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con WHONET, filter ab class
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@ -97,7 +97,7 @@ pages:
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script:
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#- Rscript -e "install.packages('pkgdown', repos = 'https://cran.rstudio.com')"
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- Rscript -e "devtools::install(build = TRUE, upgrade = FALSE)"
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- R -e "pkgdown::build_site(examples = FALSE, override = list(destination = 'public'))"
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- R -e "pkgdown::build_site(examples = FALSE, lazy = TRUE, override = list(destination = 'public'))"
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artifacts:
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paths:
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- public
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 0.5.0.9020
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Date: 2019-03-02
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Version: 0.5.0.9021
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Date: 2019-03-05
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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person(
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12
NAMESPACE
12
NAMESPACE
@ -81,8 +81,20 @@ export(count_df)
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export(eucast_exceptional_phenotypes)
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export(eucast_rules)
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export(facet_rsi)
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export(filter_1st_cephalosporins)
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export(filter_2nd_cephalosporins)
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export(filter_3rd_cephalosporins)
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export(filter_4th_cephalosporins)
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export(filter_ab_class)
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export(filter_aminoglycosides)
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export(filter_carbapenems)
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export(filter_cephalosporins)
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export(filter_first_isolate)
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export(filter_first_weighted_isolate)
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export(filter_fluoroquinolones)
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export(filter_glycopeptides)
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export(filter_macrolides)
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export(filter_tetracyclines)
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export(first_isolate)
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export(freq)
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export(frequency_tbl)
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268
R/filter_ab_class.R
Normal file
268
R/filter_ab_class.R
Normal file
@ -0,0 +1,268 @@
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# #
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# This R package was created for academic research and was publicly #
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# released in the hope that it will be useful, but it comes WITHOUT #
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# ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitab.io/AMR. #
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# ==================================================================== #
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#' Filter on antibiotic class
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#'
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#' Filter on specific antibiotic variables based on their class (ATC groups).
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#' @param tbl a data set
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#' @param ab_class an antimicrobial class, like \code{"carbapenems"}
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#' @param result an antibiotic result: S, I or R (or a combination of more of them)
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#' @param scope the scope to check which variables to check, can be \code{"any"} (default) or \code{"all"}
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#' @param ... parameters passed on to \code{\link[dplyr]{filter_at}}
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#' @details The \code{\code{antibiotics}} data set will be searched for \code{ab_class} in the columns \code{atc_group1} and \code{atc_group2} (case-insensitive). Next, \code{tbl} will be checked for column names with a value in any abbreviations, codes or official names found in the \code{antibiotics} data set.
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#' @rdname filter_ab_class
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#' @importFrom dplyr filter_at %>% select vars any_vars all_vars
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#' @importFrom crayon bold blue
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#' @export
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#' @examples
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#' library(dplyr)
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#'
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#' # filter on isolates that have any result for any aminoglycoside
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#' septic_patients %>% filter_aminoglycosides()
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#'
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#' # this is essentially the same as:
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#' septic_patients %>%
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#' filter_at(.vars = vars(c("gent", "tobr", "amik", "kana")),
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#' .vars_predicate = any_vars(. %in% c("S", "I", "R")))
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#'
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#'
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#' # filter on isolates that show resistance to ANY aminoglycoside
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#' septic_patients %>% filter_aminoglycosides("R")
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#'
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#' # filter on isolates that show resistance to ALL aminoglycosides
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#' septic_patients %>% filter_aminoglycosides("R", "all")
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#'
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#' # filter on isolates that show resistance to
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#' # any aminoglycoside and any fluoroquinolone
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#' septic_patients %>%
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#' filter_aminoglycosides("R", "any") %>%
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#' filter_fluoroquinolones("R", "any")
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filter_ab_class <- function(tbl,
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ab_class,
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result = NULL,
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scope = "any",
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...) {
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scope <- scope[1L]
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if (is.null(result)) {
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result <- c("S", "I", "R")
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}
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if (!all(result %in% c("S", "I", "R"))) {
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stop("`result` must be one or more of: S, I, R", call. = FALSE)
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}
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if (!all(scope %in% c("any", "all"))) {
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stop("`scope` must be one of: any, all", call. = FALSE)
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}
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vars_df <- colnames(tbl)[tolower(colnames(tbl)) %in% tolower(ab_class_vars(ab_class))]
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atc_groups <- ab_class_atcgroups(ab_class)
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if (length(vars_df) > 0) {
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if (length(result) == 1) {
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operator <- " is "
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} else {
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operator <- " is one of "
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}
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if (scope == "any") {
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scope_txt <- " or "
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scope_fn <- any_vars
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} else {
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scope_txt <- " and "
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scope_fn <- all_vars
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}
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message(blue(paste0("Filtering on ", atc_groups, ": ", scope, " of ",
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paste(bold(vars_df), collapse = scope_txt), operator, toString(result))))
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tbl %>%
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filter_at(.vars = vars(vars_df),
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.vars_predicate = scope_fn(. %in% result),
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...)
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} else {
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warning(paste0("no antibiotics of class ", atc_groups, " found, leaving data unchanged"), call. = FALSE)
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tbl
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}
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}
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#' @rdname filter_ab_class
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#' @export
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filter_aminoglycosides <- function(tbl,
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result = NULL,
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scope = "any",
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...) {
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filter_ab_class(tbl = tbl,
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ab_class = "aminoglycoside",
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result = result,
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scope = scope,
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...)
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}
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#' @rdname filter_ab_class
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#' @export
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filter_carbapenems <- function(tbl,
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result = NULL,
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scope = "any",
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...) {
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filter_ab_class(tbl = tbl,
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ab_class = "carbapenem",
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result = result,
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scope = scope,
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...)
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}
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#' @rdname filter_ab_class
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#' @export
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filter_cephalosporins <- function(tbl,
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result = NULL,
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scope = "any",
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...) {
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filter_ab_class(tbl = tbl,
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ab_class = "cephalosporin",
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result = result,
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scope = scope,
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...)
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}
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#' @rdname filter_ab_class
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#' @export
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filter_1st_cephalosporins <- function(tbl,
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result = NULL,
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scope = "any",
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...) {
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filter_ab_class(tbl = tbl,
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ab_class = "first-generation cephalosporin",
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result = result,
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scope = scope,
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...)
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}
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#' @rdname filter_ab_class
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#' @export
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filter_2nd_cephalosporins <- function(tbl,
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result = NULL,
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scope = "any",
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...) {
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filter_ab_class(tbl = tbl,
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ab_class = "second-generation cephalosporin",
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result = result,
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scope = scope,
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...)
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}
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#' @rdname filter_ab_class
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#' @export
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filter_3rd_cephalosporins <- function(tbl,
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result = NULL,
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scope = "any",
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...) {
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filter_ab_class(tbl = tbl,
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ab_class = "third-generation cephalosporin",
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result = result,
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scope = scope,
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...)
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}
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#' @rdname filter_ab_class
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#' @export
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filter_4th_cephalosporins <- function(tbl,
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result = NULL,
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scope = "any",
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...) {
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filter_ab_class(tbl = tbl,
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ab_class = "fourth-generation cephalosporin",
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result = result,
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scope = scope,
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...)
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}
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#' @rdname filter_ab_class
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#' @export
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filter_fluoroquinolones <- function(tbl,
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result = NULL,
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scope = "any",
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...) {
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filter_ab_class(tbl = tbl,
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ab_class = "fluoroquinolone",
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result = result,
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scope = scope,
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...)
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}
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#' @rdname filter_ab_class
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#' @export
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filter_glycopeptides <- function(tbl,
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result = NULL,
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scope = "any",
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...) {
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filter_ab_class(tbl = tbl,
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ab_class = "glycopeptide",
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result = result,
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scope = scope,
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...)
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}
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#' @rdname filter_ab_class
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#' @export
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filter_macrolides <- function(tbl,
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result = NULL,
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scope = "any",
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...) {
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filter_ab_class(tbl = tbl,
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ab_class = "macrolide",
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result = result,
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scope = scope,
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...)
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}
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#' @rdname filter_ab_class
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#' @export
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filter_tetracyclines <- function(tbl,
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result = NULL,
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scope = "any",
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...) {
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filter_ab_class(tbl = tbl,
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ab_class = "tetracycline",
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result = result,
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scope = scope,
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...)
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}
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#' @importFrom dplyr %>% filter_at any_vars select
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ab_class_vars <- function(ab_class) {
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ab_vars <- AMR::antibiotics %>%
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filter_at(vars(c("atc_group1", "atc_group2")), any_vars(. %like% ab_class)) %>%
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select(atc:trade_name) %>%
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as.matrix() %>%
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as.character() %>%
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paste(collapse = "|") %>%
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strsplit("|", fixed = TRUE) %>%
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unlist() %>%
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unique()
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ab_vars[!is.na(ab_vars)]
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}
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#' @importFrom dplyr %>% filter pull
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ab_class_atcgroups <- function(ab_class) {
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AMR::antibiotics %>%
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filter(atc %in% ab_class_vars(ab_class)) %>%
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pull("atc_group2") %>%
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unique() %>%
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tolower() %>%
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paste(collapse = "/")
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}
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51
R/mo.R
51
R/mo.R
@ -174,14 +174,26 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE,
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# check onLoad() in R/zzz.R: data tables are created there.
