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(v1.4.0.9046) get_episode
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 1.4.0.9045
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Date: 2020-12-25
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Version: 1.4.0.9046
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Date: 2020-12-27
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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person(role = c("aut", "cre"),
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@ -137,6 +137,7 @@ export(fluoroquinolones)
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export(full_join_microorganisms)
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export(g.test)
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export(geom_rsi)
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export(get_episode)
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export(get_locale)
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export(get_mo_source)
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export(ggplot_pca)
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8
NEWS.md
8
NEWS.md
@ -1,9 +1,8 @@
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# AMR 1.4.0.9045
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## <small>Last updated: 25 December 2020</small>
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# AMR 1.4.0.9046
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## <small>Last updated: 27 December 2020</small>
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### New
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* Function `is_new_episode()` to determine patient episodes which are not necessarily based on microorganisms. It also supports grouped variables with e.g. `mutate()`, `filter()` and `summarise()` of the `dplyr` package:
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* Functions `get_episode()` and `is_new_episode()` to determine (patient) episodes which are not necessarily based on microorganisms. The `get_episode()` function returns the index number of the episode per group, while the `is_new_episode()` function returns values `TRUE`/`FALSE` to indicate whether an item in a vector is the start of a new episode. They also support `dplyr`s grouping (i.e. using `group_by()`):
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```r
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library(dplyr)
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example_isolates %>%
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@ -23,7 +22,6 @@
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* If using `as.rsi()` on MICs or disk diffusion while there is intrinsic antimicrobial resistance, a warning will be thrown to remind about this
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* Fix for using `as.rsi()` on a `data.frame` that only contains one column for antibiotic interpretations
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* Some functions are now context-aware when used inside `dplyr` verbs, such as `filter()`, `mutate()` and `summarise()`. This means that then the data argument does not need to be set anymore. This is the case for the new functions `mo_is_gram_negative()`, `mo_is_gram_positive()`, `mo_is_intrinsic_resistant()` and for the existing functions `first_isolate()`, `key_antibiotics()`, `mdro()`, `brmo()`, `mrgn()`, `mdr_tb()`, `mdr_cmi2012()`, `eucast_exceptional_phenotypes()`. This was already the case for antibiotic selection functions (such as using `penicillins()` in `dplyr::select()`).
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```r
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# to select first isolates that are Gram-negative
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# and view results of cephalosporins and aminoglycosides:
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@ -536,22 +536,39 @@ get_current_data <- function(arg_name, call) {
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call = call - 4))
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}
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get_root_env_address <- function() {
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sub("<environment: (.*)>", "\\1", utils::capture.output(sys.frames()[[1]]))
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unique_call_id <- function() {
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# combination of environment ID (like "0x7fed4ee8c848")
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# and highest system call
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c(envir = gsub("<environment: (.*)>", "\\1", utils::capture.output(sys.frames()[[1]])),
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call = paste0(deparse(sys.calls()[[1]]), collapse = ""))
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}
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remember_thrown_message <- function(fn) {
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assign(x = paste0("address_", fn),
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value = get_root_env_address(),
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envir = mo_env)
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# this is to prevent that messages/notes will be printed for every dplyr group
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# e.g. this would show a msg 4 times: example_isolates %>% group_by(hospital_id) %>% filter(mo_is_gram_negative())
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assign(x = paste0("uniquecall_", fn),
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value = unique_call_id(),
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envir = pkg_env)
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}
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message_not_thrown_before <- function(fn) {
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is.null(mo_env[[paste0("address_", fn)]]) || !identical(mo_env[[paste0("address_", fn)]], get_root_env_address())
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is.null(pkg_env[[paste0("uniquecall_", fn)]]) || !identical(pkg_env[[paste0("uniquecall_", fn)]], unique_call_id())
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}
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reset_all_thrown_messages <- function() {
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# for unit tests, where the environment and highest system call do not change
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pkg_env_contents <- ls(envir = pkg_env)
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rm(list = pkg_env_contents[pkg_env_contents %like% "^uniquecall_"],
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envir = pkg_env)
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}
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has_colour <- function() {
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# this is a base R version of crayon::has_color
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# this is a base R version of crayon::has_color, but disables colours on emacs
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if (Sys.getenv("EMACS") != "" || Sys.getenv("INSIDE_EMACS") != "") {
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# disable on emacs, only supports 8 colours
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return(FALSE)
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}
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enabled <- getOption("crayon.enabled")
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if (!is.null(enabled)) {
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return(isTRUE(enabled))
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@ -581,20 +598,6 @@ has_colour <- function() {
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}
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return(FALSE)
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}
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emacs_version <- function() {
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ver <- Sys.getenv("INSIDE_EMACS")
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if (ver == "") {
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return(NA_integer_)
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}
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ver <- gsub("'", "", ver)
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ver <- strsplit(ver, ",", fixed = TRUE)[[1]]
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ver <- strsplit(ver, ".", fixed = TRUE)[[1]]
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as.numeric(ver)
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}
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if ((Sys.getenv("EMACS") != "" || Sys.getenv("INSIDE_EMACS") != "") &&
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!is.na(emacs_version()[1]) && emacs_version()[1] >= 23) {
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return(TRUE)
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}
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if ("COLORTERM" %in% names(Sys.getenv())) {
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return(TRUE)
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}
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@ -656,6 +659,15 @@ font_grey_bg <- function(..., collapse = " ") {
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font_green_bg <- function(..., collapse = " ") {
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try_colour(..., before = "\033[42m", after = "\033[49m", collapse = collapse)
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}
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font_rsi_R_bg <- function(..., collapse = " ") {
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try_colour(..., before = "\033[48;5;202m", after = "\033[49m", collapse = collapse)
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}
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font_rsi_S_bg <- function(..., collapse = " ") {
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try_colour(..., before = "\033[48;5;76m", after = "\033[49m", collapse = collapse)
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}
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font_rsi_I_bg <- function(..., collapse = " ") {
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try_colour(..., before = "\033[48;5;148m", after = "\033[49m", collapse = collapse)
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}
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font_red_bg <- function(..., collapse = " ") {
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try_colour(..., before = "\033[41m", after = "\033[49m", collapse = collapse)
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}
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@ -25,26 +25,34 @@
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#' Determine (new) episodes for patients
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#'
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#' This function determines which items in a vector can be considered (the start of) a new episode, based on the argument `episode_days`. This can be used to determine clinical episodes for any epidemiological analysis.
