ab = as.character(x),
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atc = as.character(ab_atc(x)),
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cid = ab_cid(x),
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name = ab_name(x, language = language),
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group = ab_group(x, language = language),
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@ -174,7 +173,7 @@ ab_property <- function(x, property = 'name', language = get_locale(), ...) {
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stop("invalid property: '", property, "' - use a column name of the `antibiotics` data set")
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}
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t(ab_validate(x = x, property = property, ...), language = language)
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translate_AMR(ab_validate(x = x, property = property, ...), language = language)
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}
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ab_validate <- function(x, property, ...) {
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@ -71,19 +71,17 @@
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#' # [1] "Castellani et al., 1919"
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#'
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#' # Do not get mistaken - the package only includes microorganisms
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#' mo_phylum("C. elegans")
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#' # [1] "Cyanobacteria" # Bacteria?!
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#' mo_fullname("C. elegans")
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#' mo_kingdom("C. elegans")
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#' # [1] "Bacteria" # Bacteria?!
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#' mo_name("C. elegans")
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#' # [1] "Chroococcus limneticus elegans" # Because a microorganism was found
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NULL
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#' Version info of included Catalogue of Life
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#'
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#' This function returns information about the included data from the Catalogue of Life. It also shows if the included version is their latest annual release. The Catalogue of Life releases their annual release in March each year.
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#' This function returns information about the included data from the Catalogue of Life.
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#' @seealso \code{\link{microorganisms}}
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#' @details The list item \code{...$catalogue_of_life$is_latest_annual_release} is based on the system date.
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#'
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#' For DSMZ, see \code{?microorganisms}.
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#' @details For DSMZ, see \code{?microorganisms}.
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#' @return a \code{list}, which prints in pretty format
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#' @inheritSection catalogue_of_life Catalogue of Life
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#' @inheritSection AMR Read more on our website!
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@ -99,8 +97,6 @@ catalogue_of_life_version <- function() {
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lst <- list(catalogue_of_life =
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list(version = gsub("{year}", catalogue_of_life$year, catalogue_of_life$version, fixed = TRUE),
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url = gsub("{year}", catalogue_of_life$year, catalogue_of_life$url_CoL, fixed = TRUE),
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# annual release always somewhere in May, so before June is TRUE, FALSE otherwise
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is_latest_annual_release = Sys.Date() < as.Date(paste0(catalogue_of_life$year + 1, "-06-01")),
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n = nrow(filter(AMR::microorganisms, source == "CoL"))),
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deutsche_sammlung_von_mikroorganismen_und_zellkulturen =
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list(version = "Prokaryotic Nomenclature Up-to-Date from DSMZ",
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@ -125,7 +121,6 @@ print.catalogue_of_life_version <- function(x, ...) {
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underline(lst$catalogue_of_life$version), "\n",
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" Available at: ", lst$catalogue_of_life$url, "\n",
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" Number of included species: ", format(lst$catalogue_of_life$n, big.mark = ","), "\n",
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" (based on your system time, this is most likely ", ifelse(lst$catalogue_of_life$is_latest_annual_release, "", "not "), "the latest annual release)\n\n",
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underline(paste0(lst$deutsche_sammlung_von_mikroorganismen_und_zellkulturen$version, " (",
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lst$deutsche_sammlung_von_mikroorganismen_und_zellkulturen$yearmonth, ")")), "\n",
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" Available at: ", lst$deutsche_sammlung_von_mikroorganismen_und_zellkulturen$url, "\n",
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2
R/data.R
2
R/data.R
@ -22,7 +22,7 @@
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#' Data set with ~450 antibiotics
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#'
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#' A data set containing all antibiotics. Use \code{\link{as.ab}} or one of the \code{\link{ab_property}} functions to retrieve values from this data set. Three identifiers are included in this data set: an antibiotic ID (\code{ab}, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (\code{atc}) as defined by the WHO, and a Compound ID (\code{cid}) as found in PubChem. Other properties in this data set are derived from one or more of these codes.
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#' @format A \code{\link{data.frame}} with 454 observations and 13 variables:
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#' @format A \code{\link{data.frame}} with 453 observations and 13 variables:
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#' \describe{
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#' \item{\code{ab}}{Antibiotic ID as used in this package (like \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available}
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#' \item{\code{atc}}{ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like \code{J01CR02}}
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@ -26,17 +26,17 @@
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#' @param y,z characters to compare
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#' @inheritParams first_isolate
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#' @param universal_1,universal_2,universal_3,universal_4,universal_5,universal_6 column names of \strong{broad-spectrum} antibiotics, case-insensitive. At default, the columns containing these antibiotics will be guessed with \code{\link{guess_ab_col}}.
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#' @param GramPos_1,GramPos_2,GramPos_3,GramPos_4,GramPos_5,GramPos_6 column names of antibiotics for \strong{Gram positives}, case-insensitive. At default, the columns containing these antibiotics will be guessed with \code{\link{guess_ab_col}}.
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#' @param GramNeg_1,GramNeg_2,GramNeg_3,GramNeg_4,GramNeg_5,GramNeg_6 column names of antibiotics for \strong{Gram negatives}, case-insensitive. At default, the columns containing these antibiotics will be guessed with \code{\link{guess_ab_col}}.
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#' @param GramPos_1,GramPos_2,GramPos_3,GramPos_4,GramPos_5,GramPos_6 column names of antibiotics for \strong{Gram-positives}, case-insensitive. At default, the columns containing these antibiotics will be guessed with \code{\link{guess_ab_col}}.
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#' @param GramNeg_1,GramNeg_2,GramNeg_3,GramNeg_4,GramNeg_5,GramNeg_6 column names of antibiotics for \strong{Gram-negatives}, case-insensitive. At default, the columns containing these antibiotics will be guessed with \code{\link{guess_ab_col}}.
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#' @param warnings give warning about missing antibiotic columns, they will anyway be ignored
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#' @param ... other parameters passed on to function
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#' @details The function \code{key_antibiotics} returns a character vector with 12 antibiotic results for every isolate. These isolates can then be compared using \code{key_antibiotics_equal}, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (\code{"."}). The \code{\link{first_isolate}} function only uses this function on the same microbial species from the same patient. Using this, an MRSA will be included after a susceptible \emph{S. aureus} (MSSA) found within the same episode (see \code{episode} parameter of \code{\link{first_isolate}}). Without key antibiotic comparison it would not.
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#'
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#' At default, the antibiotics that are used for \strong{Gram positive bacteria} are (colum names): \cr
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#' \code{"amox"}, \code{"amcl"}, \code{"cfur"}, \code{"pita"}, \code{"cipr"}, \code{"trsu"} (until here is universal), \code{"vanc"}, \code{"teic"}, \code{"tetr"}, \code{"eryt"}, \code{"oxac"}, \code{"rifa"}.
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#' At default, the antibiotics that are used for \strong{Gram-positive bacteria} are: \cr
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#' amoxicillin, amoxicillin/clavulanic acid, cefuroxime, piperacillin/tazobactam, ciprofloxacin, trimethoprim/sulfamethoxazole (until here is universal), vancomycin, teicoplanin, tetracycline, erythromycin, oxacillin, rifampin.
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#'
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#' At default, the antibiotics that are used for \strong{Gram negative bacteria} are (colum names): \cr
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#' \code{"amox"}, \code{"amcl"}, \code{"cfur"}, \code{"pita"}, \code{"cipr"}, \code{"trsu"} (until here is universal), \code{"gent"}, \code{"tobr"}, \code{"coli"}, \code{"cfot"}, \code{"cfta"}, \code{"mero"}.
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#' At default, the antibiotics that are used for \strong{Gram-negative bacteria} are: \cr
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#' amoxicillin, amoxicillin/clavulanic acid, cefuroxime, piperacillin/tazobactam, ciprofloxacin, trimethoprim/sulfamethoxazole (until here is universal), gentamicin, tobramycin, colistin, cefotaxime, ceftazidime, meropenem.
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#'
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#'
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#' The function \code{key_antibiotics_equal} checks the characters returned by \code{key_antibiotics} for equality, and returns a logical vector.