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}
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if (deparse(substitute(reference_df)) == "get_mo_source()"
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if (mo_source_isvalid(reference_df)
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& isFALSE(Becker)
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& isFALSE(Lancefield)
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& !is.null(reference_df)
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& all(x %in% reference_df[,1])) {
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& all(x %in% reference_df[,1][[1]])) {
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# has valid own reference_df
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# (data.table not faster here)
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reference_df <- reference_df %>% filter(!is.na(mo))
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# keep only first two columns, second must be mo
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if (colnames(reference_df)[1] == "mo") {
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reference_df <- reference_df[, c(2, 1)]
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} else {
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reference_df <- reference_df[, c(1, 2)]
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}
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colnames(reference_df)[1] <- "x"
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# remove factors, just keep characters
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suppressWarnings(
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reference_df[] <- lapply(reference_df, as.character)
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)
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suppressWarnings(
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y <- data.frame(x = x, stringsAsFactors = FALSE) %>%
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left_join(reference_df, by = "x") %>%
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@ -277,8 +289,12 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
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# only check the uniques, which is way faster
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x <- unique(x)
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# remove empty values (to later fill them in again with NAs)
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# ("xxx" is WHONET code for 'no growth')
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x <- x[!is.na(x) & !is.null(x) & !identical(x, "") & !identical(x, "xxx")]
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# ("xxx" is WHONET code for 'no growth' and "con" is WHONET code for 'contamination')
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x <- x[!is.na(x)
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& !is.null(x)
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& !identical(x, "")
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& !identical(x, "xxx")
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& !identical(x, "con")]
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# conversion of old MO codes from v0.5.0 (ITIS) to later versions (Catalogue of Life)
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if (any(x %like% "^[BFP]_[A-Z]{3,7}") & !all(x %in% microorganisms$mo)) {
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@ -292,14 +308,18 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
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# defined df to check for
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if (!is.null(reference_df)) {
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if (!is.data.frame(reference_df) | NCOL(reference_df) < 2) {
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stop('`reference_df` must be a data.frame with at least two columns.', call. = FALSE)
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}
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if (!"mo" %in% colnames(reference_df)) {
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if (!mo_source_isvalid(reference_df)) {
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stop("`reference_df` must contain a column `mo` with values from the 'microorganisms' data set.", call. = FALSE)
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}
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reference_df <- reference_df %>% filter(!is.na(mo))
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# # remove factors, just keep characters
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# keep only first two columns, second must be mo
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if (colnames(reference_df)[1] == "mo") {
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reference_df <- reference_df[, c(2, 1)]
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} else {
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reference_df <- reference_df[, c(1, 2)]
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}
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colnames(reference_df)[1] <- "x"
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# remove factors, just keep characters
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suppressWarnings(
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reference_df[] <- lapply(reference_df, as.character)
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)
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@ -314,8 +334,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
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return(rep(NA_character_, length(x_input)))
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}
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} else if (all(x %in% reference_df[, 1])
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& all(reference_df[, "mo"] %in% AMR::microorganisms$mo)) {
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} else if (all(x %in% reference_df[, 1][[1]])) {
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# all in reference df
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colnames(reference_df)[1] <- "x"
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suppressWarnings(
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@ -420,12 +439,12 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
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next
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}
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if (any(x_trimmed[i] %in% c(NA, ""))) {
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if (any(x_trimmed[i] %in% c(NA, "", "xxx", "con"))) {
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x[i] <- NA_character_
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next
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}
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if (tolower(x_trimmed[i]) %in% c("xxx", "other", "none", "unknown")) {
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if (tolower(x_trimmed[i]) %in% c("other", "none", "unknown")) {
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# empty and nonsense values, ignore without warning
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x[i] <- microorganismsDT[mo == "UNKNOWN", ..property][[1]]
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next
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@ -959,7 +978,11 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
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# Wrap up ----------------------------------------------------------------
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# comply to x, which is also unique and without empty values
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x_input_unique_nonempty <- unique(x_input[!is.na(x_input) & !is.null(x_input) & !identical(x_input, "") & !identical(x_input, "xxx")])
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x_input_unique_nonempty <- unique(x_input[!is.na(x_input)
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& !is.null(x_input)
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& !identical(x_input, "")
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& !identical(x_input, "xxx")
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& !identical(x_input, "con")])
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# left join the found results to the original input values (x_input)
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df_found <- data.frame(input = as.character(x_input_unique_nonempty),
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@ -117,22 +117,6 @@ set_mo_source <- function(path) {
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stop("File not found: ", path)
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}
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is_valid <- function(df) {
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valid <- TRUE
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if (!is.data.frame(df)) {
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valid <- FALSE
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} else if (!"mo" %in% colnames(df)) {
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valid <- FALSE
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} else if (all(as.data.frame(df)[, 1] == "")) {
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valid <- FALSE
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} else if (!all(df$mo %in% c("", AMR::microorganisms$mo))) {
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valid <- FALSE
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} else if (NCOL(df) < 2) {
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valid <- FALSE
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}
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valid
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}
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if (path %like% '[.]rds$') {
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df <- readRDS(path)
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@ -151,13 +135,13 @@ set_mo_source <- function(path) {
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try(
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df <- utils::read.table(header = TRUE, sep = ",", stringsAsFactors = FALSE),
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silent = TRUE)