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#' These functions determine which items in a vector can be considered (the start of) a new episode, based on the argument `episode_days`. This can be used to determine clinical episodes for any epidemiological analysis. The [get_episode()] function returns the index number of the episode per group, while the [is_new_episode()] function returns values `TRUE`/`FALSE` to indicate whether an item in a vector is the start of a new episode.
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#' @inheritSection lifecycle Stable lifecycle
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#' @param x vector of dates (class `Date` or `POSIXt`)
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#' @param episode_days length of the required episode in days, defaults to 365. Every element in the input will return `TRUE` after this number of days has passed since the last included date, independent of calendar years. Please see *Details*.
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#' @param episode_days length of the required episode in days, please see *Details*
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#' @param ... arguments passed on to [as.Date()]
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#' @details
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#' Dates are first sorted from old to new. The oldest date will mark the start of the first episode. After this date, the next date will be marked that is at least `episode_days` days later than the start of the first episode. From that second marked date on, the next date will be marked that is at least `episode_days` days later than the start of the second episode which will be the start of the third episode, and so on. Before the vector is being returned, the original order will be restored.
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#'
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#' The [first_isolate()] function is a wrapper around the [is_new_episode()] function, but more efficient for data sets containing microorganism codes or names.
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#' The [first_isolate()] function is a wrapper around the [is_new_episode()] function, but is more efficient for data sets containing microorganism codes or names.
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#'
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#' The `dplyr` package is not required for this function to work, but this function works conveniently inside `dplyr` verbs such as [`filter()`][dplyr::filter()], [`mutate()`][dplyr::mutate()] and [`summarise()`][dplyr::summarise()].
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#' @return a [logical] vector
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#' The `dplyr` package is not required for these functions to work, but these functions support [variable grouping][dplyr::group_by()] and work conveniently inside `dplyr` verbs such as [`filter()`][dplyr::filter()], [`mutate()`][dplyr::mutate()] and [`summarise()`][dplyr::summarise()].
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#' @return
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#' * [get_episode()]: a [double] vector
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#' * [is_new_episode()]: a [logical] vector
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#' @seealso [first_isolate()]
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#' @rdname get_episode
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#' @export
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#' @inheritSection AMR Read more on our website!
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#' @examples
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#' # `example_isolates` is a dataset available in the AMR package.
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#' # See ?example_isolates.
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#'
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#' is_new_episode(example_isolates$date)
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#' get_episode(example_isolates$date, episode_days = 60)
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#' is_new_episode(example_isolates$date, episode_days = 60)
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#'
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#' # filter on results from the third 60-day episode using base R
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#' example_isolates[which(get_episode(example_isolates$date, 60) == 3), ]
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#'
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#' \donttest{
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#' if (require("dplyr")) {
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#' # is_new_episode() can also be used in dplyr verbs to determine patient
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@ -54,7 +62,15 @@
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#' size = 2000,
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#' replace = TRUE)) %>%
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#' group_by(condition) %>%
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#' mutate(new_episode = is_new_episode(date))
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#' mutate(new_episode = is_new_episode(date, 365))
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#'
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#' example_isolates %>%
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#' group_by(hospital_id, patient_id) %>%
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#' transmute(date,
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#' patient_id,
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#' new_index = get_episode(date, 60),
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#' new_logical = is_new_episode(date, 60))
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#'
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#'
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#' example_isolates %>%
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#' group_by(hospital_id) %>%
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@ -71,7 +87,7 @@
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#'
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#' y <- example_isolates %>%
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#' group_by(patient_id, mo) %>%
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#' filter(is_new_episode(date))
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#' filter(is_new_episode(date, 365))
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#'
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#' identical(x$patient_id, y$patient_id)
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#'
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@ -79,21 +95,52 @@
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#' # since you can now group on anything that seems relevant:
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#' example_isolates %>%
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#' group_by(patient_id, mo, hospital_id, ward_icu) %>%
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#' mutate(flag_episode = is_new_episode(date))
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#' mutate(flag_episode = is_new_episode(date, 365))
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#' }
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#' }
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is_new_episode <- function(x, episode_days = 365, ...) {
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get_episode <- function(x, episode_days, ...) {
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meet_criteria(x, allow_class = c("Date", "POSIXt"))
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meet_criteria(episode_days, allow_class = c("numeric", "double", "integer"), has_length = 1)
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exec_episode(type = "sequential",
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x = x,
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episode_days = episode_days,
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... = ...)
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}
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#' @rdname get_episode
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#' @export
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is_new_episode <- function(x, episode_days, ...) {
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meet_criteria(x, allow_class = c("Date", "POSIXt"))
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meet_criteria(episode_days, allow_class = c("numeric", "double", "integer"), has_length = 1)
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exec_episode(type = "logical",
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x = x,
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episode_days = episode_days,
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... = ...)