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@ -50,7 +50,7 @@
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#' @examples
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#' # septic_patients is a dataset available in the AMR package
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#' ?septic_patients
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#'
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#' library(dplyr)
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#' # set key antibiotics to a new variable
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#' my_patients <- septic_patients %>%
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@ -78,24 +78,24 @@
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#' # FALSE, because I is not ignored and so the 4th value differs
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key_antibiotics <- function(x,
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col_mo = NULL,
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universal_1 = guess_ab_col(x, "AMX"),
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universal_2 = guess_ab_col(x, "AMC"),
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universal_3 = guess_ab_col(x, "CXM"),
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universal_4 = guess_ab_col(x, "TZP"),
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universal_5 = guess_ab_col(x, "CIP"),
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universal_6 = guess_ab_col(x, "SXT"),
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GramPos_1 = guess_ab_col(x, "VAN"),
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GramPos_2 = guess_ab_col(x, "TEC"),
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GramPos_3 = guess_ab_col(x, "TCY"),
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GramPos_4 = guess_ab_col(x, "ERY"),
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GramPos_5 = guess_ab_col(x, "OXA"),
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GramPos_6 = guess_ab_col(x, "RIF"),
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GramNeg_1 = guess_ab_col(x, "GEN"),
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GramNeg_2 = guess_ab_col(x, "TOB"),
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GramNeg_3 = guess_ab_col(x, "COL"),
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GramNeg_4 = guess_ab_col(x, "CTX"),
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GramNeg_5 = guess_ab_col(x, "CAZ"),
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GramNeg_6 = guess_ab_col(x, "MEM"),
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universal_1 = guess_ab_col(x, "amoxicillin"),
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universal_2 = guess_ab_col(x, "amoxicillin/clavulanic acid"),
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universal_3 = guess_ab_col(x, "cefuroxime"),
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universal_4 = guess_ab_col(x, "piperacillin/tazobactam"),
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universal_5 = guess_ab_col(x, "ciprofloxacin"),
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universal_6 = guess_ab_col(x, "trimethoprim/sulfamethoxazole"),
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GramPos_1 = guess_ab_col(x, "vancomycin"),
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GramPos_2 = guess_ab_col(x, "teicoplanin"),
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GramPos_3 = guess_ab_col(x, "tetracycline"),
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GramPos_4 = guess_ab_col(x, "erythromycin"),
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GramPos_5 = guess_ab_col(x, "oxacillin"),
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GramPos_6 = guess_ab_col(x, "rifampin"),
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GramNeg_1 = guess_ab_col(x, "gentamicin"),
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GramNeg_2 = guess_ab_col(x, "tobramycin"),
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GramNeg_3 = guess_ab_col(x, "colistin"),
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GramNeg_4 = guess_ab_col(x, "cefotaxime"),
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GramNeg_5 = guess_ab_col(x, "ceftazidime"),
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GramNeg_6 = guess_ab_col(x, "meropenem"),
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warnings = TRUE,
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...) {
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@ -170,7 +170,7 @@ key_antibiotics <- function(x,
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gram_positive <- gram_positive[!is.null(gram_positive)]
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gram_positive <- gram_positive[!is.na(gram_positive)]
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if (length(gram_positive) < 12) {
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warning("only using ", length(gram_positive), " different antibiotics as key antibiotics for Gram positives. See ?key_antibiotics.", call. = FALSE)
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warning("only using ", length(gram_positive), " different antibiotics as key antibiotics for Gram-positives. See ?key_antibiotics.", call. = FALSE)
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}
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gram_negative = c(universal,
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@ -179,7 +179,7 @@ key_antibiotics <- function(x,
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gram_negative <- gram_negative[!is.null(gram_negative)]
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gram_negative <- gram_negative[!is.na(gram_negative)]
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if (length(gram_negative) < 12) {
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warning("only using ", length(gram_negative), " different antibiotics as key antibiotics for Gram negatives. See ?key_antibiotics.", call. = FALSE)
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warning("only using ", length(gram_negative), " different antibiotics as key antibiotics for Gram-negatives. See ?key_antibiotics.", call. = FALSE)
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}
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# join to microorganisms data set
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@ -191,7 +191,7 @@ key_antibiotics <- function(x,
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# Gram +
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x <- x %>% mutate(key_ab =
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if_else(gramstain == "Gram positive",
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if_else(gramstain == "Gram-positive",
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apply(X = x[, gram_positive],
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MARGIN = 1,
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FUN = function(x) paste(x, collapse = "")),
|
||||
@ -199,7 +199,7 @@ key_antibiotics <- function(x,
|
||||
|
||||
# Gram -
|
||||
x <- x %>% mutate(key_ab =
|
||||
if_else(gramstain == "Gram negative",
|
||||
if_else(gramstain == "Gram-negative",
|
||||
apply(X = x[, gram_negative],
|
||||
MARGIN = 1,
|
||||
FUN = function(x) paste(x, collapse = "")),
|
||||
@ -209,7 +209,8 @@ key_antibiotics <- function(x,
|
||||
key_abs <- x %>%
|
||||
pull(key_ab) %>%
|
||||
gsub('(NA|NULL)', '.', .) %>%
|
||||
gsub('[^SIR]', '.', ., ignore.case = TRUE)
|
||||
gsub('[^SIR]', '.', ., ignore.case = TRUE) %>%
|
||||
toupper()
|
||||
|
||||
key_abs
|
||||
|
||||
@ -295,7 +296,7 @@ key_antibiotics_equal <- function(y,
|
||||
result[i] <- points >= points_threshold
|
||||
|
||||
} else {
|
||||
stop('`', type, '` is not a valid value for type, must be "points" or "keyantibiotics". See ?first_isolate.')
|
||||
stop('`', type, '` is not a valid value for type, must be "points" or "keyantibiotics". See ?key_antibiotics')
|
||||
}
|
||||
}
|
||||
}
|
||||
|
5
R/misc.R
5
R/misc.R
@ -253,7 +253,7 @@ stopifnot_installed_package <- function(package) {
|
||||
|
||||
# translate strings based on inst/translations.tsv
|
||||
#' @importFrom dplyr %>% filter
|
||||
t <- function(from, language = get_locale()) {
|
||||
translate_AMR <- function(from, language = get_locale(), only_unknown = FALSE) {
|
||||
# if (getOption("AMR_locale", "en") != language) {
|
||||
# language <- getOption("AMR_locale", "en")
|
||||
# }
|
||||
@ -274,6 +274,9 @@ t <- function(from, language = get_locale()) {
|
||||
}
|
||||
|
||||
df_trans <- df_trans %>% filter(lang == language)
|
||||
if (only_unknown == TRUE) {
|
||||
df_trans <- df_trans %>% filter(pattern %like% "unknown")
|
||||
}
|
||||
|
||||
# default case sensitive if value if 'ignore.case' is missing:
|
||||
df_trans$ignore.case[is.na(df_trans$ignore.case)] <- FALSE
|
||||
|
@ -69,8 +69,8 @@
|
||||
#' mo_shortname("E. coli") # "E. coli"
|
||||
#'
|
||||
#' ## other properties
|
||||
#' mo_gramstain("E. coli") # "Gram negative"
|
||||
#' mo_type("E. coli") # "Bacteria" (equal to kingdom)
|
||||
#' mo_gramstain("E. coli") # "Gram-negative"
|
||||
#' mo_type("E. coli") # "Bacteria" (equal to kingdom, but may be translated)
|
||||
#' mo_rank("E. coli") # "species"
|
||||
#' mo_url("E. coli") # get the direct url to the online database entry
|
||||
#'
|
||||
@ -84,7 +84,7 @@
|
||||
#' mo_genus("MRSA") # "Staphylococcus"
|
||||
#' mo_species("MRSA") # "aureus"
|
||||
#' mo_shortname("MRSA") # "S. aureus"
|
||||
#' mo_gramstain("MRSA") # "Gram positive"
|
||||
#' mo_gramstain("MRSA") # "Gram-positive"
|
||||
#'
|
||||
#' mo_genus("VISA") # "Staphylococcus"
|
||||
#' mo_species("VISA") # "aureus"
|
||||
@ -133,15 +133,15 @@
|
||||
#'
|
||||
#' # get a list with the complete taxonomy (from kingdom to subspecies)
|
||||
#' mo_taxonomy("E. coli")
|
||||
#' # get a list with the taxonomy, the authors and the URL to the online database
|
||||
#' mo_info("E. coli")
|
||||
mo_name <- function(x, language = get_locale(), ...) {
|
||||
mo_fullname(x = x, language = language, ... = ...)
|
||||
translate_AMR(mo_validate(x = x, property = "fullname", ...), language = language, only_unknown = FALSE)
|
||||
}
|
||||
|
||||
#' @rdname mo_property
|
||||
#' @export
|
||||
mo_fullname <- function(x, language = get_locale(), ...) {
|
||||
t(mo_validate(x = x, property = "fullname", ...), language = language)
|
||||
}
|
||||
mo_fullname <- mo_name
|
||||
|
||||
#' @rdname mo_property
|
||||
#' @importFrom dplyr %>% mutate pull
|
||||
@ -184,70 +184,61 @@ mo_shortname <- function(x, language = get_locale(), ...) {
|
||||
res1[res1 != res2] <- res2_fullname
|
||||
result <- as.character(res1)
|
||||
|
||||
t(result, language = language)
|
||||
translate_AMR(result, language = language, only_unknown = FALSE)
|
||||
}
|
||||
|
||||
#' @rdname mo_property
|
||||
#' @export
|
||||
mo_subspecies <- function(x, language = get_locale(), ...) {
|
||||
t(mo_validate(x = x, property = "subspecies", ...), language = language)
|
||||
translate_AMR(mo_validate(x = x, property = "subspecies", ...), language = language, only_unknown = TRUE)
|
||||
}
|
||||
|
||||
#' @rdname mo_property
|
||||
#' @export
|
||||
mo_species <- function(x, language = get_locale(), ...) {
|
||||
t(mo_validate(x = x, property = "species", ...), language = language)
|
||||
translate_AMR(mo_validate(x = x, property = "species", ...), language = language, only_unknown = TRUE)
|
||||
}
|
||||
|
||||
#' @rdname mo_property
|
||||
#' @export
|
||||
mo_genus <- function(x, language = get_locale(), ...) {
|
||||
t(mo_validate(x = x, property = "genus", ...), language = language)
|
||||
translate_AMR(mo_validate(x = x, property = "genus", ...), language = language, only_unknown = TRUE)
|
||||
}
|
||||
|
||||
#' @rdname mo_property
|
||||
#' @export
|
||||
mo_family <- function(x, language = get_locale(), ...) {
|
||||
t(mo_validate(x = x, property = "family", ...), language = language)
|
||||
translate_AMR(mo_validate(x = x, property = "family", ...), language = language, only_unknown = TRUE)
|
||||
}
|
||||
|
||||
#' @rdname mo_property
|
||||
#' @export
|
||||
mo_order <- function(x, language = get_locale(), ...) {
|
||||
t(mo_validate(x = x, property = "order", ...), language = language)
|
||||
translate_AMR(mo_validate(x = x, property = "order", ...), language = language, only_unknown = TRUE)
|
||||
}
|
||||
|
||||
#' @rdname mo_property
|
||||
#' @export
|
||||
mo_class <- function(x, language = get_locale(), ...) {
|
||||
t(mo_validate(x = x, property = "class", ...), language = language)
|
||||
translate_AMR(mo_validate(x = x, property = "class", ...), language = language, only_unknown = TRUE)
|
||||
}
|
||||
|
||||
#' @rdname mo_property
|
||||
#' @export
|
||||
mo_phylum <- function(x, language = get_locale(), ...) {
|
||||
t(mo_validate(x = x, property = "phylum", ...), language = language)
|
||||
translate_AMR(mo_validate(x = x, property = "phylum", ...), language = language, only_unknown = TRUE)
|
||||
}
|
||||
|
||||
#' @rdname mo_property
|
||||
#' @export
|
||||
mo_kingdom <- function(x, language = get_locale(), ...) {
|
||||
if (all(x %in% AMR::microorganisms$kingdom)) {
|
||||
return(x)
|
||||
}
|
||||
x <- as.mo(x, ...)