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if (!is_valid(df)) {
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if (!mo_source_isvalid(df)) {
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# try tab
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try(
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df <- utils::read.table(header = TRUE, sep = "\t", stringsAsFactors = FALSE),
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silent = TRUE)
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}
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if (!is_valid(df)) {
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if (!mo_source_isvalid(df)) {
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||||
# try pipe
|
||||
try(
|
||||
df <- utils::read.table(header = TRUE, sep = "|", stringsAsFactors = FALSE),
|
||||
@ -165,10 +149,12 @@ set_mo_source <- function(path) {
|
||||
}
|
||||
}
|
||||
|
||||
if (!is_valid(df)) {
|
||||
if (!mo_source_isvalid(df)) {
|
||||
stop("File must contain a column with self-defined values and a reference column `mo` with valid values from the `microorganisms` data set.")
|
||||
}
|
||||
|
||||
df <- df %>% filter(!is.na(mo))
|
||||
|
||||
# keep only first two columns, second must be mo
|
||||
if (colnames(df)[1] == "mo") {
|
||||
df <- df[, c(2, 1)]
|
||||
@ -213,3 +199,22 @@ get_mo_source <- function() {
|
||||
|
||||
readRDS("~/.mo_source.rds")
|
||||
}
|
||||
|
||||
mo_source_isvalid <- function(x) {
|
||||
if (deparse(substitute(x)) == "get_mo_source()") {
|
||||
return(TRUE)
|
||||
}
|
||||
if (identical(x, get_mo_source())) {
|
||||
return(TRUE)
|
||||
}
|
||||
if (is.null(x)) {
|
||||
return(TRUE)
|
||||
}
|
||||
if (!is.data.frame(x)) {
|
||||
return(FALSE)
|
||||
}
|
||||
if (!"mo" %in% colnames(x)) {
|
||||
return(FALSE)
|
||||
}
|
||||
all(x$mo %in% c("", AMR::microorganisms$mo))
|
||||
}
|
||||
|
||||
@ -78,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -40,7 +40,7 @@
|
||||
</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">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -192,7 +192,7 @@
|
||||
<h1>How to conduct AMR analysis</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">02 March 2019</h4>
|
||||
<h4 class="date">05 March 2019</h4>
|
||||
|
||||
|
||||
<div class="hidden name"><code>AMR.Rmd</code></div>
|
||||
@ -201,7 +201,7 @@
|
||||
|
||||
|
||||
|
||||
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">RMarkdown</a>. However, the methodology remains unchanged. This page was generated on 02 March 2019.</p>
|
||||
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">RMarkdown</a>. However, the methodology remains unchanged. This page was generated on 05 March 2019.</p>
|
||||
<div id="introduction" class="section level1">
|
||||
<h1 class="hasAnchor">
|
||||
<a href="#introduction" class="anchor"></a>Introduction</h1>
|
||||
@ -217,21 +217,21 @@
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">2019-03-02</td>
|
||||
<td align="center">2019-03-05</td>
|
||||
<td align="center">abcd</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2019-03-02</td>
|
||||
<td align="center">2019-03-05</td>
|
||||
<td align="center">abcd</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2019-03-02</td>
|
||||
<td align="center">2019-03-05</td>
|
||||
<td align="center">efgh</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">R</td>
|
||||
@ -327,30 +327,52 @@
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">2012-06-30</td>
|
||||
<td align="center">2010-01-23</td>
|
||||
<td align="center">E2</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Staphylococcus aureus</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2017-12-07</td>
|
||||
<td align="center">L8</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Staphylococcus aureus</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2012-07-19</td>
|
||||
<td align="center">W5</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">Staphylococcus aureus</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2012-07-07</td>
|
||||
<td align="center">T4</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">2013-11-26</td>
|
||||
<td align="center">L7</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2011-02-19</td>
|
||||
<td align="center">H3</td>
|
||||
<td align="center">2016-01-24</td>
|
||||
<td align="center">M7</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
@ -360,37 +382,15 @@
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2012-12-15</td>
|
||||
<td align="center">G10</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">Klebsiella pneumoniae</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2010-09-11</td>
|
||||
<td align="center">L4</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">Staphylococcus aureus</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2011-03-27</td>
|
||||
<td align="center">H5</td>
|
||||
<td align="center">2016-11-13</td>
|
||||
<td align="center">V10</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -411,8 +411,8 @@
|
||||
#>
|
||||
#> Item Count Percent Cum. Count Cum. Percent
|
||||
#> --- ----- ------- -------- ----------- -------------
|
||||
#> 1 M 10,433 52.2% 10,433 52.2%
|
||||
#> 2 F 9,567 47.8% 20,000 100.0%</code></pre>
|
||||
#> 1 M 10,562 52.8% 10,562 52.8%
|
||||
#> 2 F 9,438 47.2% 20,000 100.0%</code></pre>
|
||||
<p>So, we can draw at least two conclusions immediately. From a data scientist perspective, the data looks clean: only values <code>M</code> and <code>F</code>. From a researcher perspective: there are slightly more men. Nothing we didn’t already know.</p>
|
||||
<p>The data is already quite clean, but we still need to transform some variables. The <code>bacteria</code> column now consists of text, and we want to add more variables based on microbial IDs later on. So, we will transform this column to valid IDs. The <code><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate()</a></code> function of the <code>dplyr</code> package makes this really easy:</p>
|
||||
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" title="1">data <-<span class="st"> </span>data <span class="op">%>%</span></a>
|
||||
@ -443,10 +443,10 @@
|
||||
<a class="sourceLine" id="cb14-19" title="19"><span class="co">#> Kingella kingae (no changes)</span></a>
|
||||
<a class="sourceLine" id="cb14-20" title="20"><span class="co">#> </span></a>
|
||||
<a class="sourceLine" id="cb14-21" title="21"><span class="co">#> EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)</span></a>
|
||||
<a class="sourceLine" id="cb14-22" title="22"><span class="co">#> Table 1: Intrinsic resistance in Enterobacteriaceae (1323 changes)</span></a>
|
||||
<a class="sourceLine" id="cb14-22" title="22"><span class="co">#> Table 1: Intrinsic resistance in Enterobacteriaceae (1344 changes)</span></a>
|
||||
<a class="sourceLine" id="cb14-23" title="23"><span class="co">#> Table 2: Intrinsic resistance in non-fermentative Gram-negative bacteria (no changes)</span></a>
|
||||
<a class="sourceLine" id="cb14-24" title="24"><span class="co">#> Table 3: Intrinsic resistance in other Gram-negative bacteria (no changes)</span></a>
|
||||
<a class="sourceLine" id="cb14-25" title="25"><span class="co">#> Table 4: Intrinsic resistance in Gram-positive bacteria (2834 changes)</span></a>
|
||||
<a class="sourceLine" id="cb14-25" title="25"><span class="co">#> Table 4: Intrinsic resistance in Gram-positive bacteria (2767 changes)</span></a>
|
||||
<a class="sourceLine" id="cb14-26" title="26"><span class="co">#> Table 8: Interpretive rules for B-lactam agents and Gram-positive cocci (no changes)</span></a>
|
||||
<a class="sourceLine" id="cb14-27" title="27"><span class="co">#> Table 9: Interpretive rules for B-lactam agents and Gram-negative rods (no changes)</span></a>
|
||||
<a class="sourceLine" id="cb14-28" title="28"><span class="co">#> Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria (no changes)</span></a>
|
||||
@ -462,9 +462,9 @@
|
||||
<a class="sourceLine" id="cb14-38" title="38"><span class="co">#> Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no changes)</span></a>
|
||||
<a class="sourceLine" id="cb14-39" title="39"><span class="co">#> Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no changes)</span></a>
|
||||
<a class="sourceLine" id="cb14-40" title="40"><span class="co">#> </span></a>
|
||||
<a class="sourceLine" id="cb14-41" title="41"><span class="co">#> => EUCAST rules affected 7,524 out of 20,000 rows</span></a>
|
||||
<a class="sourceLine" id="cb14-41" title="41"><span class="co">#> => EUCAST rules affected 7,383 out of 20,000 rows</span></a>
|
||||
<a class="sourceLine" id="cb14-42" title="42"><span class="co">#> -> added 0 test results</span></a>
|
||||
<a class="sourceLine" id="cb14-43" title="43"><span class="co">#> -> changed 4,157 test results (0 to S; 0 to I; 4,157 to R)</span></a></code></pre></div>
|
||||
<a class="sourceLine" id="cb14-43" title="43"><span class="co">#> -> changed 4,111 test results (0 to S; 0 to I; 4,111 to R)</span></a></code></pre></div>
|
||||
</div>
|
||||
<div id="adding-new-variables" class="section level1">
|
||||
<h1 class="hasAnchor">
|
||||
@ -489,8 +489,8 @@
|
||||
<a class="sourceLine" id="cb16-3" title="3"><span class="co">#> </span><span class="al">NOTE</span><span class="co">: Using column `bacteria` as input for `col_mo`.</span></a>
|
||||
<a class="sourceLine" id="cb16-4" title="4"><span class="co">#> </span><span class="al">NOTE</span><span class="co">: Using column `date` as input for `col_date`.</span></a>
|
||||
<a class="sourceLine" id="cb16-5" title="5"><span class="co">#> </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></a>
|
||||
<a class="sourceLine" id="cb16-6" title="6"><span class="co">#> => Found 5,698 first isolates (28.5% of total)</span></a></code></pre></div>
|
||||
<p>So only 28.5% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
|
||||
<a class="sourceLine" id="cb16-6" title="6"><span class="co">#> => Found 5,676 first isolates (28.4% of total)</span></a></code></pre></div>
|
||||
<p>So only 28.4% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
|
||||
<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1">data_1st <-<span class="st"> </span>data <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb17-2" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(first <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>)</a></code></pre></div>
|
||||
<p>For future use, the above two syntaxes can be shortened with the <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> function:</p>
|
||||
@ -516,21 +516,21 @@
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">1</td>
|
||||