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}
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exec_episode <- function(type, x, episode_days, ...) {
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x <- as.double(as.Date(x, ...)) # as.Date() for POSIX classes
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if (length(x) == 1) {
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return(TRUE)
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if (type == "logical") {
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return(TRUE)
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} else if (type == "sequential") {
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return(1)
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}
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} else if (length(x) == 2) {
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if (max(x) - min(x) >= episode_days) {
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return(c(TRUE, TRUE))
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if (type == "logical") {
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return(c(TRUE, TRUE))
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} else if (type == "sequential") {
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return(c(1, 2))
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}
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} else {
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return(c(TRUE, FALSE))
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if (type == "logical") {
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return(c(TRUE, FALSE))
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} else if (type == "sequential") {
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return(c(1, 1))
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}
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}
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}
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@ -107,13 +154,22 @@ is_new_episode <- function(x, episode_days = 365, ...) {
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for (i in 2:length(x)) {
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if (isTRUE((x[i] - start) >= episode_days)) {
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ind <- ind + 1
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indices[ind] <- i
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if (type == "logical") {
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indices[ind] <- i
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}
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start <- x[i]
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}
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if (type == "sequential") {
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indices[i] <- ind
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}
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}
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if (type == "logical") {
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result <- rep(FALSE, length(x))
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result[indices] <- TRUE
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result
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} else if (type == "sequential") {
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indices
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}
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result <- rep(FALSE, length(x))
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result[indices] <- TRUE
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result
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}
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df <- data.frame(x = x,
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58
R/mo.R
58
R/mo.R
@ -361,11 +361,11 @@ exec_as.mo <- function(x,
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# keep track of time - give some hints to improve speed if it takes a long time
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start_time <- Sys.time()
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mo_env$mo_failures <- NULL
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mo_env$mo_uncertainties <- NULL
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mo_env$mo_renamed <- NULL
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pkg_env$mo_failures <- NULL
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pkg_env$mo_uncertainties <- NULL
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pkg_env$mo_renamed <- NULL
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}
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mo_env$mo_renamed_last_run <- NULL
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pkg_env$mo_renamed_last_run <- NULL
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failures <- character(0)
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uncertainty_level <- translate_allow_uncertain(allow_uncertain)
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@ -598,7 +598,7 @@ exec_as.mo <- function(x,
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} else {
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x[i] <- lookup(fullname == found["fullname_new"], haystack = MO_lookup)
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}
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mo_env$mo_renamed_last_run <- found["fullname"]
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pkg_env$mo_renamed_last_run <- found["fullname"]
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was_renamed(name_old = found["fullname"],
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name_new = lookup(fullname == found["fullname_new"], "fullname", haystack = MO_lookup),
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ref_old = found["ref"],
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@ -973,7 +973,7 @@ exec_as.mo <- function(x,
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} else {
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x[i] <- lookup(fullname == found["fullname_new"], haystack = MO_lookup)
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}
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mo_env$mo_renamed_last_run <- found["fullname"]
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pkg_env$mo_renamed_last_run <- found["fullname"]
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was_renamed(name_old = found["fullname"],
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name_new = lookup(fullname == found["fullname_new"], "fullname", haystack = MO_lookup),
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ref_old = found["ref"],
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@ -1025,7 +1025,7 @@ exec_as.mo <- function(x,
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ref_old = found["ref"],
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ref_new = lookup(fullname == found["fullname_new"], "ref", haystack = MO_lookup),