|
||||
kngdm <- mo_validate(x = x, property = "kingdom", ...)
|
||||
if (language != "en") {
|
||||
# translate only unknown, so "Bacteria" (the official taxonomic name) would not change
|
||||
kngdm[identical(x, "UNKNOWN")] <- t(kngdm[identical(x, "UNKNOWN")], language = language)
|
||||
}
|
||||
kngdm
|
||||
translate_AMR(mo_validate(x = x, property = "kingdom", ...), language = language, only_unknown = TRUE)
|
||||
}
|
||||
|
||||
#' @rdname mo_property
|
||||
#' @export
|
||||
mo_type <- function(x, language = get_locale(), ...) {
|
||||
t(mo_validate(x = x, property = "kingdom", ...), language = language)
|
||||
translate_AMR(mo_validate(x = x, property = "kingdom", ...), language = language, only_unknown = FALSE)
|
||||
}
|
||||
|
||||
#' @rdname mo_property
|
||||
@ -255,16 +246,26 @@ mo_type <- function(x, language = get_locale(), ...) {
|
||||
mo_gramstain <- function(x, language = get_locale(), ...) {
|
||||
x.mo <- as.mo(x, ...)
|
||||
x.phylum <- mo_phylum(x.mo, language = "en")
|
||||
# DETERMINE GRAM STAIN FOR BACTERIA
|
||||
# Source: https://itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=956097
|
||||
# It says this:
|
||||
# Kingdom Bacteria (Cavalier-Smith, 2002)
|
||||
# Subkingdom Posibacteria (Cavalier-Smith, 2002)
|
||||
# Direct Children:
|
||||
# Phylum Actinobacteria (Cavalier-Smith, 2002)
|
||||
# Phylum Chloroflexi (Garrity and Holt, 2002)
|
||||
# Phylum Firmicutes (corrig. Gibbons and Murray, 1978)
|
||||
# Phylum Tenericutes (Murray, 1984)
|
||||
x <- NA_character_
|
||||
# make all bacteria Gram negative
|
||||
x[mo_kingdom(x.mo, language = "en") == "Bacteria"] <- "Gram-negative"
|
||||
# overwrite these phyla with Gram positive
|
||||
x[x.phylum %in% c("Actinobacteria",
|
||||
"Chloroflexi",
|
||||
"Firmicutes",
|
||||
"Tenericutes")] <- "Gram positive"
|
||||
x[x != "Gram positive"] <- "Gram negative"
|
||||
x[mo_kingdom(x.mo, language = "en") != "Bacteria"] <- NA_character_
|
||||
x[x.mo == "B_GRAMP"] <- "Gram positive"
|
||||
x[x.mo == "B_GRAMN"] <- "Gram negative"
|
||||
|
||||
t(x, language = language)
|
||||
"Tenericutes")
|
||||
| x.mo == "B_GRAMP"] <- "Gram-positive"
|
||||
translate_AMR(x, language = language, only_unknown = FALSE)
|
||||
}
|
||||
|
||||
#' @rdname mo_property
|
||||
@ -311,6 +312,15 @@ mo_taxonomy <- function(x, language = get_locale(), ...) {
|
||||
subspecies = mo_subspecies(x, language = language))
|
||||
}
|
||||
|
||||
#' @rdname mo_property
|
||||
#' @export
|
||||
mo_info <- function(x, language = get_locale(), ...) {
|
||||
x <- AMR::as.mo(x, ...)
|
||||
c(mo_taxonomy(x, language = language),
|
||||
list(url = unname(mo_url(x, open = FALSE)),
|
||||
ref = mo_ref(x)))
|
||||
}
|
||||
|
||||
#' @rdname mo_property
|
||||
#' @importFrom utils browseURL
|
||||
#' @importFrom dplyr %>% left_join select mutate case_when
|
||||
@ -349,7 +359,7 @@ mo_property <- function(x, property = 'fullname', language = get_locale(), ...)
|
||||
stop("invalid property: '", property, "' - use a column name of the `microorganisms` data set")
|
||||
}
|
||||
|
||||
t(mo_validate(x = x, property = property, ...), language = language)
|
||||
translate_AMR(mo_validate(x = x, property = property, ...), language = language, only_unknown = TRUE)
|
||||
}
|
||||
|
||||
mo_validate <- function(x, property, ...) {
|
||||
|
BIN
R/sysdata.rda
BIN
R/sysdata.rda
Binary file not shown.
@ -59,12 +59,12 @@ genus_species is Moraxella catarrhalis ERY S AZM, CLR, RXT S Moraxella catarrhal
|
||||
genus_species is Moraxella catarrhalis ERY I AZM, CLR, RXT I Moraxella catarrhalis Breakpoints
|
||||
genus_species is Moraxella catarrhalis ERY R AZM, CLR, RXT R Moraxella catarrhalis Breakpoints
|
||||
genus_species is Moraxella catarrhalis TCY S DOX, MNO S Moraxella catarrhalis Breakpoints
|
||||
genus one_of Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN S AMP, AMX, PIP, TZP, TIC S Anaerobic Gram positives Breakpoints
|
||||
genus one_of Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN I AMP, AMX, PIP, TZP, TIC I Anaerobic Gram positives Breakpoints
|
||||
genus one_of Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN R AMP, AMX, PIP, TZP, TIC R Anaerobic Gram positives Breakpoints
|
||||
genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN S AMP, AMX, PIP, TZP, TIC S Anaerobic Gram negatives Breakpoints
|
||||
genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN I AMP, AMX, PIP, TZP, TIC I Anaerobic Gram negatives Breakpoints
|
||||
genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN R AMP, AMX, PIP, TZP, TIC R Anaerobic Gram negatives Breakpoints
|
||||
genus one_of Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN S AMP, AMX, PIP, TZP, TIC S Anaerobic Gram-positives Breakpoints
|
||||
genus one_of Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN I AMP, AMX, PIP, TZP, TIC I Anaerobic Gram-positives Breakpoints
|
||||
genus one_of Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus, Propionibacterium PEN R AMP, AMX, PIP, TZP, TIC R Anaerobic Gram-positives Breakpoints
|
||||
genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN S AMP, AMX, PIP, TZP, TIC S Anaerobic Gram-negatives Breakpoints
|
||||
genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN I AMP, AMX, PIP, TZP, TIC I Anaerobic Gram-negatives Breakpoints
|
||||
genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella PEN R AMP, AMX, PIP, TZP, TIC R Anaerobic Gram-negatives Breakpoints
|
||||
genus_species is Pasteurella multocida PEN S AMP, AMX S Pasteurella multocida Breakpoints
|
||||
genus_species is Pasteurella multocida PEN I AMP, AMX I Pasteurella multocida Breakpoints
|
||||
genus_species is Pasteurella multocida PEN R AMP, AMX R Pasteurella multocida Breakpoints
|
||||
@ -135,7 +135,7 @@ genus is Neisseria TMP R Table 03: Intrinsic resistance in other Gram-negative
|
||||
genus_species is Campylobacter fetus FUS, streptogramins, TMP, NAL R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules
|
||||
genus_species is Campylobacter jejuni FUS, streptogramins, TMP R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules
|
||||
genus_species is Campylobacter coli FUS, streptogramins, TMP R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules
|
||||
gramstain is Gram positive ATM, polymyxins, NAL R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
|
||||
gramstain is Gram-positive ATM, polymyxins, NAL R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
|
||||
genus_species is Staphylococcus saprophyticus FUS, CAZ, FOS, NOV R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
|
||||
genus_species is Staphylococcus cohnii CAZ, NOV R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
|
||||
genus_species is Staphylococcus xylosus CAZ, NOV R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules
|
||||
|
|
@ -5,8 +5,8 @@
|
||||
# "minopenicillins", "ureidopenicillins", "fluoroquinolones", "all_betalactams",
|
||||
# and all separate EARS-Net letter codes like "AMC". They can be separated by comma: "AMC, fluoroquinolones".
|
||||
# The mo_property can be any column name from the AMR::microorganisms data set, or "genus_species" or "gramstain".
|
||||
# This file contains references to the 'Burkholderia cepacia complex'. The species in this group can be found in:
|
||||
# LiPuma JJ, 2015 (PMID 16217180).
|
||||
# The EUCAST guideline contains references to the 'Burkholderia cepacia complex'. The species in this group can be found in:
|
||||
# LiPuma JJ, Curr Opin Pulm Med. 2005 Nov;11(6):528-33. (PMID 16217180).
|
||||
eucast_rules_file <- dplyr::arrange(
|
||||
.data = utils::read.delim(file = "data-raw/eucast_rules.tsv",
|
||||
sep = "\t",
|
||||
|
@ -289,6 +289,9 @@ antibiotics <- filter(antibiotics, ab != "MOX")
|
||||
antibiotics <- filter(antibiotics, ab != "RFP")
|
||||
antibiotics[which(antibiotics$ab == "RFP1"), "ab"] <- "RFP"
|
||||
antibiotics[which(antibiotics$ab == "RFP"), "abbreviations"][[1]] <- list(c("rifp"))
|
||||
# PME and PVM1 (the J0 one) both mean 'Pivmecillinam', so:
|
||||
antibiotics <- filter(antibiotics, ab != "PME")
|
||||
antibiotics[which(antibiotics$ab == "PVM1"), "ab"] <- "PME"
|
||||
# ESBL E-test codes:
|
||||
antibiotics[which(antibiotics$ab == "CCV"), "abbreviations"][[1]] <- list(c("xtzl"))
|
||||
antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]] <- list(c(antibiotics[which(antibiotics$ab == "CAZ"), "abbreviations"][[1]], "xtz", "cefta"))
|
||||
|
@ -318,13 +318,13 @@ MOs <- MOs %>%
|
||||
stringsAsFactors = FALSE),
|
||||
data.frame(mo = "B_GRAMN",
|
||||
col_id = NA_integer_,
|
||||
fullname = "(unknown Gram negatives)",
|
||||
fullname = "(unknown Gram-negatives)",
|
||||
kingdom = "Bacteria",
|
||||
phylum = "(unknown phylum)",
|
||||
class = "(unknown class)",
|
||||
order = "(unknown order)",
|
||||
family = "(unknown family)",
|
||||
genus = "(unknown Gram negatives)",
|
||||
genus = "(unknown Gram-negatives)",
|
||||
species = "(unknown species)",
|
||||
subspecies = "(unknown subspecies)",
|
||||
rank = "species",
|
||||
@ -334,13 +334,13 @@ MOs <- MOs %>%
|
||||
stringsAsFactors = FALSE),
|
||||
data.frame(mo = "B_GRAMP",
|
||||
col_id = NA_integer_,
|
||||
fullname = "(unknown Gram positives)",
|
||||
fullname = "(unknown Gram-positives)",
|
||||
kingdom = "Bacteria",
|
||||
phylum = "(unknown phylum)",
|
||||
class = "(unknown class)",
|
||||
order = "(unknown order)",
|
||||
family = "(unknown family)",
|
||||
genus = "(unknown Gram positives)",
|
||||
genus = "(unknown Gram-positives)",
|
||||
species = "(unknown species)",
|
||||
subspecies = "(unknown subspecies)",
|
||||
rank = "species",
|
||||
@ -457,7 +457,7 @@ MOs <- MOs %>%
|
||||
mutate(prevalence = case_when(
|
||||
class == "Gammaproteobacteria"
|
||||
| genus %in% c("Enterococcus", "Staphylococcus", "Streptococcus")
|
||||
| mo == "UNKNOWN"
|
||||
| mo %in% c("UNKNOWN", "B_GRAMN", "B_GRAMP")
|
||||
~ 1,
|
||||
phylum %in% c("Proteobacteria",
|
||||
"Firmicutes",
|
||||
@ -494,8 +494,8 @@ saveRDS(MOs, "microorganisms.rds")
|
||||
saveRDS(MOs.old, "microorganisms.old.rds")
|
||||
|
||||
# on the server:
|
||||
usethis::use_data(microorganisms, overwrite = TRUE)
|
||||
usethis::use_data(microorganisms.old, overwrite = TRUE)
|
||||
usethis::use_data(microorganisms, overwrite = TRUE, version = 2)
|
||||
usethis::use_data(microorganisms.old, overwrite = TRUE, version = 2)
|
||||
rm(microorganisms)
|
||||
rm(microorganisms.old)
|
||||
# and update the year in R/data.R
|
||||
|
@ -2,8 +2,8 @@ lang pattern replacement fixed ignore.case
|
||||
de Coagulase-negative Staphylococcus Koagulase-negative Staphylococcus FALSE FALSE
|
||||
de Coagulase-positive Staphylococcus Koagulase-positive Staphylococcus FALSE FALSE
|
||||
de Beta-haemolytic Streptococcus Beta-hämolytischer Streptococcus FALSE FALSE
|
||||
de unknown Gram negatives unbekannte Gramnegativen FALSE FALSE
|
||||
de unknown Gram positives unbekannte Grampositiven FALSE FALSE
|
||||
de unknown Gram-negatives unbekannte Gramnegativen FALSE FALSE
|
||||
de unknown Gram-positives unbekannte Grampositiven FALSE FALSE
|
||||
de unknown name unbekannte Name FALSE FALSE
|
||||
de unknown kingdom unbekanntes Reich FALSE FALSE
|
||||
de unknown phylum unbekannter Stamm FALSE FALSE
|
||||
@ -16,8 +16,8 @@ de unknown subspecies unbekannte Unterart FALSE FALSE
|
||||
de unknown rank unbekannter Rang FALSE FALSE
|
||||
de (CoNS) (KNS) TRUE FALSE
|
||||
de (CoPS) (KPS) TRUE FALSE
|
||||
de Gram negative Gramnegativ FALSE FALSE
|
||||
de Gram positive Grampositiv FALSE FALSE
|
||||
de Gram-negative Gramnegativ FALSE FALSE
|
||||
de Gram-positive Grampositiv FALSE FALSE
|
||||
de Bacteria Bakterien FALSE FALSE
|
||||
de Fungi Hefen/Pilze FALSE FALSE
|
||||
de Protozoa Protozoen FALSE FALSE
|
||||
@ -29,8 +29,8 @@ de ([([ ]*?)Group \\1Gruppe FALSE FALSE
|
||||
nl Coagulase-negative Staphylococcus Coagulase-negatieve Staphylococcus FALSE FALSE
|
||||
nl Coagulase-positive Staphylococcus Coagulase-positieve Staphylococcus FALSE FALSE
|
||||
nl Beta-haemolytic Streptococcus Beta-hemolytische Streptococcus FALSE FALSE
|
||||
nl unknown Gram negatives onbekende Gram-negatieven FALSE FALSE
|
||||
nl unknown Gram positives onbekende Gram-positieven FALSE FALSE
|
||||
nl unknown Gram-negatives onbekende Gram-negatieven FALSE FALSE
|
||||
nl unknown Gram-positives onbekende Gram-positieven FALSE FALSE
|
||||
nl unknown name onbekende naam FALSE FALSE
|
||||
nl unknown kingdom onbekend koninkrijk FALSE FALSE
|
||||
nl unknown phylum onbekend fylum FALSE FALSE
|
||||
@ -43,8 +43,8 @@ nl unknown subspecies onbekende ondersoort FALSE FALSE
|
||||
nl unknown rank onbekende rang FALSE FALSE
|
||||
nl (CoNS) (CNS) TRUE FALSE
|
||||
nl (CoPS) (CPS) TRUE FALSE
|
||||
nl Gram negative Gram-negatief FALSE FALSE
|
||||
nl Gram positive Gram-positief FALSE FALSE
|
||||
nl Gram-negative Gram-negatief FALSE FALSE
|
||||
nl Gram-positive Gram-positief FALSE FALSE
|
||||
nl Bacteria Bacteriën FALSE FALSE
|
||||
nl Fungi Schimmels/gisten FALSE FALSE
|
||||
nl Protozoa protozoën FALSE FALSE
|
||||
@ -55,8 +55,8 @@ nl ([([ ]*?)Group \\1Groep FALSE FALSE
|
||||
es Coagulase-negative Staphylococcus Staphylococcus coagulasa negativo FALSE FALSE
|
||||
es Coagulase-positive Staphylococcus Staphylococcus coagulasa positivo FALSE FALSE
|
||||
es Beta-haemolytic Streptococcus Streptococcus Beta-hemolítico FALSE FALSE
|
||||
es unknown Gram negatives Gram negativos desconocidos FALSE FALSE
|
||||
es unknown Gram positives Gram positivos desconocidos FALSE FALSE
|
||||
es unknown Gram-negatives Gram negativos desconocidos FALSE FALSE
|
||||
es unknown Gram-positives Gram positivos desconocidos FALSE FALSE
|
||||
es unknown name nombre desconocido FALSE FALSE
|
||||
es unknown kingdom reino desconocido FALSE FALSE
|
||||
es unknown phylum filo desconocido FALSE FALSE
|
||||
@ -69,8 +69,8 @@ es unknown subspecies subespecie desconocida FALSE FALSE
|
||||
es unknown rank rango desconocido FALSE FALSE
|
||||
es (CoNS) (SCN) TRUE FALSE
|
||||
es (CoPS) (SCP) TRUE FALSE
|
||||
es Gram negative Gram negativo FALSE FALSE
|
||||
es Gram positive Gram positivo FALSE FALSE
|
||||
es Gram-negative Gram negativo FALSE FALSE
|
||||
es Gram-positive Gram positivo FALSE FALSE
|
||||
es Bacteria Bacterias FALSE FALSE
|
||||
es Fungi Hongos FALSE FALSE
|
||||
es Protozoa Protozoarios FALSE FALSE
|
||||
@ -82,8 +82,8 @@ es ([([ ]*?)Group \\1Grupo FALSE FALSE
|
||||
it Coagulase-negative Staphylococcus Staphylococcus negativo coagulasi FALSE FALSE
|
||||
it Coagulase-positive Staphylococcus Staphylococcus positivo coagulasi FALSE FALSE
|
||||
it Beta-haemolytic Streptococcus Streptococcus Beta-emolitico FALSE FALSE
|
||||
it unknown Gram negatives Gram negativi sconosciuti FALSE FALSE
|
||||
it unknown Gram positives Gram positivi sconosciuti FALSE FALSE
|
||||
it unknown Gram-negatives Gram negativi sconosciuti FALSE FALSE
|
||||
it unknown Gram-positives Gram positivi sconosciuti FALSE FALSE
|
||||
it unknown name nome sconosciuto FALSE FALSE
|
||||
it unknown kingdom regno sconosciuto FALSE FALSE
|
||||
it unknown phylum phylum sconosciuto FALSE FALSE
|
||||
@ -94,8 +94,8 @@ it unknown genus genere sconosciuto FALSE FALSE
|
||||
it unknown species specie sconosciute FALSE FALSE
|
||||
it unknown subspecies sottospecie sconosciute FALSE FALSE
|
||||
it unknown rank grado sconosciuto FALSE FALSE
|
||||
it Gram negative Gram negativo FALSE FALSE
|
||||
it Gram positive Gram positivo FALSE FALSE
|
||||
it Gram-negative Gram negativo FALSE FALSE
|
||||
it Gram-positive Gram positivo FALSE FALSE
|
||||
it Bacteria Batteri FALSE FALSE
|
||||
it Fungi Fungo FALSE FALSE
|
||||
it Protozoa Protozoi FALSE FALSE
|
||||
@ -107,8 +107,8 @@ it ([([ ]*?)Group \\1Gruppo FALSE FALSE
|
||||
fr Coagulase-negative Staphylococcus Staphylococcus à coagulase négative FALSE FALSE
|
||||
fr Coagulase-positive Staphylococcus Staphylococcus à coagulase positif FALSE FALSE
|
||||
fr Beta-haemolytic Streptococcus Streptococcus Bêta-hémolytique FALSE FALSE
|
||||
fr unknown Gram negatives Gram négatifs inconnus FALSE FALSE
|
||||
fr unknown Gram positives Gram positifs inconnus FALSE FALSE
|
||||
fr unknown Gram-negatives Gram négatifs inconnus FALSE FALSE
|
||||
fr unknown Gram-positives Gram positifs inconnus FALSE FALSE
|
||||
fr unknown name nom inconnu FALSE FALSE
|
||||
fr unknown kingdom règme inconnu FALSE FALSE
|
||||
fr unknown phylum embranchement inconnu FALSE FALSE
|
||||
@ -119,8 +119,8 @@ fr unknown genus genre inconnu FALSE FALSE
|
||||
fr unknown species espèce inconnue FALSE FALSE
|
||||
fr unknown subspecies sous-espèce inconnue FALSE FALSE
|
||||
fr unknown rank rang inconnu FALSE FALSE
|
||||
fr Gram negative Gram négatif FALSE FALSE
|
||||