<td align="center">2010-01-18</td>
|
||||
<td align="center">C7</td>
|
||||
<td align="center">2010-01-20</td>
|
||||
<td align="center">L10</td>
|
||||
<td align="center">B_ESCHR_COL</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2</td>
|
||||
<td align="center">2010-02-27</td>
|
||||
<td align="center">C7</td>
|
||||
<td align="center">2010-03-26</td>
|
||||
<td align="center">L10</td>
|
||||
<td align="center">B_ESCHR_COL</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
@ -538,8 +538,8 @@
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">3</td>
|
||||
<td align="center">2010-04-22</td>
|
||||
<td align="center">C7</td>
|
||||
<td align="center">2010-05-05</td>
|
||||
<td align="center">L10</td>
|
||||
<td align="center">B_ESCHR_COL</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
@ -549,8 +549,8 @@
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">4</td>
|
||||
<td align="center">2010-06-09</td>
|
||||
<td align="center">C7</td>
|
||||
<td align="center">2010-06-20</td>
|
||||
<td align="center">L10</td>
|
||||
<td align="center">B_ESCHR_COL</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
@ -560,19 +560,19 @@
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">5</td>
|
||||
<td align="center">2011-04-13</td>
|
||||
<td align="center">C7</td>
|
||||
<td align="center">2010-07-10</td>
|
||||
<td align="center">L10</td>
|
||||
<td align="center">B_ESCHR_COL</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">TRUE</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">6</td>
|
||||
<td align="center">2011-04-25</td>
|
||||
<td align="center">C7</td>
|
||||
<td align="center">2010-08-01</td>
|
||||
<td align="center">L10</td>
|
||||
<td align="center">B_ESCHR_COL</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
@ -582,32 +582,32 @@
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">7</td>
|
||||
<td align="center">2011-08-02</td>
|
||||
<td align="center">C7</td>
|
||||
<td align="center">2010-08-27</td>
|
||||
<td align="center">L10</td>
|
||||
<td align="center">B_ESCHR_COL</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">8</td>
|
||||
<td align="center">2011-10-19</td>
|
||||
<td align="center">C7</td>
|
||||
<td align="center">2010-09-09</td>
|
||||
<td align="center">L10</td>
|
||||
<td align="center">B_ESCHR_COL</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">9</td>
|
||||
<td align="center">2011-10-23</td>
|
||||
<td align="center">C7</td>
|
||||
<td align="center">2010-09-26</td>
|
||||
<td align="center">L10</td>
|
||||
<td align="center">B_ESCHR_COL</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
@ -615,18 +615,18 @@
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">10</td>
|
||||
<td align="center">2011-11-10</td>
|
||||
<td align="center">C7</td>
|
||||
<td align="center">2010-10-11</td>
|
||||
<td align="center">L10</td>
|
||||
<td align="center">B_ESCHR_COL</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<p>Only 2 isolates are marked as ‘first’ according to CLSI guideline. But when reviewing the antibiogram, it is obvious that some isolates are absolutely different strains and should be included too. This is why we weigh isolates, based on their antibiogram. The <code><a href="../reference/key_antibiotics.html">key_antibiotics()</a></code> function adds a vector with 18 key antibiotics: 6 broad spectrum ones, 6 small spectrum for Gram negatives and 6 small spectrum for Gram positives. These can be defined by the user.</p>
|
||||
<p>Only 1 isolates are marked as ‘first’ according to CLSI guideline. But when reviewing the antibiogram, it is obvious that some isolates are absolutely different strains and should be included too. This is why we weigh isolates, based on their antibiogram. The <code><a href="../reference/key_antibiotics.html">key_antibiotics()</a></code> function adds a vector with 18 key antibiotics: 6 broad spectrum ones, 6 small spectrum for Gram negatives and 6 small spectrum for Gram positives. These can be defined by the user.</p>
|
||||
<p>If a column exists with a name like ‘key(…)ab’ the <code><a href="../reference/first_isolate.html">first_isolate()</a></code> function will automatically use it and determine the first weighted isolates. Mind the NOTEs in below output:</p>
|
||||
<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" title="1">data <-<span class="st"> </span>data <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb19-2" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="dt">keyab =</span> <span class="kw"><a href="../reference/key_antibiotics.html">key_antibiotics</a></span>(.)) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
@ -637,7 +637,7 @@
|
||||
<a class="sourceLine" id="cb19-7" title="7"><span class="co">#> </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></a>
|
||||
<a class="sourceLine" id="cb19-8" title="8"><span class="co">#> </span><span class="al">NOTE</span><span class="co">: Using column `keyab` as input for `col_keyantibiotics`. Use col_keyantibiotics = FALSE to prevent this.</span></a>
|
||||
<a class="sourceLine" id="cb19-9" title="9"><span class="co">#> [Criterion] Inclusion based on key antibiotics, ignoring I.</span></a>
|
||||
<a class="sourceLine" id="cb19-10" title="10"><span class="co">#> => Found 15,826 first weighted isolates (79.1% of total)</span></a></code></pre></div>
|
||||
<a class="sourceLine" id="cb19-10" title="10"><span class="co">#> => Found 15,767 first weighted isolates (78.8% of total)</span></a></code></pre></div>
|
||||
<table class="table">
|
||||
<thead><tr class="header">
|
||||
<th align="center">isolate</th>
|
||||
@ -654,11 +654,11 @@
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">1</td>
|
||||
<td align="center">2010-01-18</td>
|
||||
<td align="center">C7</td>
|
||||
<td align="center">2010-01-20</td>
|
||||
<td align="center">L10</td>
|
||||
<td align="center">B_ESCHR_COL</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">TRUE</td>
|
||||
@ -666,32 +666,32 @@
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2</td>
|
||||
<td align="center">2010-02-27</td>
|
||||
<td align="center">C7</td>
|
||||
<td align="center">2010-03-26</td>
|
||||
<td align="center">L10</td>
|
||||
<td align="center">B_ESCHR_COL</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
<td align="center">FALSE</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">3</td>
|
||||
<td align="center">2010-04-22</td>
|
||||
<td align="center">C7</td>
|
||||
<td align="center">2010-05-05</td>
|
||||
<td align="center">L10</td>
|
||||
<td align="center">B_ESCHR_COL</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
<td align="center">FALSE</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">4</td>
|
||||
<td align="center">2010-06-09</td>
|
||||
<td align="center">C7</td>
|
||||
<td align="center">2010-06-20</td>
|
||||
<td align="center">L10</td>
|
||||
<td align="center">B_ESCHR_COL</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
@ -702,83 +702,83 @@
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">5</td>
|
||||
<td align="center">2011-04-13</td>
|
||||
<td align="center">C7</td>
|
||||
<td align="center">B_ESCHR_COL</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">TRUE</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">6</td>
|
||||
<td align="center">2011-04-25</td>
|
||||
<td align="center">C7</td>
|
||||
<td align="center">2010-07-10</td>
|
||||
<td align="center">L10</td>
|
||||
<td align="center">B_ESCHR_COL</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
<td align="center">TRUE</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">6</td>
|
||||
<td align="center">2010-08-01</td>
|
||||
<td align="center">L10</td>
|
||||
<td align="center">B_ESCHR_COL</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">7</td>
|
||||
<td align="center">2011-08-02</td>
|
||||
<td align="center">C7</td>
|
||||
<td align="center">2010-08-27</td>
|
||||
<td align="center">L10</td>
|
||||
<td align="center">B_ESCHR_COL</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">8</td>
|
||||
<td align="center">2011-10-19</td>
|
||||
<td align="center">C7</td>
|
||||
<td align="center">2010-09-09</td>
|
||||
<td align="center">L10</td>
|
||||
<td align="center">B_ESCHR_COL</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
<td align="center">TRUE</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">9</td>
|
||||
<td align="center">2011-10-23</td>
|
||||
<td align="center">C7</td>
|
||||
<td align="center">2010-09-26</td>
|
||||
<td align="center">L10</td>
|
||||
<td align="center">B_ESCHR_COL</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
<td align="center">TRUE</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">10</td>
|
||||
<td align="center">2011-11-10</td>
|
||||
<td align="center">C7</td>
|
||||
<td align="center">2010-10-11</td>
|
||||
<td align="center">L10</td>
|
||||
<td align="center">B_ESCHR_COL</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
<td align="center">FALSE</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<p>Instead of 2, now 7 isolates are flagged. In total, 79.1% of all isolates are marked ‘first weighted’ - 50.6% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
|
||||
<p>Instead of 1, now 4 isolates are flagged. In total, 78.8% of all isolates are marked ‘first weighted’ - 50.5% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
|
||||
<p>As with <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code>, there’s a shortcut for this new algorithm too:</p>
|
||||
<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1">data_1st <-<span class="st"> </span>data <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb20-2" title="2"><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_weighted_isolate</a></span>()</a></code></pre></div>
|
||||
<p>So we end up with 15,826 isolates for analysis.</p>
|
||||
<p>So we end up with 15,767 isolates for analysis.</p>
|
||||
<p>We can remove unneeded columns:</p>
|
||||
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" title="1">data_1st <-<span class="st"> </span>data_1st <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb21-2" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(first, keyab))</a></code></pre></div>
|
||||
@ -786,7 +786,6 @@
|
||||
<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/head">head</a></span>(data_1st)</a></code></pre></div>
|
||||
<table class="table">
|
||||
<thead><tr class="header">
|
||||
<th></th>
|
||||
<th align="center">date</th>
|
||||
<th align="center">patient_id</th>
|
||||
<th align="center">hospital</th>
|
||||
@ -803,79 +802,44 @@
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td>2</td>
|
||||
<td align="center">2012-07-07</td>