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mo = lookup(fullname == found["fullname_new"], "mo", haystack = MO_lookup))
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mo_env$mo_renamed_last_run <- found["fullname"]
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pkg_env$mo_renamed_last_run <- found["fullname"]
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uncertainties <<- rbind(uncertainties,
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format_uncertainty_as_df(uncertainty_level = now_checks_for_uncertainty_level,
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input = a.x_backup,
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@ -1396,7 +1396,7 @@ exec_as.mo <- function(x,
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# handling failures ----
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failures <- failures[!failures %in% c(NA, NULL, NaN)]
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if (length(failures) > 0 & initial_search == TRUE) {
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mo_env$mo_failures <- sort(unique(failures))
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pkg_env$mo_failures <- sort(unique(failures))
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plural <- c("value", "it", "was")
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if (pm_n_distinct(failures) > 1) {
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plural <- c("values", "them", "were")
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@ -1423,7 +1423,7 @@ exec_as.mo <- function(x,
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# handling uncertainties ----
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if (NROW(uncertainties) > 0 & initial_search == TRUE) {
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uncertainties <- as.list(pm_distinct(uncertainties, input, .keep_all = TRUE))
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mo_env$mo_uncertainties <- uncertainties
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pkg_env$mo_uncertainties <- uncertainties
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plural <- c("", "it", "was")
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if (length(uncertainties$input) > 1) {
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@ -1559,13 +1559,13 @@ was_renamed <- function(name_old, name_new, ref_old = "", ref_new = "", mo = "")
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new_ref = ref_new,
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mo = mo,
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stringsAsFactors = FALSE)
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already_set <- mo_env$mo_renamed
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already_set <- pkg_env$mo_renamed
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if (!is.null(already_set)) {
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mo_env$mo_renamed = rbind(already_set,
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pkg_env$mo_renamed = rbind(already_set,
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newly_set,
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stringsAsFactors = FALSE)
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} else {
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mo_env$mo_renamed <- newly_set
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pkg_env$mo_renamed <- newly_set
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}
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}
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@ -1573,9 +1573,9 @@ format_uncertainty_as_df <- function(uncertainty_level,
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input,
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result_mo,
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candidates = NULL) {
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if (!is.null(mo_env$mo_renamed_last_run)) {
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fullname <- mo_env$mo_renamed_last_run
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mo_env$mo_renamed_last_run <- NULL
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if (!is.null(pkg_env$mo_renamed_last_run)) {
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fullname <- pkg_env$mo_renamed_last_run
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pkg_env$mo_renamed_last_run <- NULL
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renamed_to <- MO_lookup[match(result_mo, MO_lookup$mo), "fullname", drop = TRUE][1]
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} else {
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fullname <- MO_lookup[match(result_mo, MO_lookup$mo), "fullname", drop = TRUE][1]
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@ -1764,16 +1764,16 @@ unique.mo <- function(x, incomparables = FALSE, ...) {
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#' @rdname as.mo
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#' @export
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mo_failures <- function() {
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mo_env$mo_failures
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pkg_env$mo_failures
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}
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||||
|
||||
#' @rdname as.mo
|
||||
#' @export
|
||||
mo_uncertainties <- function() {
|
||||
if (is.null(mo_env$mo_uncertainties)) {
|
||||
if (is.null(pkg_env$mo_uncertainties)) {
|
||||
return(NULL)
|
||||
}
|
||||
set_clean_class(as.data.frame(mo_env$mo_uncertainties,
|
||||
set_clean_class(as.data.frame(pkg_env$mo_uncertainties,
|
||||
stringsAsFactors = FALSE),
|
||||
new_class = c("mo_uncertainties", "data.frame"))
|
||||
}
|
||||
@ -1842,7 +1842,7 @@ print.mo_uncertainties <- function(x, ...) {
|
||||
#' @rdname as.mo
|
||||
#' @export
|
||||
mo_renamed <- function() {
|
||||
items <- mo_env$mo_renamed
|
||||
items <- pkg_env$mo_renamed
|
||||
if (is.null(items)) {
|
||||
items <- data.frame(stringsAsFactors = FALSE)
|
||||
} else {
|
||||
@ -1906,20 +1906,20 @@ translate_allow_uncertain <- function(allow_uncertain) {
|
||||
}
|
||||
|
||||
get_mo_failures_uncertainties_renamed <- function() {
|
||||
remember <- list(failures = mo_env$mo_failures,
|
||||
uncertainties = mo_env$mo_uncertainties,
|
||||
renamed = mo_env$mo_renamed)
|
||||
remember <- list(failures = pkg_env$mo_failures,
|
||||
uncertainties = pkg_env$mo_uncertainties,
|
||||
renamed = pkg_env$mo_renamed)
|
||||
# empty them, otherwise mo_shortname("Chlamydophila psittaci") will give 3 notes
|
||||
mo_env$mo_failures <- NULL
|
||||
mo_env$mo_uncertainties <- NULL
|
||||
mo_env$mo_renamed <- NULL
|
||||
pkg_env$mo_failures <- NULL
|
||||
pkg_env$mo_uncertainties <- NULL
|
||||
pkg_env$mo_renamed <- NULL
|
||||
remember
|
||||
}
|
||||
|
||||
load_mo_failures_uncertainties_renamed <- function(metadata) {
|
||||
mo_env$mo_failures <- metadata$failures
|
||||
mo_env$mo_uncertainties <- metadata$uncertainties
|
||||
mo_env$mo_renamed <- metadata$renamed
|
||||
pkg_env$mo_failures <- metadata$failures
|
||||
pkg_env$mo_uncertainties <- metadata$uncertainties
|
||||
pkg_env$mo_renamed <- metadata$renamed