fr Gram positive Gram positif FALSE FALSE
|
||||
fr Gram-negative Gram négatif FALSE FALSE
|
||||
fr Gram-positive Gram positif FALSE FALSE
|
||||
fr Bacteria Bactéries FALSE FALSE
|
||||
fr Fungi Champignons FALSE FALSE
|
||||
fr Protozoa Protozoaires FALSE FALSE
|
||||
@ -131,8 +131,8 @@ fr ([([ ]*?)Group \\1Groupe FALSE FALSE
|
||||
pt Coagulase-negative Staphylococcus Staphylococcus coagulase negativo FALSE FALSE
|
||||
pt Coagulase-positive Staphylococcus Staphylococcus coagulase positivo FALSE FALSE
|
||||
pt Beta-haemolytic Streptococcus Streptococcus Beta-hemolítico FALSE FALSE
|
||||
pt unknown Gram negatives Gram negativos desconhecidos FALSE FALSE
|
||||
pt unknown Gram positives Gram positivos desconhecidos FALSE FALSE
|
||||
pt unknown Gram-negatives Gram negativos desconhecidos FALSE FALSE
|
||||
pt unknown Gram-positives Gram positivos desconhecidos FALSE FALSE
|
||||
pt unknown name nome desconhecido FALSE FALSE
|
||||
pt unknown kingdom reino desconhecido FALSE FALSE
|
||||
pt unknown phylum filo desconhecido FALSE FALSE
|
||||
@ -143,8 +143,8 @@ pt unknown genus gênero desconhecido FALSE FALSE
|
||||
pt unknown species espécies desconhecida FALSE FALSE
|
||||
pt unknown subspecies subespécies desconhecida FALSE FALSE
|
||||
pt unknown rank classificação desconhecido FALSE FALSE
|
||||
pt Gram negative Gram negativo FALSE FALSE
|
||||
pt Gram positive Gram positivo FALSE FALSE
|
||||
pt Gram-negative Gram negativo FALSE FALSE
|
||||
pt Gram-positive Gram positivo FALSE FALSE
|
||||
pt Bacteria Bactérias FALSE FALSE
|
||||
pt Fungi Fungos FALSE FALSE
|
||||
pt Protozoa Protozoários FALSE FALSE
|
||||
|
|
Binary file not shown.
Binary file not shown.
@ -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="Latest development version">0.7.0.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9005</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="Latest development version">0.7.0.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9005</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="Latest development version">0.7.0.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
@ -42,7 +42,7 @@
|
||||
</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="Latest development version">0.7.0.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9005</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="Latest development version">0.7.0.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -232,9 +232,9 @@
|
||||
|
||||
</div>
|
||||
|
||||
<div id="amr-0709004" class="section level1">
|
||||
<div id="amr-0709005" class="section level1">
|
||||
<h1 class="page-header">
|
||||
<a href="#amr-0709004" class="anchor"></a>AMR 0.7.0.9004<small> Unreleased </small>
|
||||
<a href="#amr-0709005" class="anchor"></a>AMR 0.7.0.9005<small> Unreleased </small>
|
||||
</h1>
|
||||
<div id="new" class="section level4">
|
||||
<h4 class="hasAnchor">
|
||||
@ -247,6 +247,7 @@
|
||||
<a class="sourceLine" id="cb1-3" title="3"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"UPEC"</span>)</a>
|
||||
<a class="sourceLine" id="cb1-4" title="4"><span class="co"># "Escherichia coli"</span></a></code></pre></div>
|
||||
</li>
|
||||
<li><p>Function <code><a href="../reference/mo_property.html">mo_info()</a></code> as an analogy to <code><a href="../reference/ab_property.html">ab_info()</a></code>. The <code><a href="../reference/mo_property.html">mo_info()</a></code> prints a list with the full taxonomy, authors, and the URL to the online database of a microorganism</p></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="changed" class="section level4">
|
||||
@ -256,6 +257,7 @@
|
||||
<li>Fixed bug in translation of microorganism names</li>
|
||||
<li>Fixed bug in determining taxonomic kingdoms</li>
|
||||
<li>Algorithm improvements for <code><a href="../reference/as.ab.html">as.ab()</a></code> and <code><a href="../reference/as.mo.html">as.mo()</a></code> to understand even more severely misspelled input</li>
|
||||
<li>Function <code><a href="../reference/as.ab.html">as.ab()</a></code> now allows spaces for coercing antibiotics names</li>
|
||||
<li>Added <code>ggplot2</code> methods for automatically determining the scale type of classes <code>mo</code> and <code>ab</code>
|
||||
</li>
|
||||
<li>Added names of object in the header in frequency tables, even when using pipes</li>
|
||||
@ -263,6 +265,9 @@
|
||||
<li>Fixed a bug where setting an antibiotic would not work for <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> and <code><a href="../reference/mdro.html">mdro()</a></code>
|
||||
</li>
|
||||
<li>Fixed a EUCAST rule for Staphylococci, where amikacin resistance would not be inferred from tobramycin</li>
|
||||
<li>Removed <code>latest_annual_release</code> from the <code><a href="../reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code> function</li>
|
||||
<li>Removed antibiotic code <code>PVM1</code> from the <code>antibiotics</code> data set as this was a duplicate of <code>PME</code>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="other" class="section level4">
|
||||
@ -1101,7 +1106,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
|
||||
<div id="tocnav">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#amr-0709004">0.7.0.9004</a></li>
|
||||
<li><a href="#amr-0709005">0.7.0.9005</a></li>
|
||||
<li><a href="#amr-070">0.7.0</a></li>
|
||||
<li><a href="#amr-061">0.6.1</a></li>
|
||||
<li><a href="#amr-060">0.6.0</a></li>
|
||||
|
@ -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">0.7.0.9000</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -165,13 +165,6 @@
|
||||
Create frequency tables
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/g.test.html">
|
||||
<span class="fa fa-clipboard-check"></span>
|
||||
|
||||
Use the G-test
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/benchmarks.html">
|
||||
<span class="fa fa-shipping-fast"></span>
|
||||
@ -252,7 +245,7 @@
|
||||
|
||||
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
|
||||
|
||||
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 454 observations and 13 variables:</p><dl class='dl-horizontal'>
|
||||
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 453 observations and 13 variables:</p><dl class='dl-horizontal'>
|
||||
<dt><code>ab</code></dt><dd><p>Antibiotic ID as used in this package (like <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></dd>
|
||||
<dt><code>atc</code></dt><dd><p>ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like <code>J01CR02</code></p></dd>
|
||||
<dt><code>cid</code></dt><dd><p>Compound ID as found in PubChem</p></dd>
|
||||
|
@ -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">0.7.0.9000</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -165,13 +165,6 @@
|
||||
Create frequency tables
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/g.test.html">
|
||||
<span class="fa fa-clipboard-check"></span>
|
||||
|
||||
Use the G-test
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/benchmarks.html">
|
||||
<span class="fa fa-shipping-fast"></span>
|
||||
@ -307,9 +300,9 @@ Function <code><a href='as.mo.html'>as.mo</a>()</code> to use the data for intel
|
||||
<span class='co'># [1] "Castellani et al., 1919"</span>
|
||||
|
||||
<span class='co'># Do not get mistaken - the package only includes microorganisms</span>
|
||||
<span class='fu'><a href='mo_property.html'>mo_phylum</a></span>(<span class='st'>"C. elegans"</span>)
|
||||
<span class='co'># [1] "Cyanobacteria" # Bacteria?!</span>
|
||||
<span class='fu'><a href='mo_property.html'>mo_fullname</a></span>(<span class='st'>"C. elegans"</span>)
|
||||
<span class='fu'><a href='mo_property.html'>mo_kingdom</a></span>(<span class='st'>"C. elegans"</span>)
|
||||
<span class='co'># [1] "Bacteria" # Bacteria?!</span>
|
||||
<span class='fu'><a href='mo_property.html'>mo_name</a></span>(<span class='st'>"C. elegans"</span>)
|
||||
<span class='co'># [1] "Chroococcus limneticus elegans" # Because a microorganism was found</span>
|
||||
<span class='co'># }</span></pre>
|
||||
</div>
|
||||
|
@ -47,7 +47,7 @@
|
||||
<script src="../extra.js"></script>
|
||||
<meta property="og:title" content="Version info of included Catalogue of Life — catalogue_of_life_version" />
|
||||
|
||||
<meta property="og:description" content="This function returns information about the included data from the Catalogue of Life. It also shows if the included version is their latest annual release. The Catalogue of Life releases their annual release in March each year." />
|
||||
<meta property="og:description" content="This function returns information about the included data from the Catalogue of Life." />
|
||||
|
||||
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
|
||||
<meta name="twitter:card" content="summary" />
|
||||
@ -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">0.7.0.9000</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -165,13 +165,6 @@
|
||||
Create frequency tables
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/g.test.html">
|
||||
<span class="fa fa-clipboard-check"></span>
|
||||
|
||||
Use the G-test
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/benchmarks.html">
|
||||
<span class="fa fa-shipping-fast"></span>
|
||||
@ -244,7 +237,7 @@