|
||||
<td align="center">T4</td>
|
||||
<td align="center">2010-01-23</td>
|
||||
<td align="center">E2</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_ESCHR_COL</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">B_STPHY_AUR</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram positive</td>
|
||||
<td align="center">Staphylococcus</td>
|
||||
<td align="center">aureus</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td>3</td>
|
||||
<td align="center">2011-02-19</td>
|
||||
<td align="center">H3</td>
|
||||
<td align="center">2017-12-07</td>
|
||||
<td align="center">L8</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_ESCHR_COL</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td>4</td>
|
||||
<td align="center">2012-12-15</td>
|
||||
<td align="center">G10</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">B_KLBSL_PNE</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram negative</td>
|
||||
<td align="center">Klebsiella</td>
|
||||
<td align="center">pneumoniae</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td>6</td>
|
||||
<td align="center">2011-03-27</td>
|
||||
<td align="center">H5</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_ESCHR_COL</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td>7</td>
|
||||
<td align="center">2012-06-22</td>
|
||||
<td align="center">Q8</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_STPHY_AUR</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram positive</td>
|
||||
<td align="center">Staphylococcus</td>
|
||||
<td align="center">aureus</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2012-07-19</td>
|
||||
<td align="center">W5</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_STPHY_AUR</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram positive</td>
|
||||
<td align="center">Staphylococcus</td>
|
||||
@ -883,12 +847,41 @@
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td>8</td>
|
||||
<td align="center">2015-06-27</td>
|
||||
<td align="center">Q2</td>
|
||||
<td align="center">2013-11-26</td>
|
||||
<td align="center">L7</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_ESCHR_COL</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2016-01-24</td>
|
||||
<td align="center">M7</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_ESCHR_COL</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
<td align="center">Gram negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2016-11-13</td>
|
||||
<td align="center">V10</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_ESCHR_COL</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
@ -915,9 +908,9 @@
|
||||
<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" title="1"><span class="kw"><a href="../reference/freq.html">freq</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/paste">paste</a></span>(data_1st<span class="op">$</span>genus, data_1st<span class="op">$</span>species))</a></code></pre></div>
|
||||
<p>Or can be used like the <code>dplyr</code> way, which is easier readable:</p>
|
||||
<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" title="1">data_1st <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(genus, species)</a></code></pre></div>
|
||||
<p><strong>Frequency table of <code>genus</code> and <code>species</code> from a <code>data.frame</code> (15,826 x 13)</strong></p>
|
||||
<p><strong>Frequency table of <code>genus</code> and <code>species</code> from a <code>data.frame</code> (15,767 x 13)</strong></p>
|
||||
<p>Columns: 2<br>
|
||||
Length: 15,826 (of which NA: 0 = 0.00%)<br>
|
||||
Length: 15,767 (of which NA: 0 = 0.00%)<br>
|
||||
Unique: 4</p>
|
||||
<p>Shortest: 16<br>
|
||||
Longest: 24</p>
|
||||
@ -934,33 +927,33 @@ Longest: 24</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">Escherichia coli</td>
|
||||
<td align="right">7,714</td>
|
||||
<td align="right">48.7%</td>
|
||||
<td align="right">7,714</td>
|
||||
<td align="right">48.7%</td>
|
||||
<td align="right">7,762</td>
|
||||
<td align="right">49.2%</td>
|
||||
<td align="right">7,762</td>
|
||||
<td align="right">49.2%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">Staphylococcus aureus</td>
|
||||
<td align="right">3,977</td>
|
||||
<td align="right">25.1%</td>
|
||||
<td align="right">11,691</td>
|
||||
<td align="right">73.9%</td>
|
||||
<td align="right">4,014</td>
|
||||
<td align="right">25.5%</td>
|
||||
<td align="right">11,776</td>
|
||||
<td align="right">74.7%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">3</td>
|
||||
<td align="left">Streptococcus pneumoniae</td>
|
||||
<td align="right">2,514</td>
|
||||
<td align="right">15.9%</td>
|
||||
<td align="right">14,205</td>
|
||||
<td align="right">89.8%</td>
|
||||
<td align="right">2,450</td>
|
||||
<td align="right">15.5%</td>
|
||||
<td align="right">14,226</td>
|
||||
<td align="right">90.2%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">4</td>
|
||||
<td align="left">Klebsiella pneumoniae</td>
|
||||
<td align="right">1,621</td>
|
||||
<td align="right">10.2%</td>
|
||||
<td align="right">15,826</td>
|
||||
<td align="right">1,541</td>
|
||||
<td align="right">9.8%</td>
|
||||
<td align="right">15,767</td>
|
||||
<td align="right">100.0%</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
@ -971,7 +964,7 @@ Longest: 24</p>
|
||||
<a href="#resistance-percentages" class="anchor"></a>Resistance percentages</h2>
|
||||
<p>The functions <code><a href="../reference/portion.html">portion_R()</a></code>, <code>portion_RI()</code>, <code><a href="../reference/portion.html">portion_I()</a></code>, <code>portion_IS()</code> and <code><a href="../reference/portion.html">portion_S()</a></code> can be used to determine the portion of a specific antimicrobial outcome. They can be used on their own:</p>
|
||||
<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" title="1">data_1st <span class="op">%>%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_IR</a></span>(amox)</a>
|
||||
<a class="sourceLine" id="cb25-2" title="2"><span class="co">#> [1] 0.4830027</span></a></code></pre></div>
|
||||
<a class="sourceLine" id="cb25-2" title="2"><span class="co">#> [1] 0.4762479</span></a></code></pre></div>
|
||||
<p>Or can be used in conjuction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
|
||||
<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" title="1">data_1st <span class="op">%>%</span><span class="st"> </span></a>
|
||||
<a class="sourceLine" id="cb26-2" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(hospital) <span class="op">%>%</span><span class="st"> </span></a>
|
||||
@ -984,19 +977,19 @@ Longest: 24</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">0.4798820</td>
|
||||
<td align="center">0.4717496</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">0.4792835</td>
|
||||
<td align="center">0.4754662</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">0.4863714</td>
|
||||
<td align="center">0.4748170</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">0.4915730</td>
|
||||
<td align="center">0.4854430</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1014,23 +1007,23 @@ Longest: 24</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">0.4798820</td>
|
||||
<td align="center">4747</td>
|
||||
<td align="center">0.4717496</td>
|
||||
<td align="center">4761</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">0.4792835</td>
|
||||
<td align="center">5527</td>
|
||||
<td align="center">0.4754662</td>
|
||||
<td align="center">5523</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">0.4863714</td>
|
||||
<td align="center">2348</td>
|
||||
<td align="center">0.4748170</td>
|
||||
<td align="center">2323</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">0.4915730</td>
|
||||
<td align="center">3204</td>
|
||||
<td align="center">0.4854430</td>
|
||||
<td align="center">3160</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1050,27 +1043,27 @@ Longest: 24</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">0.7313975</td>
|
||||
<td align="center">0.8940887</td>
|
||||
<td align="center">0.9752398</td>
|
||||
<td align="center">0.7333162</td>
|
||||
<td align="center">0.9035043</td>
|
||||
<td align="center">0.9748776</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Klebsiella</td>
|
||||
<td align="center">0.7143738</td>
|
||||
<td align="center">0.8994448</td>
|
||||
<td align="center">0.9697717</td>
|
||||
<td align="center">0.7352369</td>
|
||||
<td align="center">0.9104478</td>
|
||||
<td align="center">0.9733939</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Staphylococcus</td>
|
||||
<td align="center">0.7301986</td>
|
||||
<td align="center">0.9104853</td>
|
||||
<td align="center">0.9786271</td>
|
||||
<td align="center">0.7416542</td>
|
||||
<td align="center">0.9160438</td>
|
||||
<td align="center">0.9763328</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">0.7430390</td>
|
||||
<td align="center">0.7473469</td>
|
||||
<td align="center">0.0000000</td>
|
||||
<td align="center">0.7430390</td>
|
||||
<td align="center">0.7473469</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 35 KiB After Width: | Height: | Size: 35 KiB |
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|
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|
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|
Before Width: | Height: | Size: 50 KiB After Width: | Height: | Size: 50 KiB |
@ -40,7 +40,7 @@
|
||||
</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">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -192,7 +192,7 @@
|
||||
<h1>How to apply EUCAST rules</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">02 March 2019</h4>
|
||||
<h4 class="date">05 March 2019</h4>
|
||||
|
||||
|
||||
<div class="hidden name"><code>EUCAST.Rmd</code></div>
|
||||
|
||||
@ -40,7 +40,7 @@
|
||||
</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">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -192,7 +192,7 @@
|
||||
<h1>How to use the <em>G</em>-test</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">02 March 2019</h4>
|
||||
<h4 class="date">05 March 2019</h4>
|
||||
|
||||
|
||||
<div class="hidden name"><code>G_test.Rmd</code></div>
|
||||
|
||||
@ -40,7 +40,7 @@
|
||||
</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">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -40,7 +40,7 @@
|
||||
</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">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -192,7 +192,7 @@
|
||||
<h1>How to work with WHONET data</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">02 March 2019</h4>
|
||||
<h4 class="date">05 March 2019</h4>
|
||||
|
||||
|
||||