|
||||
}
|
||||
|
||||
trimws2 <- function(x) {
|
||||
@ -2007,4 +2007,4 @@ repair_reference_df <- function(reference_df) {
|
||||
reference_df
|
||||
}
|
||||
|
||||
mo_env <- new.env(hash = FALSE)
|
||||
pkg_env <- new.env(hash = FALSE)
|
||||
|
||||
@ -163,7 +163,7 @@
|
||||
mo_name <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
x <- find_mo_col("mo_name")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
@ -180,7 +180,7 @@ mo_fullname <- mo_name
|
||||
mo_shortname <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
x <- find_mo_col("mo_shortname")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
@ -218,7 +218,7 @@ mo_shortname <- function(x, language = get_locale(), ...) {
|
||||
mo_subspecies <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
x <- find_mo_col("mo_subspecies")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
@ -231,7 +231,7 @@ mo_subspecies <- function(x, language = get_locale(), ...) {
|
||||
mo_species <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
x <- find_mo_col("mo_species")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
@ -244,7 +244,7 @@ mo_species <- function(x, language = get_locale(), ...) {
|
||||
mo_genus <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
x <- find_mo_col("mo_genus")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
@ -257,7 +257,7 @@ mo_genus <- function(x, language = get_locale(), ...) {
|
||||
mo_family <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
x <- find_mo_col("mo_family")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
@ -270,7 +270,7 @@ mo_family <- function(x, language = get_locale(), ...) {
|
||||
mo_order <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
x <- find_mo_col("mo_order")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
@ -283,7 +283,7 @@ mo_order <- function(x, language = get_locale(), ...) {
|
||||
mo_class <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
x <- find_mo_col("mo_class")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
@ -296,7 +296,7 @@ mo_class <- function(x, language = get_locale(), ...) {
|
||||
mo_phylum <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
x <- find_mo_col("mo_phylum")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
@ -309,7 +309,7 @@ mo_phylum <- function(x, language = get_locale(), ...) {
|
||||
mo_kingdom <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
x <- find_mo_col("mo_kingdom")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
@ -326,7 +326,7 @@ mo_domain <- mo_kingdom
|
||||
mo_type <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
x <- find_mo_col("mo_type")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
@ -339,7 +339,7 @@ mo_type <- function(x, language = get_locale(), ...) {
|
||||
mo_gramstain <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
x <- find_mo_col("mo_gramstain")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
@ -377,7 +377,7 @@ mo_gramstain <- function(x, language = get_locale(), ...) {
|
||||
mo_is_gram_negative <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
x <- find_mo_col("mo_is_gram_negative")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
@ -396,7 +396,7 @@ mo_is_gram_negative <- function(x, language = get_locale(), ...) {
|
||||
mo_is_gram_positive <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
x <- find_mo_col("mo_is_gram_positive")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
@ -450,7 +450,7 @@ mo_is_intrinsic_resistant <- function(x, ab, language = get_locale(), ...) {
|
||||
mo_snomed <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
x <- find_mo_col("mo_snomed")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
@ -463,7 +463,7 @@ mo_snomed <- function(x, language = get_locale(), ...) {
|
||||
mo_ref <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
x <- find_mo_col("mo_ref")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
@ -476,7 +476,7 @@ mo_ref <- function(x, language = get_locale(), ...) {
|
||||
mo_authors <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
x <- find_mo_col("mo_authors")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
@ -492,7 +492,7 @@ mo_authors <- function(x, language = get_locale(), ...) {
|
||||
mo_year <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
x <- find_mo_col("mo_year")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
@ -508,7 +508,7 @@ mo_year <- function(x, language = get_locale(), ...) {
|
||||
mo_rank <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
x <- find_mo_col("mo_rank")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
@ -521,7 +521,7 @@ mo_rank <- function(x, language = get_locale(), ...) {
|
||||
mo_taxonomy <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
x <- find_mo_col("mo_taxonomy")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
@ -547,7 +547,7 @@ mo_taxonomy <- function(x, language = get_locale(), ...) {
|
||||
mo_synonyms <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
x <- find_mo_col("mo_synonyms")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
@ -580,7 +580,7 @@ mo_synonyms <- function(x, language = get_locale(), ...) {
|
||||
mo_info <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
x <- find_mo_col("mo_info")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
@ -610,7 +610,7 @@ mo_info <- function(x, language = get_locale(), ...) {
|
||||
mo_url <- function(x, open = FALSE, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
x <- find_mo_col("mo_url")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(open, allow_class = "logical", has_length = 1)
|
||||
@ -647,7 +647,7 @@ mo_url <- function(x, open = FALSE, language = get_locale(), ...) {
|
||||
mo_property <- function(x, property = "fullname", language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
x <- find_mo_col("mo_property")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(property, allow_class = "character", has_length = 1, is_in = colnames(microorganisms))
|
||||
|
||||
@ -132,7 +132,7 @@ set_mo_source <- function(path, destination = getOption("AMR_mo_source", "~/mo_s
|
||||
stop_ifnot(interactive(), "this function can only be used in interactive mode, since it must ask for the user's permission to write a file to their home folder.")
|
||||
|
||||
if (is.null(path) || path %in% c(FALSE, "")) {
|
||||
mo_env$mo_source <- NULL
|
||||
pkg_env$mo_source <- NULL
|
||||
if (file.exists(mo_source_destination)) {
|
||||
unlink(mo_source_destination)
|
||||
message_("Removed mo_source file '", font_bold(mo_source_destination), "'",
|
||||
@ -214,7 +214,7 @@ set_mo_source <- function(path, destination = getOption("AMR_mo_source", "~/mo_s
|
||||
attr(df, "mo_source_destination") <- mo_source_destination
|
||||
attr(df, "mo_source_timestamp") <- file.mtime(path)
|
||||
saveRDS(df, mo_source_destination)
|
||||
mo_env$mo_source <- df
|
||||
pkg_env$mo_source <- df
|
||||
message_(action, " mo_source file '", font_bold(mo_source_destination),
|
||||
"' (", formatted_filesize(mo_source_destination),
|
||||
") from '", font_bold(path),
|
||||
@ -232,17 +232,17 @@ get_mo_source <- function(destination = getOption("AMR_mo_source", "~/mo_source.
|
||||
}
|
||||
return(NULL)
|
||||
}
|
||||