|
||||
|
||||
<div class="ref-description">
|
||||
|
||||
<p>This function returns information about the included data from the Catalogue of Life. It also shows if the included version is their latest annual release. The Catalogue of Life releases their annual release in March each year.</p>
|
||||
<p>This function returns information about the included data from the Catalogue of Life.</p>
|
||||
|
||||
</div>
|
||||
|
||||
@ -256,8 +249,7 @@
|
||||
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p>The list item <code>...$catalogue_of_life$is_latest_annual_release</code> is based on the system date.</p>
|
||||
<p>For DSMZ, see <code><a href='microorganisms.html'>?microorganisms</a></code>.</p>
|
||||
<p>For DSMZ, see <code><a href='microorganisms.html'>?microorganisms</a></code>.</p>
|
||||
|
||||
<h2 class="hasAnchor" id="catalogue-of-life"><a class="anchor" href="#catalogue-of-life"></a>Catalogue of Life</h2>
|
||||
|
||||
|
@ -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="Latest development version">0.7.0.9004</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -373,7 +373,7 @@
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="mo_property.html">mo_name()</a></code> <code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_rank()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_url()</a></code> <code><a href="mo_property.html">mo_property()</a></code> </p>
|
||||
<p><code><a href="mo_property.html">mo_name()</a></code> <code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_rank()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_info()</a></code> <code><a href="mo_property.html">mo_url()</a></code> <code><a href="mo_property.html">mo_property()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Property of a microorganism</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">0.7.0.9000</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -165,13 +165,6 @@
|
||||
Create frequency tables
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/g.test.html">
|
||||
<span class="fa fa-clipboard-check"></span>
|
||||
|
||||
Use the G-test
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/benchmarks.html">
|
||||
<span class="fa fa-shipping-fast"></span>
|
||||
@ -248,19 +241,22 @@
|
||||
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>key_antibiotics</span>(<span class='no'>x</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>universal_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"AMX"</span>),
|
||||
<span class='kw'>universal_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"AMC"</span>), <span class='kw'>universal_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
|
||||
<span class='st'>"CXM"</span>), <span class='kw'>universal_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"TZP"</span>),
|
||||
<span class='kw'>universal_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"CIP"</span>), <span class='kw'>universal_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
|
||||
<span class='st'>"SXT"</span>), <span class='kw'>GramPos_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"VAN"</span>),
|
||||
<span class='kw'>GramPos_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"TEC"</span>), <span class='kw'>GramPos_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
|
||||
<span class='st'>"TCY"</span>), <span class='kw'>GramPos_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"ERY"</span>),
|
||||
<span class='kw'>GramPos_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"OXA"</span>), <span class='kw'>GramPos_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
|
||||
<span class='st'>"RIF"</span>), <span class='kw'>GramNeg_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"GEN"</span>),
|
||||
<span class='kw'>GramNeg_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"TOB"</span>), <span class='kw'>GramNeg_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
|
||||
<span class='st'>"COL"</span>), <span class='kw'>GramNeg_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"CTX"</span>),
|
||||
<span class='kw'>GramNeg_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"CAZ"</span>), <span class='kw'>GramNeg_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
|
||||
<span class='st'>"MEM"</span>), <span class='kw'>warnings</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
|
||||
<pre class="usage"><span class='fu'>key_antibiotics</span>(<span class='no'>x</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>universal_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
|
||||
<span class='st'>"amoxicillin"</span>), <span class='kw'>universal_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
|
||||
<span class='st'>"amoxicillin/clavulanic acid"</span>), <span class='kw'>universal_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
|
||||
<span class='st'>"cefuroxime"</span>), <span class='kw'>universal_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
|
||||
<span class='st'>"piperacillin/tazobactam"</span>), <span class='kw'>universal_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
|
||||
<span class='st'>"ciprofloxacin"</span>), <span class='kw'>universal_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
|
||||
<span class='st'>"trimethoprim/sulfamethoxazole"</span>), <span class='kw'>GramPos_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
|
||||
<span class='st'>"vancomycin"</span>), <span class='kw'>GramPos_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"teicoplanin"</span>),
|
||||
<span class='kw'>GramPos_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"tetracycline"</span>),
|
||||
<span class='kw'>GramPos_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"erythromycin"</span>),
|
||||
<span class='kw'>GramPos_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"oxacillin"</span>), <span class='kw'>GramPos_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
|
||||
<span class='st'>"rifampin"</span>), <span class='kw'>GramNeg_1</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"gentamicin"</span>),
|
||||
<span class='kw'>GramNeg_2</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"tobramycin"</span>),
|
||||
<span class='kw'>GramNeg_3</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"colistin"</span>), <span class='kw'>GramNeg_4</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>,
|
||||
<span class='st'>"cefotaxime"</span>), <span class='kw'>GramNeg_5</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"ceftazidime"</span>),
|
||||
<span class='kw'>GramNeg_6</span> <span class='kw'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span>(<span class='no'>x</span>, <span class='st'>"meropenem"</span>), <span class='kw'>warnings</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>key_antibiotics_equal</span>(<span class='no'>y</span>, <span class='no'>z</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"keyantibiotics"</span>, <span class='st'>"points"</span>),
|
||||
<span class='kw'>ignore_I</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>points_threshold</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
|
||||
@ -282,11 +278,11 @@
|
||||
</tr>
|
||||
<tr>
|
||||
<th>GramPos_1, GramPos_2, GramPos_3, GramPos_4, GramPos_5, GramPos_6</th>
|
||||
<td><p>column names of antibiotics for <strong>Gram positives</strong>, case-insensitive. At default, the columns containing these antibiotics will be guessed with <code><a href='guess_ab_col.html'>guess_ab_col</a></code>.</p></td>
|
||||
<td><p>column names of antibiotics for <strong>Gram-positives</strong>, case-insensitive. At default, the columns containing these antibiotics will be guessed with <code><a href='guess_ab_col.html'>guess_ab_col</a></code>.</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>GramNeg_1, GramNeg_2, GramNeg_3, GramNeg_4, GramNeg_5, GramNeg_6</th>
|
||||
<td><p>column names of antibiotics for <strong>Gram negatives</strong>, case-insensitive. At default, the columns containing these antibiotics will be guessed with <code><a href='guess_ab_col.html'>guess_ab_col</a></code>.</p></td>
|
||||
<td><p>column names of antibiotics for <strong>Gram-negatives</strong>, case-insensitive. At default, the columns containing these antibiotics will be guessed with <code><a href='guess_ab_col.html'>guess_ab_col</a></code>.</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>warnings</th>
|
||||
@ -321,10 +317,10 @@
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p>The function <code>key_antibiotics</code> returns a character vector with 12 antibiotic results for every isolate. These isolates can then be compared using <code>key_antibiotics_equal</code>, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (<code>"."</code>). The <code><a href='first_isolate.html'>first_isolate</a></code> function only uses this function on the same microbial species from the same patient. Using this, an MRSA will be included after a susceptible <em>S. aureus</em> (MSSA) found within the same episode (see <code>episode</code> parameter of <code><a href='first_isolate.html'>first_isolate</a></code>). Without key antibiotic comparison it would not.</p>
|
||||
<p>At default, the antibiotics that are used for <strong>Gram positive bacteria</strong> are (colum names): <br />