<div class="hidden name"><code>WHONET.Rmd</code></div>
|
||||
|
||||
@ -40,7 +40,7 @@
|
||||
</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">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -192,7 +192,7 @@
|
||||
<h1>How to get properties of an antibiotic</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">02 March 2019</h4>
|
||||
<h4 class="date">05 March 2019</h4>
|
||||
|
||||
|
||||
<div class="hidden name"><code>atc_property.Rmd</code></div>
|
||||
|
||||
@ -40,7 +40,7 @@
|
||||
</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">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -192,7 +192,7 @@
|
||||
<h1>Benchmarks</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">02 March 2019</h4>
|
||||
<h4 class="date">05 March 2019</h4>
|
||||
|
||||
|
||||
<div class="hidden name"><code>benchmarks.Rmd</code></div>
|
||||
@ -218,13 +218,13 @@
|
||||
<a class="sourceLine" id="cb2-9" title="9"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(S.aureus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
|
||||
<a class="sourceLine" id="cb2-10" title="10"><span class="co">#> Unit: milliseconds</span></a>
|
||||
<a class="sourceLine" id="cb2-11" title="11"><span class="co">#> expr min lq mean median uq max neval</span></a>
|
||||
<a class="sourceLine" id="cb2-12" title="12"><span class="co">#> as.mo("sau") 16.60 16.70 16.90 16.70 16.80 18.20 10</span></a>
|
||||
<a class="sourceLine" id="cb2-13" title="13"><span class="co">#> as.mo("stau") 31.80 32.00 44.30 32.10 72.40 73.60 10</span></a>
|
||||
<a class="sourceLine" id="cb2-14" title="14"><span class="co">#> as.mo("staaur") 16.70 16.70 16.80 16.70 16.80 17.30 10</span></a>
|
||||
<a class="sourceLine" id="cb2-15" title="15"><span class="co">#> as.mo("STAAUR") 16.70 16.80 35.20 18.60 58.00 73.00 10</span></a>
|
||||
<a class="sourceLine" id="cb2-16" title="16"><span class="co">#> as.mo("S. aureus") 24.60 24.60 33.50 24.70 24.90 68.70 10</span></a>
|
||||
<a class="sourceLine" id="cb2-17" title="17"><span class="co">#> as.mo("S. aureus") 24.50 24.70 25.30 24.90 26.00 26.40 10</span></a>
|
||||
<a class="sourceLine" id="cb2-18" title="18"><span class="co">#> as.mo("Staphylococcus aureus") 7.35 7.45 7.53 7.51 7.56 7.97 10</span></a></code></pre></div>
|
||||
<a class="sourceLine" id="cb2-12" title="12"><span class="co">#> as.mo("sau") 16.80 17.20 25.80 18.10 32.10 52.8 10</span></a>
|
||||
<a class="sourceLine" id="cb2-13" title="13"><span class="co">#> as.mo("stau") 32.20 33.10 43.30 34.00 42.40 82.3 10</span></a>
|
||||
<a class="sourceLine" id="cb2-14" title="14"><span class="co">#> as.mo("staaur") 16.70 16.80 25.40 17.20 19.80 60.4 10</span></a>
|
||||
<a class="sourceLine" id="cb2-15" title="15"><span class="co">#> as.mo("STAAUR") 16.70 16.80 22.40 17.90 20.20 61.7 10</span></a>
|
||||
<a class="sourceLine" id="cb2-16" title="16"><span class="co">#> as.mo("S. aureus") 24.90 25.10 42.00 26.20 67.50 88.8 10</span></a>
|
||||
<a class="sourceLine" id="cb2-17" title="17"><span class="co">#> as.mo("S. aureus") 24.50 25.00 43.70 25.30 67.90 78.2 10</span></a>
|
||||
<a class="sourceLine" id="cb2-18" title="18"><span class="co">#> as.mo("Staphylococcus aureus") 7.47 7.48 9.63 7.53 7.69 28.3 10</span></a></code></pre></div>
|
||||
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 100 milliseconds, this is only 10 input values per second. The second input is the only one that has to be looked up thoroughly. All the others are known codes (the first one is a WHONET code) or common laboratory codes, or common full organism names like the last one. Full organism names are always preferred.</p>
|
||||
<p>To achieve this speed, the <code>as.mo</code> function also takes into account the prevalence of human pathogenic microorganisms. The downside is of course that less prevalent microorganisms will be determined less fast. See this example for the ID of <em>Thermus islandicus</em> (<code>B_THERMS_ISL</code>), a bug probably never found before in humans:</p>
|
||||
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1">T.islandicus <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"theisl"</span>),</a>
|
||||
@ -236,12 +236,12 @@
|
||||
<a class="sourceLine" id="cb3-7" title="7"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(T.islandicus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
|
||||
<a class="sourceLine" id="cb3-8" title="8"><span class="co">#> Unit: milliseconds</span></a>
|
||||
<a class="sourceLine" id="cb3-9" title="9"><span class="co">#> expr min lq mean median uq max neval</span></a>
|
||||
<a class="sourceLine" id="cb3-10" title="10"><span class="co">#> as.mo("theisl") 265.0 268.0 294.0 307.0 312 321 10</span></a>
|
||||
<a class="sourceLine" id="cb3-11" title="11"><span class="co">#> as.mo("THEISL") 264.0 264.0 312.0 307.0 316 464 10</span></a>
|
||||
<a class="sourceLine" id="cb3-12" title="12"><span class="co">#> as.mo("T. islandicus") 142.0 142.0 159.0 143.0 187 216 10</span></a>
|
||||
<a class="sourceLine" id="cb3-13" title="13"><span class="co">#> as.mo("T. islandicus") 142.0 143.0 173.0 185.0 187 190 10</span></a>
|
||||
<a class="sourceLine" id="cb3-14" title="14"><span class="co">#> as.mo("Thermus islandicus") 68.1 68.4 81.9 68.6 111 115 10</span></a></code></pre></div>
|
||||
<p>That takes 8 times as much time on average. A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like <em>Thermus islandicus</em>) are almost fast - these are the most probable input from most data sets.</p>
|
||||
<a class="sourceLine" id="cb3-10" title="10"><span class="co">#> as.mo("theisl") 275.0 304.0 310 309.0 316 337 10</span></a>
|
||||
<a class="sourceLine" id="cb3-11" title="11"><span class="co">#> as.mo("THEISL") 263.0 304.0 311 306.0 312 391 10</span></a>
|
||||
<a class="sourceLine" id="cb3-12" title="12"><span class="co">#> as.mo("T. islandicus") 142.0 143.0 168 148.0 188 220 10</span></a>
|
||||
<a class="sourceLine" id="cb3-13" title="13"><span class="co">#> as.mo("T. islandicus") 142.0 142.0 169 143.0 185 312 10</span></a>
|
||||
<a class="sourceLine" id="cb3-14" title="14"><span class="co">#> as.mo("Thermus islandicus") 68.1 68.6 101 89.8 122 179 10</span></a></code></pre></div>
|
||||
<p>That takes 7 times as much time on average. A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like <em>Thermus islandicus</em>) are almost fast - these are the most probable input from most data sets.</p>
|
||||
<p>In the figure below, we compare <em>Escherichia coli</em> (which is very common) with <em>Prevotella brevis</em> (which is moderately common) and with <em>Thermus islandicus</em> (which is very uncommon):</p>
|
||||
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/par">par</a></span>(<span class="dt">mar =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">5</span>, <span class="dv">16</span>, <span class="dv">4</span>, <span class="dv">2</span>)) <span class="co"># set more space for left margin text (16)</span></a>
|
||||
<a class="sourceLine" id="cb4-2" title="2"></a>
|
||||
@ -287,8 +287,8 @@
|
||||
<a class="sourceLine" id="cb5-24" title="24"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
|
||||
<a class="sourceLine" id="cb5-25" title="25"><span class="co">#> Unit: milliseconds</span></a>
|
||||
<a class="sourceLine" id="cb5-26" title="26"><span class="co">#> expr min lq mean median uq max neval</span></a>
|
||||
<a class="sourceLine" id="cb5-27" title="27"><span class="co">#> mo_fullname(x) 732 772 823 819 858 1020 10</span></a></code></pre></div>
|
||||
<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.82 seconds (819 ms). You only lose time on your unique input values.</p>
|
||||
<a class="sourceLine" id="cb5-27" title="27"><span class="co">#> mo_fullname(x) 687 738 767 770 774 887 10</span></a></code></pre></div>
|
||||
<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.77 seconds (770 ms). You only lose time on your unique input values.</p>
|
||||
</div>
|
||||
<div id="precalculated-results" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
@ -301,9 +301,9 @@
|
||||
<a class="sourceLine" id="cb6-5" title="5"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
|
||||
<a class="sourceLine" id="cb6-6" title="6"><span class="co">#> Unit: milliseconds</span></a>
|
||||
<a class="sourceLine" id="cb6-7" title="7"><span class="co">#> expr min lq mean median uq max neval</span></a>
|
||||
<a class="sourceLine" id="cb6-8" title="8"><span class="co">#> A 11.100 11.400 16.700 11.700 14.400 43.200 10</span></a>
|
||||
<a class="sourceLine" id="cb6-9" title="9"><span class="co">#> B 22.300 22.400 22.800 22.700 22.900 24.100 10</span></a>
|
||||
<a class="sourceLine" id="cb6-10" title="10"><span class="co">#> C 0.324 0.439 0.532 0.577 0.582 0.677 10</span></a></code></pre></div>
|
||||
<a class="sourceLine" id="cb6-8" title="8"><span class="co">#> A 11.100 11.300 15.600 11.400 11.600 53.4 10</span></a>
|
||||
<a class="sourceLine" id="cb6-9" title="9"><span class="co">#> B 22.200 22.500 22.800 22.800 23.000 23.7 10</span></a>
|
||||
<a class="sourceLine" id="cb6-10" title="10"><span class="co">#> C 0.322 0.326 0.518 0.563 0.578 0.8 10</span></a></code></pre></div>
|
||||
<p>So going from <code><a href="../reference/mo_property.html">mo_fullname("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0006 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
|
||||
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1">run_it <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">A =</span> <span class="kw"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),</a>
|
||||
<a class="sourceLine" id="cb7-2" title="2"> <span class="dt">B =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),</a>
|
||||
@ -317,14 +317,14 @@
|
||||
<a class="sourceLine" id="cb7-10" title="10"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
|
||||
<a class="sourceLine" id="cb7-11" title="11"><span class="co">#> Unit: milliseconds</span></a>
|
||||
<a class="sourceLine" id="cb7-12" title="12"><span class="co">#> expr min lq mean median uq max neval</span></a>
|
||||
<a class="sourceLine" id="cb7-13" title="13"><span class="co">#> A 0.322 0.338 0.397 0.384 0.415 0.569 10</span></a>
|
||||
<a class="sourceLine" id="cb7-14" title="14"><span class="co">#> B 0.316 0.370 0.442 0.442 0.508 0.601 10</span></a>
|
||||
<a class="sourceLine" id="cb7-15" title="15"><span class="co">#> C 0.335 0.385 0.502 0.504 0.566 0.724 10</span></a>
|
||||
<a class="sourceLine" id="cb7-16" title="16"><span class="co">#> D 0.283 0.324 0.362 0.366 0.389 0.437 10</span></a>
|
||||
<a class="sourceLine" id="cb7-17" title="17"><span class="co">#> E 0.252 0.274 0.317 0.323 0.355 0.383 10</span></a>
|
||||