if (is.null(mo_env$mo_source)) {
|
||||
mo_env$mo_source <- readRDS(path.expand(destination))
|
||||
if (is.null(pkg_env$mo_source)) {
|
||||
pkg_env$mo_source <- readRDS(path.expand(destination))
|
||||
}
|
||||
|
||||
old_time <- attributes(mo_env$mo_source)$mo_source_timestamp
|
||||
new_time <- file.mtime(attributes(mo_env$mo_source)$mo_source_location)
|
||||
old_time <- attributes(pkg_env$mo_source)$mo_source_timestamp
|
||||
new_time <- file.mtime(attributes(pkg_env$mo_source)$mo_source_location)
|
||||
if (interactive() && !identical(old_time, new_time)) {
|
||||
# source file was updated, also update reference
|
||||
set_mo_source(attributes(mo_env$mo_source)$mo_source_location)
|
||||
set_mo_source(attributes(pkg_env$mo_source)$mo_source_location)
|
||||
}
|
||||
mo_env$mo_source
|
||||
pkg_env$mo_source
|
||||
}
|
||||
|
||||
check_validity_mo_source <- function(x, refer_to_name = "`reference_df`", stop_on_error = TRUE) {
|
||||
@ -251,7 +251,7 @@ check_validity_mo_source <- function(x, refer_to_name = "`reference_df`", stop_o
|
||||
if (paste(deparse(substitute(x)), collapse = "") == "get_mo_source()") {
|
||||
return(TRUE)
|
||||
}
|
||||
if (is.null(mo_env$mo_source) && (identical(x, get_mo_source()))) {
|
||||
if (is.null(pkg_env$mo_source) && (identical(x, get_mo_source()))) {
|
||||
return(TRUE)
|
||||
}
|
||||
if (is.null(x)) {
|
||||
|
||||
6
R/rsi.R
6
R/rsi.R
@ -844,9 +844,9 @@ exec_as.rsi <- function(method,
|
||||
pillar_shaft.rsi <- function(x, ...) {
|
||||
out <- trimws(format(x))
|
||||
out[is.na(x)] <- font_grey(" NA")
|
||||
out[x == "S"] <- font_green_bg(font_white(" S "))
|
||||
out[x == "I"] <- font_yellow_bg(font_black(" I "))
|
||||
out[x == "R"] <- font_red_bg(font_white(" R "))
|
||||
out[x == "R"] <- font_rsi_R_bg(font_black(" R "))
|
||||
out[x == "S"] <- font_rsi_S_bg(font_black(" S "))
|
||||
out[x == "I"] <- font_rsi_I_bg(font_black(" I "))
|
||||
create_pillar_column(out, align = "left", width = 5)
|
||||
}
|
||||
|
||||
|
||||
@ -147,12 +147,10 @@ rsi_calc <- function(...,
|
||||
}
|
||||
|
||||
if (print_warning == TRUE) {
|
||||
# since rsi_calc() is always called from a count() or proportion() function, we use -1:
|
||||
cll <- gsub("[^a-zA-Z0-9_]+", "_", paste(deparse(sys.calls()[[length(sys.calls()) - 1]]), collapse = ""))
|
||||
if (message_not_thrown_before(cll)) {
|
||||
if (message_not_thrown_before("rsi_calc")) {
|
||||
warning_("Increase speed by transforming to class <rsi> on beforehand: your_data %>% mutate_if(is.rsi.eligible, as.rsi)",
|
||||
call = FALSE)
|
||||
remember_thrown_message(cll)
|
||||
remember_thrown_message("rsi_calc")
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@ -217,4 +217,4 @@ template:
|
||||
assets: "pkgdown/logos" # use logos in this folder
|
||||
params:
|
||||
noindex: false
|
||||
template: "flatly"
|
||||
bootswatch: "flatly"
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9045</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9045</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -12,7 +12,7 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
|
||||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
|
||||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
|
||||
@ -39,7 +39,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -193,7 +193,7 @@
|
||||
<h1 data-toc-skip>How to conduct AMR analysis</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">24 December 2020</h4>
|
||||
<h4 class="date">26 December 2020</h4>
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/AMR.Rmd"><code>vignettes/AMR.Rmd</code></a></small>
|
||||
<div class="hidden name"><code>AMR.Rmd</code></div>
|
||||
@ -202,7 +202,7 @@
|
||||
|
||||
|
||||
|
||||
<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/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 24 December 2020.</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/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 26 December 2020.</p>
|
||||
<div id="introduction" class="section level1">
|
||||
<h1 class="hasAnchor">
|
||||
<a href="#introduction" class="anchor"></a>Introduction</h1>
|
||||
@ -233,21 +233,21 @@
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">2020-12-24</td>
|
||||
<td align="center">2020-12-26</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">2020-12-24</td>
|
||||
<td align="center">2020-12-26</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">2020-12-24</td>
|
||||
<td align="center">2020-12-26</td>
|
||||
<td align="center">efgh</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">R</td>
|
||||
@ -352,31 +352,9 @@
|
||||
</tr></thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">2012-10-07</td>
|
||||
<td align="center">D7</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Escherichia coli</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="even">
|
||||
<td align="center">2016-11-19</td>
|
||||
<td align="center">V9</td>
|
||||
<td align="center">2011-10-28</td>
|
||||
<td align="center">I1</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">Klebsiella pneumoniae</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2015-03-30</td>
|
||||
<td align="center">D9</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">Staphylococcus aureus</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
@ -385,38 +363,60 @@
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2012-06-28</td>
|
||||
<td align="center">Z4</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">F</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2014-03-04</td>
|
||||
<td align="center">M4</td>
|
||||
<td align="center">Hospital C</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">2014-08-18</td>
|
||||
<td align="center">D2</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">2011-06-05</td>
|
||||
<td align="center">G5</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">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2014-05-12</td>
|
||||
<td align="center">X7</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">Streptococcus pneumoniae</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>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2011-02-23</td>
|
||||
<td align="center">K5</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">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">M</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">2017-09-20</td>
|
||||
<td align="center">T5</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">Escherichia coli</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>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2017-02-10</td>
|
||||
<td align="center">Y6</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">Escherichia coli</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<p>Now, let’s start the cleaning and the analysis!</p>
|
||||
@ -449,16 +449,16 @@ Longest: 1</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">M</td>
|
||||
<td align="right">10,392</td>
|
||||
<td align="right">51.96%</td>
|
||||
<td align="right">10,392</td>
|
||||
<td align="right">51.96%</td>
|
||||
<td align="right">10,426</td>
|
||||
<td align="right">52.13%</td>
|
||||
<td align="right">10,426</td>
|
||||