|
||||
<code>"amox"</code>, <code>"amcl"</code>, <code>"cfur"</code>, <code>"pita"</code>, <code>"cipr"</code>, <code>"trsu"</code> (until here is universal), <code>"vanc"</code>, <code>"teic"</code>, <code>"tetr"</code>, <code>"eryt"</code>, <code>"oxac"</code>, <code>"rifa"</code>.</p>
|
||||
<p>At default, the antibiotics that are used for <strong>Gram negative bacteria</strong> are (colum names): <br />
|
||||
<code>"amox"</code>, <code>"amcl"</code>, <code>"cfur"</code>, <code>"pita"</code>, <code>"cipr"</code>, <code>"trsu"</code> (until here is universal), <code>"gent"</code>, <code>"tobr"</code>, <code>"coli"</code>, <code>"cfot"</code>, <code>"cfta"</code>, <code>"mero"</code>.</p>
|
||||
<p>At default, the antibiotics that are used for <strong>Gram-positive bacteria</strong> are: <br />
|
||||
amoxicillin, amoxicillin/clavulanic acid, cefuroxime, piperacillin/tazobactam, ciprofloxacin, trimethoprim/sulfamethoxazole (until here is universal), vancomycin, teicoplanin, tetracycline, erythromycin, oxacillin, rifampin.</p>
|
||||
<p>At default, the antibiotics that are used for <strong>Gram-negative bacteria</strong> are: <br />
|
||||
amoxicillin, amoxicillin/clavulanic acid, cefuroxime, piperacillin/tazobactam, ciprofloxacin, trimethoprim/sulfamethoxazole (until here is universal), gentamicin, tobramycin, colistin, cefotaxime, ceftazidime, meropenem.</p>
|
||||
<p>The function <code>key_antibiotics_equal</code> checks the characters returned by <code>key_antibiotics</code> for equality, and returns a logical vector.</p>
|
||||
|
||||
<h2 class="hasAnchor" id="key-antibiotics"><a class="anchor" href="#key-antibiotics"></a>Key antibiotics</h2>
|
||||
@ -350,6 +346,7 @@
|
||||
<pre class="examples"><span class='co'># NOT RUN {</span>
|
||||
<span class='co'># septic_patients is a dataset available in the AMR package</span>
|
||||
?<span class='no'>septic_patients</span>
|
||||
|
||||
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
|
||||
<span class='co'># set key antibiotics to a new variable</span>
|
||||
<span class='no'>my_patients</span> <span class='kw'><-</span> <span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
|
@ -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">0.7.0.9000</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9005</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -165,13 +165,6 @@
|
||||
Create frequency tables
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/g.test.html">
|
||||
<span class="fa fa-clipboard-check"></span>
|
||||
|
||||
Use the G-test
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/benchmarks.html">
|
||||
<span class="fa fa-shipping-fast"></span>
|
||||
@ -284,6 +277,8 @@
|
||||
|
||||
<span class='fu'>mo_taxonomy</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>mo_info</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>mo_url</span>(<span class='no'>x</span>, <span class='kw'>open</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>mo_property</span>(<span class='no'>x</span>, <span class='kw'>property</span> <span class='kw'>=</span> <span class='st'>"fullname"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='no'>...</span>)</pre>
|
||||
@ -378,8 +373,8 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
<span class='fu'>mo_shortname</span>(<span class='st'>"E. coli"</span>) <span class='co'># "E. coli"</span>
|
||||
|
||||
<span class='co'>## other properties</span>
|
||||
<span class='fu'>mo_gramstain</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Gram negative"</span>
|
||||
<span class='fu'>mo_type</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Bacteria" (equal to kingdom)</span>
|
||||
<span class='fu'>mo_gramstain</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Gram-negative"</span>
|
||||
<span class='fu'>mo_type</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Bacteria" (equal to kingdom, but may be translated)</span>
|
||||
<span class='fu'>mo_rank</span>(<span class='st'>"E. coli"</span>) <span class='co'># "species"</span>
|
||||
<span class='fu'>mo_url</span>(<span class='st'>"E. coli"</span>) <span class='co'># get the direct url to the online database entry</span>
|
||||
|
||||
@ -393,7 +388,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
<span class='fu'>mo_genus</span>(<span class='st'>"MRSA"</span>) <span class='co'># "Staphylococcus"</span>
|
||||
<span class='fu'>mo_species</span>(<span class='st'>"MRSA"</span>) <span class='co'># "aureus"</span>
|
||||
<span class='fu'>mo_shortname</span>(<span class='st'>"MRSA"</span>) <span class='co'># "S. aureus"</span>
|
||||
<span class='fu'>mo_gramstain</span>(<span class='st'>"MRSA"</span>) <span class='co'># "Gram positive"</span>
|
||||
<span class='fu'>mo_gramstain</span>(<span class='st'>"MRSA"</span>) <span class='co'># "Gram-positive"</span>
|
||||
|
||||
<span class='fu'>mo_genus</span>(<span class='st'>"VISA"</span>) <span class='co'># "Staphylococcus"</span>
|
||||
<span class='fu'>mo_species</span>(<span class='st'>"VISA"</span>) <span class='co'># "aureus"</span>
|
||||
@ -442,6 +437,8 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
|
||||
<span class='co'># get a list with the complete taxonomy (from kingdom to subspecies)</span>
|
||||
<span class='fu'>mo_taxonomy</span>(<span class='st'>"E. coli"</span>)
|
||||
<span class='co'># get a list with the taxonomy, the authors and the URL to the online database</span>
|
||||
<span class='fu'>mo_info</span>(<span class='st'>"E. coli"</span>)
|
||||
<span class='co'># }</span></pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
|
@ -4,7 +4,7 @@
|
||||
\name{antibiotics}
|
||||
\alias{antibiotics}
|
||||
\title{Data set with ~450 antibiotics}
|
||||
\format{A \code{\link{data.frame}} with 454 observations and 13 variables:
|
||||
\format{A \code{\link{data.frame}} with 453 observations and 13 variables:
|
||||
\describe{
|
||||
\item{\code{ab}}{Antibiotic ID as used in this package (like \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available}
|
||||
\item{\code{atc}}{ATC code (Anatomical Therapeutic Chemical) as defined by the WHOCC, like \code{J01CR02}}
|
||||
|
@ -61,9 +61,9 @@ mo_ref("E. coli")
|
||||
# [1] "Castellani et al., 1919"
|
||||
|
||||
# Do not get mistaken - the package only includes microorganisms
|
||||
mo_phylum("C. elegans")
|
||||
# [1] "Cyanobacteria" # Bacteria?!
|
||||
mo_fullname("C. elegans")
|
||||
mo_kingdom("C. elegans")
|
||||
# [1] "Bacteria" # Bacteria?!
|
||||
mo_name("C. elegans")
|
||||
# [1] "Chroococcus limneticus elegans" # Because a microorganism was found
|
||||
}
|
||||
\seealso{
|
||||
|
@ -10,11 +10,9 @@ catalogue_of_life_version()
|
||||
a \code{list}, which prints in pretty format
|
||||
}
|
||||
\description{
|
||||
This function returns information about the included data from the Catalogue of Life. It also shows if the included version is their latest annual release. The Catalogue of Life releases their annual release in March each year.
|
||||
This function returns information about the included data from the Catalogue of Life.
|
||||
}
|
||||
\details{
|
||||
The list item \code{...$catalogue_of_life$is_latest_annual_release} is based on the system date.
|
||||
|
||||
For DSMZ, see \code{?microorganisms}.
|
||||
}
|
||||
\section{Catalogue of Life}{
|
||||
|
@ -5,19 +5,22 @@
|
||||
\alias{key_antibiotics_equal}
|
||||
\title{Key antibiotics for first \emph{weighted} isolates}
|
||||
\usage{
|
||||
key_antibiotics(x, col_mo = NULL, universal_1 = guess_ab_col(x, "AMX"),
|
||||
universal_2 = guess_ab_col(x, "AMC"), universal_3 = guess_ab_col(x,
|
||||
"CXM"), universal_4 = guess_ab_col(x, "TZP"),
|
||||
universal_5 = guess_ab_col(x, "CIP"), universal_6 = guess_ab_col(x,
|
||||
"SXT"), GramPos_1 = guess_ab_col(x, "VAN"),
|
||||
GramPos_2 = guess_ab_col(x, "TEC"), GramPos_3 = guess_ab_col(x,
|
||||
"TCY"), GramPos_4 = guess_ab_col(x, "ERY"),
|
||||
GramPos_5 = guess_ab_col(x, "OXA"), GramPos_6 = guess_ab_col(x,
|
||||
"RIF"), GramNeg_1 = guess_ab_col(x, "GEN"),
|
||||
GramNeg_2 = guess_ab_col(x, "TOB"), GramNeg_3 = guess_ab_col(x,
|
||||
"COL"), GramNeg_4 = guess_ab_col(x, "CTX"),
|
||||
GramNeg_5 = guess_ab_col(x, "CAZ"), GramNeg_6 = guess_ab_col(x,
|
||||
"MEM"), warnings = TRUE, ...)
|
||||
key_antibiotics(x, col_mo = NULL, universal_1 = guess_ab_col(x,
|
||||
"amoxicillin"), universal_2 = guess_ab_col(x,
|
||||
"amoxicillin/clavulanic acid"), universal_3 = guess_ab_col(x,
|
||||
"cefuroxime"), universal_4 = guess_ab_col(x,
|
||||
"piperacillin/tazobactam"), universal_5 = guess_ab_col(x,
|
||||
"ciprofloxacin"), universal_6 = guess_ab_col(x,
|
||||
"trimethoprim/sulfamethoxazole"), GramPos_1 = guess_ab_col(x,
|
||||
"vancomycin"), GramPos_2 = guess_ab_col(x, "teicoplanin"),
|
||||
GramPos_3 = guess_ab_col(x, "tetracycline"),
|
||||
GramPos_4 = guess_ab_col(x, "erythromycin"),
|
||||
GramPos_5 = guess_ab_col(x, "oxacillin"), GramPos_6 = guess_ab_col(x,
|
||||
"rifampin"), GramNeg_1 = guess_ab_col(x, "gentamicin"),
|
||||
GramNeg_2 = guess_ab_col(x, "tobramycin"),
|
||||
GramNeg_3 = guess_ab_col(x, "colistin"), GramNeg_4 = guess_ab_col(x,
|
||||
"cefotaxime"), GramNeg_5 = guess_ab_col(x, "ceftazidime"),
|
||||
GramNeg_6 = guess_ab_col(x, "meropenem"), warnings = TRUE, ...)