<a class="sourceLine" id="cb7-18" title="18"><span class="co">#> F 0.255 0.275 0.325 0.332 0.348 0.411 10</span></a>
|
||||
<a class="sourceLine" id="cb7-19" title="19"><span class="co">#> G 0.259 0.272 0.307 0.299 0.318 0.412 10</span></a>
|
||||
<a class="sourceLine" id="cb7-20" title="20"><span class="co">#> H 0.271 0.319 0.338 0.334 0.362 0.418 10</span></a></code></pre></div>
|
||||
<a class="sourceLine" id="cb7-13" title="13"><span class="co">#> A 0.330 0.345 0.421 0.441 0.461 0.525 10</span></a>
|
||||
<a class="sourceLine" id="cb7-14" title="14"><span class="co">#> B 0.355 0.378 0.453 0.435 0.464 0.754 10</span></a>
|
||||
<a class="sourceLine" id="cb7-15" title="15"><span class="co">#> C 0.315 0.374 0.506 0.516 0.633 0.700 10</span></a>
|
||||
<a class="sourceLine" id="cb7-16" title="16"><span class="co">#> D 0.273 0.329 0.353 0.365 0.385 0.391 10</span></a>
|
||||
<a class="sourceLine" id="cb7-17" title="17"><span class="co">#> E 0.279 0.322 0.330 0.335 0.343 0.366 10</span></a>
|
||||
<a class="sourceLine" id="cb7-18" title="18"><span class="co">#> F 0.247 0.263 0.315 0.319 0.355 0.429 10</span></a>
|
||||
<a class="sourceLine" id="cb7-19" title="19"><span class="co">#> G 0.276 0.320 0.342 0.328 0.371 0.447 10</span></a>
|
||||
<a class="sourceLine" id="cb7-20" title="20"><span class="co">#> H 0.251 0.258 0.315 0.329 0.360 0.368 10</span></a></code></pre></div>
|
||||
<p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> too, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.</p>
|
||||
</div>
|
||||
<div id="results-in-other-languages" class="section level3">
|
||||
@ -351,13 +351,13 @@
|
||||
<a class="sourceLine" id="cb8-18" title="18"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">4</span>)</a>
|
||||
<a class="sourceLine" id="cb8-19" title="19"><span class="co">#> Unit: milliseconds</span></a>
|
||||
<a class="sourceLine" id="cb8-20" title="20"><span class="co">#> expr min lq mean median uq max neval</span></a>
|
||||
<a class="sourceLine" id="cb8-21" title="21"><span class="co">#> en 14.92 15.11 15.44 15.31 15.83 16.30 10</span></a>
|
||||
<a class="sourceLine" id="cb8-22" title="22"><span class="co">#> de 27.88 27.89 32.32 28.03 28.37 69.82 10</span></a>
|
||||
<a class="sourceLine" id="cb8-23" title="23"><span class="co">#> nl 27.39 28.01 40.70 28.48 69.20 70.26 10</span></a>
|
||||
<a class="sourceLine" id="cb8-24" title="24"><span class="co">#> es 27.69 27.93 38.06 28.12 29.21 84.95 10</span></a>
|
||||
<a class="sourceLine" id="cb8-25" title="25"><span class="co">#> it 27.73 27.95 28.16 28.00 28.15 29.40 10</span></a>
|
||||
<a class="sourceLine" id="cb8-26" title="26"><span class="co">#> fr 27.13 27.65 32.76 28.41 29.50 69.48 10</span></a>
|
||||
<a class="sourceLine" id="cb8-27" title="27"><span class="co">#> pt 27.08 27.34 27.89 27.99 28.05 29.40 10</span></a></code></pre></div>
|
||||
<a class="sourceLine" id="cb8-21" title="21"><span class="co">#> en 14.98 15.35 19.58 15.51 15.58 56.78 10</span></a>
|
||||
<a class="sourceLine" id="cb8-22" title="22"><span class="co">#> de 27.26 27.69 28.05 27.85 28.01 29.44 10</span></a>
|
||||
<a class="sourceLine" id="cb8-23" title="23"><span class="co">#> nl 27.07 27.73 31.89 27.87 28.00 69.50 10</span></a>
|
||||
<a class="sourceLine" id="cb8-24" title="24"><span class="co">#> es 26.98 27.43 31.98 27.84 28.09 69.30 10</span></a>
|
||||
<a class="sourceLine" id="cb8-25" title="25"><span class="co">#> it 27.26 27.57 28.38 27.82 28.92 32.14 10</span></a>
|
||||
<a class="sourceLine" id="cb8-26" title="26"><span class="co">#> fr 27.21 27.72 36.16 27.83 28.19 70.08 10</span></a>
|
||||
<a class="sourceLine" id="cb8-27" title="27"><span class="co">#> pt 27.21 27.78 36.17 27.96 28.54 69.43 10</span></a></code></pre></div>
|
||||
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
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||||
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||||
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|
||||
|
||||
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|
||||
<h1>How to create frequency tables</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">02 March 2019</h4>
|
||||
<h4 class="date">05 March 2019</h4>
|
||||
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||||
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||||
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||||
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||||
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|
||||
<h1>How to get properties of a microorganism</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">02 March 2019</h4>
|
||||
<h4 class="date">05 March 2019</h4>
|
||||
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||||
<div class="hidden name"><code>mo_property.Rmd</code></div>
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||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
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||||
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||||
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||||
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|
||||
<h1>How to predict antimicrobial resistance</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">02 March 2019</h4>
|
||||
<h4 class="date">05 March 2019</h4>
|
||||
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||||
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||||
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|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -81,7 +81,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
369
docs/reference/filter_ab_class.html
Normal file
369
docs/reference/filter_ab_class.html
Normal file
@ -0,0 +1,369 @@
|
||||
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||||
Conduct AMR analysis
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||||
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|
||||
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|
||||
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|
||||
<a href="../articles/resistance_predict.html">
|
||||
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|
||||
|
||||
Predict antimicrobial resistance
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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|
||||
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|
||||
|
||||
Get properties of a microorganism
|
||||
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|
||||
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|
||||
<li>
|
||||
<a href="../reference/atc_property.html">
|
||||
<span class="fa fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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||||
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||||
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|
||||
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||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
Source Code
|
||||
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|
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|
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</header>
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||||
|
||||
<div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header">
|
||||
<h1>Filter on antibiotic class</h1>
|
||||
|
||||
<div class="hidden name"><code>filter_ab_class.Rd</code></div>
|
||||
</div>
|
||||
|
||||
<div class="ref-description">
|
||||
|
||||
<p>Filter on specific antibiotic variables based on their class (ATC groups).</p>
|
||||
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>filter_ab_class</span>(<span class='no'>tbl</span>, <span class='no'>ab_class</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>filter_aminoglycosides</span>(<span class='no'>tbl</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>filter_carbapenems</span>(<span class='no'>tbl</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>filter_cephalosporins</span>(<span class='no'>tbl</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>filter_1st_cephalosporins</span>(<span class='no'>tbl</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>filter_2nd_cephalosporins</span>(<span class='no'>tbl</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>filter_3rd_cephalosporins</span>(<span class='no'>tbl</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>filter_4th_cephalosporins</span>(<span class='no'>tbl</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>filter_fluoroquinolones</span>(<span class='no'>tbl</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>filter_glycopeptides</span>(<span class='no'>tbl</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>filter_macrolides</span>(<span class='no'>tbl</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)
|
||||
|
||||
<span class='fu'>filter_tetracyclines</span>(<span class='no'>tbl</span>, <span class='kw'>result</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>scope</span> <span class='kw'>=</span> <span class='st'>"any"</span>, <span class='no'>...</span>)</pre>
|
||||
|
||||
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
|
||||
<table class="ref-arguments">
|
||||
<colgroup><col class="name" /><col class="desc" /></colgroup>
|
||||
<tr>
|
||||
<th>tbl</th>
|
||||
<td><p>a data set</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>ab_class</th>
|
||||
<td><p>an antimicrobial class, like <code>"carbapenems"</code></p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>result</th>
|
||||
<td><p>an antibiotic result: S, I or R (or a combination of more of them)</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>scope</th>
|
||||
<td><p>the scope to check which variables to check, can be <code>"any"</code> (default) or <code>"all"</code></p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>...</th>
|
||||
<td><p>parameters passed on to <code><a href='https://dplyr.tidyverse.org/reference/filter_all.html'>filter_at</a></code></p></td>
|
||||
</tr>
|
||||
</table>
|
||||
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p>The <code><code>antibiotics</code></code> data set will be searched for <code>ab_class</code> in the columns <code>atc_group1</code> and <code>atc_group2</code> (case-insensitive). Next, <code>tbl</code> will be checked for column names with a value in any abbreviations, codes or official names found in the <code>antibiotics</code> data set.</p>
|
||||
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># NOT RUN {</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'># filter on isolates that have any result for any aminoglycoside</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'>filter_aminoglycosides</span>()
|
||||
|
||||