<td align="right">52.13%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">F</td>
|
||||
<td align="right">9,608</td>
|
||||
<td align="right">48.04%</td>
|
||||
<td align="right">9,574</td>
|
||||
<td align="right">47.87%</td>
|
||||
<td align="right">20,000</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
@ -515,7 +515,7 @@ Longest: 1</p>
|
||||
<div id="first-weighted-isolates" class="section level2">
|
||||
<h2 class="hasAnchor">
|
||||
<a href="#first-weighted-isolates" class="anchor"></a>First <em>weighted</em> isolates</h2>
|
||||
<p>We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient M9, sorted on date:</p>
|
||||
<p>We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient F3, sorted on date:</p>
|
||||
<table class="table">
|
||||
<thead><tr class="header">
|
||||
<th align="center">isolate</th>
|
||||
@ -531,19 +531,19 @@ Longest: 1</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">1</td>
|
||||
<td align="center">2010-01-25</td>
|
||||
<td align="center">M9</td>
|
||||
<td align="center">2010-01-17</td>
|
||||
<td align="center">F3</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2</td>
|
||||
<td align="center">2010-02-01</td>
|
||||
<td align="center">M9</td>
|
||||
<td align="center">2010-03-13</td>
|
||||
<td align="center">F3</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
@ -553,21 +553,21 @@ Longest: 1</p>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">3</td>
|
||||
<td align="center">2010-02-22</td>
|
||||
<td align="center">M9</td>
|
||||
<td align="center">2010-04-21</td>
|
||||
<td align="center">F3</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">4</td>
|
||||
<td align="center">2010-08-12</td>
|
||||
<td align="center">M9</td>
|
||||
<td align="center">2010-06-24</td>
|
||||
<td align="center">F3</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
@ -575,19 +575,19 @@ Longest: 1</p>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">5</td>
|
||||
<td align="center">2010-08-17</td>
|
||||
<td align="center">M9</td>
|
||||
<td align="center">2010-08-02</td>
|
||||
<td align="center">F3</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</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">FALSE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">6</td>
|
||||
<td align="center">2010-09-18</td>
|
||||
<td align="center">M9</td>
|
||||
<td align="center">2010-08-14</td>
|
||||
<td align="center">F3</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
@ -597,19 +597,19 @@ Longest: 1</p>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">7</td>
|
||||
<td align="center">2011-07-05</td>
|
||||
<td align="center">M9</td>
|
||||
<td align="center">2010-10-06</td>
|
||||
<td align="center">F3</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">TRUE</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">2011-07-19</td>
|
||||
<td align="center">M9</td>
|
||||
<td align="center">2010-10-17</td>
|
||||
<td align="center">F3</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
@ -619,19 +619,8 @@ Longest: 1</p>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">9</td>
|
||||
<td align="center">2011-07-20</td>
|
||||
<td align="center">M9</td>
|
||||
<td align="center">B_ESCHR_COLI</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>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">10</td>
|
||||
<td align="center">2011-09-04</td>
|
||||
<td align="center">M9</td>
|
||||
<td align="center">2010-11-17</td>
|
||||
<td align="center">F3</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">I</td>
|
||||
@ -639,6 +628,17 @@ Longest: 1</p>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">10</td>
|
||||
<td align="center">2011-02-21</td>
|
||||
<td align="center">F3</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">TRUE</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>
|
||||
@ -665,20 +665,20 @@ Longest: 1</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">1</td>
|
||||
<td align="center">2010-01-25</td>
|
||||
<td align="center">M9</td>
|
||||
<td align="center">2010-01-17</td>
|
||||
<td align="center">F3</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">TRUE</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">2</td>
|
||||
<td align="center">2010-02-01</td>
|
||||
<td align="center">M9</td>
|
||||
<td align="center">2010-03-13</td>
|
||||
<td align="center">F3</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
@ -689,68 +689,68 @@ Longest: 1</p>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">3</td>
|
||||
<td align="center">2010-02-22</td>
|
||||
<td align="center">M9</td>
|
||||
<td align="center">2010-04-21</td>
|
||||
<td align="center">F3</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</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">2010-08-12</td>
|
||||
<td align="center">M9</td>
|
||||
<td align="center">2010-06-24</td>
|
||||
<td align="center">F3</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">I</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="odd">
|
||||
<td align="center">5</td>
|
||||
<td align="center">2010-08-17</td>
|
||||
<td align="center">M9</td>
|
||||
<td align="center">2010-08-02</td>
|
||||
<td align="center">F3</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</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">FALSE</td>
|
||||
<td align="center">TRUE</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">6</td>
|
||||
<td align="center">2010-09-18</td>
|
||||
<td align="center">M9</td>
|
||||
<td align="center">2010-08-14</td>
|
||||
<td align="center">F3</td>
|
||||
<td align="center">B_ESCHR_COLI</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="odd">
|
||||
<td align="center">7</td>
|
||||
<td align="center">2011-07-05</td>
|
||||
<td align="center">M9</td>
|
||||
<td align="center">2010-10-06</td>
|
||||
<td align="center">F3</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">TRUE</td>
|
||||
<td align="center">TRUE</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">8</td>
|
||||
<td align="center">2011-07-19</td>
|
||||
<td align="center">M9</td>
|
||||
<td align="center">2010-10-17</td>
|
||||
<td align="center">F3</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
@ -761,36 +761,36 @@ Longest: 1</p>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">9</td>
|
||||
<td align="center">2011-07-20</td>
|
||||
<td align="center">M9</td>
|
||||
<td align="center">B_ESCHR_COLI</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>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">10</td>
|
||||
<td align="center">2011-09-04</td>
|
||||
<td align="center">M9</td>
|
||||
<td align="center">2010-11-17</td>
|
||||
<td align="center">F3</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">I</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">FALSE</td>
|
||||
<td align="center">FALSE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">10</td>
|
||||
<td align="center">2011-02-21</td>
|
||||