|
||||
|
||||
key_antibiotics_equal(y, z, type = c("keyantibiotics", "points"),
|
||||
ignore_I = TRUE, points_threshold = 2, info = FALSE)
|
||||
@ -29,9 +32,9 @@ key_antibiotics_equal(y, z, type = c("keyantibiotics", "points"),
|
||||
|
||||
\item{universal_1, universal_2, universal_3, universal_4, universal_5, universal_6}{column names of \strong{broad-spectrum} antibiotics, case-insensitive. At default, the columns containing these antibiotics will be guessed with \code{\link{guess_ab_col}}.}
|
||||
|
||||
\item{GramPos_1, GramPos_2, GramPos_3, GramPos_4, GramPos_5, GramPos_6}{column names of antibiotics for \strong{Gram positives}, case-insensitive. At default, the columns containing these antibiotics will be guessed with \code{\link{guess_ab_col}}.}
|
||||
\item{GramPos_1, GramPos_2, GramPos_3, GramPos_4, GramPos_5, GramPos_6}{column names of antibiotics for \strong{Gram-positives}, case-insensitive. At default, the columns containing these antibiotics will be guessed with \code{\link{guess_ab_col}}.}
|
||||
|
||||
\item{GramNeg_1, GramNeg_2, GramNeg_3, GramNeg_4, GramNeg_5, GramNeg_6}{column names of antibiotics for \strong{Gram negatives}, case-insensitive. At default, the columns containing these antibiotics will be guessed with \code{\link{guess_ab_col}}.}
|
||||
\item{GramNeg_1, GramNeg_2, GramNeg_3, GramNeg_4, GramNeg_5, GramNeg_6}{column names of antibiotics for \strong{Gram-negatives}, case-insensitive. At default, the columns containing these antibiotics will be guessed with \code{\link{guess_ab_col}}.}
|
||||
|
||||
\item{warnings}{give warning about missing antibiotic columns, they will anyway be ignored}
|
||||
|
||||
@ -53,11 +56,11 @@ These function can be used to determine first isolates (see \code{\link{first_is
|
||||
\details{
|
||||
The function \code{key_antibiotics} returns a character vector with 12 antibiotic results for every isolate. These isolates can then be compared using \code{key_antibiotics_equal}, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (\code{"."}). The \code{\link{first_isolate}} function only uses this function on the same microbial species from the same patient. Using this, an MRSA will be included after a susceptible \emph{S. aureus} (MSSA) found within the same episode (see \code{episode} parameter of \code{\link{first_isolate}}). Without key antibiotic comparison it would not.
|
||||
|
||||
At default, the antibiotics that are used for \strong{Gram positive bacteria} are (colum names): \cr
|
||||
\code{"amox"}, \code{"amcl"}, \code{"cfur"}, \code{"pita"}, \code{"cipr"}, \code{"trsu"} (until here is universal), \code{"vanc"}, \code{"teic"}, \code{"tetr"}, \code{"eryt"}, \code{"oxac"}, \code{"rifa"}.
|
||||
At default, the antibiotics that are used for \strong{Gram-positive bacteria} are: \cr
|
||||
amoxicillin, amoxicillin/clavulanic acid, cefuroxime, piperacillin/tazobactam, ciprofloxacin, trimethoprim/sulfamethoxazole (until here is universal), vancomycin, teicoplanin, tetracycline, erythromycin, oxacillin, rifampin.
|
||||
|
||||
At default, the antibiotics that are used for \strong{Gram negative bacteria} are (colum names): \cr
|
||||
\code{"amox"}, \code{"amcl"}, \code{"cfur"}, \code{"pita"}, \code{"cipr"}, \code{"trsu"} (until here is universal), \code{"gent"}, \code{"tobr"}, \code{"coli"}, \code{"cfot"}, \code{"cfta"}, \code{"mero"}.
|
||||
At default, the antibiotics that are used for \strong{Gram-negative bacteria} are: \cr
|
||||
amoxicillin, amoxicillin/clavulanic acid, cefuroxime, piperacillin/tazobactam, ciprofloxacin, trimethoprim/sulfamethoxazole (until here is universal), gentamicin, tobramycin, colistin, cefotaxime, ceftazidime, meropenem.
|
||||
|
||||
|
||||
The function \code{key_antibiotics_equal} checks the characters returned by \code{key_antibiotics} for equality, and returns a logical vector.
|
||||
@ -81,6 +84,7 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
|
||||
\examples{
|
||||
# septic_patients is a dataset available in the AMR package
|
||||
?septic_patients
|
||||
|
||||
library(dplyr)
|
||||
# set key antibiotics to a new variable
|
||||
my_patients <- septic_patients \%>\%
|
||||
|
@ -20,6 +20,7 @@
|
||||
\alias{mo_year}
|
||||
\alias{mo_rank}
|
||||
\alias{mo_taxonomy}
|
||||
\alias{mo_info}
|
||||
\alias{mo_url}
|
||||
\title{Property of a microorganism}
|
||||
\usage{
|
||||
@ -59,6 +60,8 @@ mo_rank(x, ...)
|
||||
|
||||
mo_taxonomy(x, language = get_locale(), ...)
|
||||
|
||||
mo_info(x, language = get_locale(), ...)
|
||||
|
||||
mo_url(x, open = FALSE, ...)
|
||||
|
||||
mo_property(x, property = "fullname", language = get_locale(), ...)
|
||||
@ -140,8 +143,8 @@ mo_fullname("E. coli") # "Escherichia coli", same as mo_name()
|
||||
mo_shortname("E. coli") # "E. coli"
|
||||
|
||||
## other properties
|
||||
mo_gramstain("E. coli") # "Gram negative"
|
||||
mo_type("E. coli") # "Bacteria" (equal to kingdom)
|
||||
mo_gramstain("E. coli") # "Gram-negative"
|
||||
mo_type("E. coli") # "Bacteria" (equal to kingdom, but may be translated)
|
||||
mo_rank("E. coli") # "species"
|
||||
mo_url("E. coli") # get the direct url to the online database entry
|
||||
|
||||
@ -155,7 +158,7 @@ mo_year("E. coli") # 1919
|
||||
mo_genus("MRSA") # "Staphylococcus"
|
||||
mo_species("MRSA") # "aureus"
|
||||
mo_shortname("MRSA") # "S. aureus"
|
||||
mo_gramstain("MRSA") # "Gram positive"
|
||||
mo_gramstain("MRSA") # "Gram-positive"
|
||||
|
||||
mo_genus("VISA") # "Staphylococcus"
|
||||
mo_species("VISA") # "aureus"
|
||||
@ -204,6 +207,8 @@ mo_fullname("S. pyogenes",
|
||||
|
||||
# get a list with the complete taxonomy (from kingdom to subspecies)
|
||||
mo_taxonomy("E. coli")
|
||||
# get a list with the taxonomy, the authors and the URL to the online database
|
||||
mo_info("E. coli")
|
||||
}
|
||||
\seealso{
|
||||
\code{\link{microorganisms}}
|
||||
|
@ -24,12 +24,17 @@ context("data.R")
|
||||
test_that("data sets are valid", {
|
||||
# IDs should always be unique
|
||||
expect_identical(nrow(antibiotics), length(unique(antibiotics$ab)))
|
||||
expect_identical(class(antibiotics$ab), "ab")
|
||||
expect_identical(nrow(microorganisms), length(unique(microorganisms$mo)))
|
||||
expect_identical(class(microorganisms$mo), "mo")
|
||||
|
||||
# check cross table reference
|
||||
expect_true(all(microorganisms.codes$mo %in% microorganisms$mo))
|
||||
|
||||
# there should be no diacritics (i.e. non ASCII) characters in the datasets
|
||||
# antibiotic names must always be coercible to their original AB code
|
||||
expect_identical(antibiotics$ab, as.ab(antibiotics$name))
|
||||
|
||||
# there should be no diacritics (i.e. non ASCII) characters in the datasets (CRAN policy)
|
||||
datasets <- data(package = "AMR", envir = asNamespace("AMR"))$results[, "Item"]
|
||||
for (i in 1:length(datasets)) {
|
||||
dataset <- get(datasets[i], envir = asNamespace("AMR"))
|
||||
|
@ -33,10 +33,13 @@ test_that("mo_property works", {
|
||||
expect_equal(mo_fullname("E. coli"), "Escherichia coli")
|
||||
expect_equal(mo_name("E. coli"), "Escherichia coli")
|
||||
expect_equal(mo_type("E. coli", language = "en"), "Bacteria")
|
||||
expect_equal(mo_gramstain("E. coli", language = "en"), "Gram negative")
|
||||
expect_equal(mo_gramstain("E. coli", language = "en"), "Gram-negative")
|
||||
expect_equal(class(mo_taxonomy("E. coli")), "list")
|
||||
expect_equal(names(mo_taxonomy("E. coli")), c("kingdom", "phylum", "class", "order",
|
||||
"family", "genus", "species", "subspecies"))
|
||||
expect_equal(names(mo_info("E. coli")), c("kingdom", "phylum", "class", "order",
|
||||
"family", "genus", "species", "subspecies",
|
||||
"url", "ref"))
|
||||
|
||||
expect_equal(mo_ref("E. coli"), "Castellani et al., 1919")
|
||||
expect_equal(mo_authors("E. coli"), "Castellani et al.")
|
||||
|
Loading…
Reference in New Issue
Block a user