<span class='co'># this is essentially the same as:</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter_all.html'>filter_at</a></span>(<span class='kw'>.vars</span> <span class='kw'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"gent"</span>, <span class='st'>"tobr"</span>, <span class='st'>"amik"</span>, <span class='st'>"kana"</span>)),
|
||||
<span class='kw'>.vars_predicate</span> <span class='kw'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/all_vars.html'>any_vars</a></span>(<span class='no'>.</span> <span class='kw'>%in%</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"S"</span>, <span class='st'>"I"</span>, <span class='st'>"R"</span>)))
|
||||
|
||||
|
||||
<span class='co'># filter on isolates that show resistance to ANY aminoglycoside</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'>filter_aminoglycosides</span>(<span class='st'>"R"</span>)
|
||||
|
||||
<span class='co'># filter on isolates that show resistance to ALL aminoglycosides</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span> <span class='fu'>filter_aminoglycosides</span>(<span class='st'>"R"</span>, <span class='st'>"all"</span>)
|
||||
|
||||
<span class='co'># filter on isolates that show resistance to</span>
|
||||
<span class='co'># any aminoglycoside and any fluoroquinolone</span>
|
||||
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
|
||||
<span class='fu'>filter_aminoglycosides</span>(<span class='st'>"R"</span>, <span class='st'>"any"</span>) <span class='kw'>%>%</span>
|
||||
<span class='fu'>filter_fluoroquinolones</span>(<span class='st'>"R"</span>, <span class='st'>"any"</span>)
|
||||
<span class='co'># }</span></pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
|
||||
<h2>Contents</h2>
|
||||
<ul class="nav nav-pills nav-stacked">
|
||||
<li><a href="#arguments">Arguments</a></li>
|
||||
|
||||
<li><a href="#details">Details</a></li>
|
||||
|
||||
<li><a href="#examples">Examples</a></li>
|
||||
</ul>
|
||||
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<footer>
|
||||
<div class="copyright">
|
||||
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
|
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</div>
|
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</footer>
|
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</div>
|
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|
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|
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<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
|
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<script>
|
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docsearch({
|
||||
|
||||
|
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apiKey: 'f737050abfd4d726c63938e18f8c496e',
|
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indexName: 'amr',
|
||||
inputSelector: 'input#search-input.form-control',
|
||||
transformData: function(hits) {
|
||||
return hits.map(function (hit) {
|
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hit.url = updateHitURL(hit);
|
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return hit;
|
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|
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||||
|
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</body>
|
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</html>
|
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|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -81,7 +81,7 @@ top_freq can be used to get the top/bottom n items of a frequency table, with co
|
||||
</button>
|
||||
<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
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|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
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<span class="navbar-brand">
|
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
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|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
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|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -78,7 +78,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -81,7 +81,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -81,7 +81,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -80,7 +80,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -81,7 +81,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9020</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9021</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -60,6 +60,9 @@
|
||||
<url>
|
||||
<loc>https://msberends.gitlab.io/AMR/reference/eucast_rules.html</loc>
|
||||
</url>
|
||||
<url>
|
||||
<loc>https://msberends.gitlab.io/AMR/reference/filter_ab_class.html</loc>
|
||||
</url>
|
||||
<url>
|
||||
<loc>https://msberends.gitlab.io/AMR/reference/first_isolate.html</loc>
|
||||
</url>
|
||||
|
||||
82
man/filter_ab_class.Rd
Normal file
82
man/filter_ab_class.Rd
Normal file
@ -0,0 +1,82 @@
|
||||
% Generated by roxygen2: do not edit by hand
|
||||
% Please edit documentation in R/filter_ab_class.R
|
||||
\name{filter_ab_class}
|
||||
\alias{filter_ab_class}
|
||||
\alias{filter_aminoglycosides}
|
||||
\alias{filter_carbapenems}
|
||||
\alias{filter_cephalosporins}
|
||||
\alias{filter_1st_cephalosporins}
|
||||
\alias{filter_2nd_cephalosporins}
|
||||
\alias{filter_3rd_cephalosporins}
|
||||
\alias{filter_4th_cephalosporins}
|
||||
\alias{filter_fluoroquinolones}
|
||||
\alias{filter_glycopeptides}
|
||||
\alias{filter_macrolides}
|
||||
\alias{filter_tetracyclines}
|
||||
\title{Filter on antibiotic class}
|
||||
\usage{
|
||||
filter_ab_class(tbl, ab_class, result = NULL, scope = "any", ...)
|
||||
|
||||
filter_aminoglycosides(tbl, result = NULL, scope = "any", ...)
|
||||
|
||||
filter_carbapenems(tbl, result = NULL, scope = "any", ...)
|
||||
|
||||
filter_cephalosporins(tbl, result = NULL, scope = "any", ...)
|
||||
|
||||
filter_1st_cephalosporins(tbl, result = NULL, scope = "any", ...)
|
||||
|
||||
filter_2nd_cephalosporins(tbl, result = NULL, scope = "any", ...)
|
||||
|
||||
filter_3rd_cephalosporins(tbl, result = NULL, scope = "any", ...)
|
||||
|
||||
filter_4th_cephalosporins(tbl, result = NULL, scope = "any", ...)
|
||||
|
||||
filter_fluoroquinolones(tbl, result = NULL, scope = "any", ...)
|
||||
|
||||
filter_glycopeptides(tbl, result = NULL, scope = "any", ...)
|
||||
|
||||
filter_macrolides(tbl, result = NULL, scope = "any", ...)
|
||||
|
||||
filter_tetracyclines(tbl, result = NULL, scope = "any", ...)
|
||||
}
|
||||
\arguments{
|
||||
\item{tbl}{a data set}
|
||||
|
||||
\item{ab_class}{an antimicrobial class, like \code{"carbapenems"}}
|
||||
|
||||
\item{result}{an antibiotic result: S, I or R (or a combination of more of them)}
|
||||
|
||||
\item{scope}{the scope to check which variables to check, can be \code{"any"} (default) or \code{"all"}}
|
||||
|
||||
\item{...}{parameters passed on to \code{\link[dplyr]{filter_at}}}
|
||||
}
|
||||
\description{
|
||||
Filter on specific antibiotic variables based on their class (ATC groups).
|
||||
}
|
||||
\details{
|
||||
The \code{\code{antibiotics}} data set will be searched for \code{ab_class} in the columns \code{atc_group1} and \code{atc_group2} (case-insensitive). Next, \code{tbl} will be checked for column names with a value in any abbreviations, codes or official names found in the \code{antibiotics} data set.
|
||||
}
|
||||
\examples{
|
||||
library(dplyr)
|
||||
|
||||
# filter on isolates that have any result for any aminoglycoside
|
||||
septic_patients \%>\% filter_aminoglycosides()
|
||||
|
||||
# this is essentially the same as:
|
||||
septic_patients \%>\%
|
||||
filter_at(.vars = vars(c("gent", "tobr", "amik", "kana")),
|
||||
.vars_predicate = any_vars(. \%in\% c("S", "I", "R")))
|
||||
|
||||
|
||||
# filter on isolates that show resistance to ANY aminoglycoside
|
||||
septic_patients \%>\% filter_aminoglycosides("R")
|
||||
|
||||
# filter on isolates that show resistance to ALL aminoglycosides
|
||||
septic_patients \%>\% filter_aminoglycosides("R", "all")
|
||||
|
||||
# filter on isolates that show resistance to
|
||||
# any aminoglycoside and any fluoroquinolone
|
||||
septic_patients \%>\%
|
||||
filter_aminoglycosides("R", "any") \%>\%
|
||||
filter_fluoroquinolones("R", "any")
|
||||
}
|
||||
44
tests/testthat/test-filter_ab_class.R
Normal file
44
tests/testthat/test-filter_ab_class.R
Normal file
@ -0,0 +1,44 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antimicrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://gitlab.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# This R package is free software; you can freely use and distribute #
|
||||
# it for both personal and commercial purposes under the terms of the #
|
||||
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
|
||||
# the Free Software Foundation. #
|
||||
# #
|
||||
# This R package was created for academic research and was publicly #
|
||||
# released in the hope that it will be useful, but it comes WITHOUT #
|
||||
# ANY WARRANTY OR LIABILITY. #
|
||||
# Visit our website for more info: https://msberends.gitab.io/AMR. #
|
||||
# ==================================================================== #
|
||||
|
||||
context("filter_ab_class.R")
|
||||
|
||||
test_that("ATC-group filtering works", {
|
||||
library(dplyr)
|
||||
expect_gt(septic_patients %>% filter_ab_class("carbapenem") %>% nrow(), 0)
|
||||
expect_gt(septic_patients %>% filter_aminoglycosides() %>% nrow(), 0)
|
||||
expect_gt(septic_patients %>% filter_carbapenems() %>% nrow(), 0)
|
||||
expect_gt(septic_patients %>% filter_cephalosporins() %>% nrow(), 0)
|
||||
expect_gt(septic_patients %>% filter_1st_cephalosporins() %>% nrow(), 0)
|
||||
expect_gt(septic_patients %>% filter_2nd_cephalosporins() %>% nrow(), 0)
|
||||
expect_gt(septic_patients %>% filter_3rd_cephalosporins() %>% nrow(), 0)
|
||||
expect_gt(septic_patients %>% filter_4th_cephalosporins() %>% nrow(), 0)
|
||||
expect_gt(septic_patients %>% filter_fluoroquinolones() %>% nrow(), 0)
|
||||
expect_gt(septic_patients %>% filter_glycopeptides() %>% nrow(), 0)
|
||||
expect_gt(septic_patients %>% filter_macrolides() %>% nrow(), 0)
|
||||
expect_gt(septic_patients %>% filter_tetracyclines() %>% nrow(), 0)
|
||||
|
||||
expect_gt(septic_patients %>% filter_carbapenems("R", "all") %>% nrow(), 0)
|
||||
|
||||
expect_error(septic_patients %>% filter_carbapenems(result = "test"))
|
||||
expect_error(septic_patients %>% filter_carbapenems(scope = "test"))
|
||||
expect_warning(septic_patients %>% select(1:3) %>% filter_carbapenems())
|
||||
})
|
||||
Loading…
Reference in New Issue
Block a user