<td align="center">F3</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">TRUE</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<p>Instead of 2, now 8 isolates are flagged. In total, 78.4% of all isolates are marked ‘first weighted’ - 50.0% 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 2, now 6 isolates are flagged. In total, 78.5% of all isolates are marked ‘first weighted’ - 50.1% 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="cb19"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op"><-</span> <span class="va">data</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="../reference/first_isolate.html">filter_first_weighted_isolate</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
|
||||
<p>So we end up with 15,683 isolates for analysis.</p>
|
||||
<p>So we end up with 15,695 isolates for analysis.</p>
|
||||
<p>We can remove unneeded columns:</p>
|
||||
<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op"><-</span> <span class="va">data_1st</span> <span class="op">%>%</span>
|
||||
@ -834,13 +834,29 @@ Longest: 1</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="center">2012-10-07</td>
|
||||
<td align="center">D7</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">2011-10-28</td>
|
||||
<td align="center">I1</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_STPHY_AURS</td>
|
||||
<td align="center">R</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="even">
|
||||
<td align="left">2</td>
|
||||
<td align="center">2011-06-05</td>
|
||||
<td align="center">G5</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_ESCHR_COLI</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">M</td>
|
||||
<td align="center">Gram-negative</td>
|
||||
@ -848,63 +864,15 @@ Longest: 1</p>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="center">2016-11-19</td>
|
||||
<td align="center">V9</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_KLBSL_PNMN</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">F</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="odd">
|
||||
<td align="left">3</td>
|
||||
<td align="center">2015-03-30</td>
|
||||
<td align="center">D9</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">B_STPHY_AURS</td>
|
||||
<td align="center">R</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="even">
|
||||
<td align="left">5</td>
|
||||
<td align="center">2014-03-04</td>
|
||||
<td align="center">M4</td>
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">B_STPHY_AURS</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="left">7</td>
|
||||
<td align="center">2011-02-08</td>
|
||||
<td align="center">S3</td>
|
||||
<td align="center">2014-05-12</td>
|
||||
<td align="center">X7</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">B_STRPT_PNMN</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">F</td>
|
||||
<td align="center">Gram-positive</td>
|
||||
@ -913,16 +881,48 @@ Longest: 1</p>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">8</td>
|
||||
<td align="center">2015-12-31</td>
|
||||
<td align="center">I5</td>
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="center">R</td>
|
||||
<td align="left">4</td>
|
||||
<td align="center">2011-02-23</td>
|
||||
<td align="center">K5</td>
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">B_STPHY_AURS</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="left">5</td>
|
||||
<td align="center">2017-09-20</td>
|
||||
<td align="center">T5</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_ESCHR_COLI</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">Gram-negative</td>
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">coli</td>
|
||||
<td align="center">TRUE</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">7</td>
|
||||
<td align="center">2017-12-17</td>
|
||||
<td align="center">Z3</td>
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">B_ESCHR_COLI</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</td>
|
||||
<td align="center">S</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>
|
||||
@ -949,8 +949,8 @@ Longest: 1</p>
|
||||
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%>%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></code></pre></div>
|
||||
<p><strong>Frequency table</strong></p>
|
||||
<p>Class: character<br>
|
||||
Length: 15,683<br>
|
||||
Available: 15,683 (100%, NA: 0 = 0%)<br>
|
||||
Length: 15,695<br>
|
||||
Available: 15,695 (100%, NA: 0 = 0%)<br>
|
||||
Unique: 4</p>
|
||||
<p>Shortest: 16<br>
|
||||
Longest: 24</p>
|
||||
@ -967,33 +967,33 @@ Longest: 24</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">Escherichia coli</td>
|
||||
<td align="right">7,815</td>
|
||||
<td align="right">49.83%</td>
|
||||
<td align="right">7,815</td>
|
||||
<td align="right">49.83%</td>
|
||||
<td align="right">7,828</td>
|
||||
<td align="right">49.88%</td>
|
||||
<td align="right">7,828</td>
|
||||
<td align="right">49.88%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">Staphylococcus aureus</td>
|
||||
<td align="right">4,001</td>
|
||||
<td align="right">25.51%</td>
|
||||
<td align="right">11,816</td>
|
||||
<td align="right">75.34%</td>
|
||||
<td align="right">3,977</td>
|
||||
<td align="right">25.34%</td>
|
||||
<td align="right">11,805</td>
|
||||
<td align="right">75.22%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">3</td>
|
||||
<td align="left">Streptococcus pneumoniae</td>
|
||||
<td align="right">2,330</td>
|
||||
<td align="right">14.86%</td>
|
||||
<td align="right">14,146</td>
|
||||
<td align="right">90.20%</td>
|
||||
<td align="right">2,320</td>
|
||||
<td align="right">14.78%</td>
|
||||
<td align="right">14,125</td>
|
||||
<td align="right">90.00%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">4</td>
|
||||
<td align="left">Klebsiella pneumoniae</td>
|
||||
<td align="right">1,537</td>
|
||||
<td align="right">9.80%</td>
|
||||
<td align="right">15,683</td>
|
||||
<td align="right">1,570</td>
|
||||
<td align="right">10.00%</td>
|
||||
<td align="right">15,695</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
@ -1020,50 +1020,50 @@ Longest: 24</p>
|
||||
<tr class="odd">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">AMX</td>
|
||||
<td align="center">3744</td>
|
||||
<td align="center">257</td>
|
||||
<td align="center">3814</td>
|
||||
<td align="center">7815</td>
|
||||
<td align="center">3731</td>
|
||||
<td align="center">275</td>
|
||||
<td align="center">3822</td>
|
||||
<td align="center">7828</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">AMC</td>
|
||||
<td align="center">6185</td>
|
||||
<td align="center">294</td>
|
||||
<td align="center">1336</td>
|
||||
<td align="center">7815</td>
|
||||
<td align="center">6146</td>
|
||||
<td align="center">297</td>
|
||||
<td align="center">1385</td>
|
||||
<td align="center">7828</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">CIP</td>
|
||||
<td align="center">5934</td>
|
||||
<td align="center">5918</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">1881</td>
|
||||
<td align="center">7815</td>
|
||||
<td align="center">1910</td>
|
||||
<td align="center">7828</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">GEN</td>
|
||||
<td align="center">7005</td>
|
||||
<td align="center">7087</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">810</td>
|
||||
<td align="center">7815</td>
|
||||
<td align="center">741</td>
|
||||
<td align="center">7828</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">K. pneumoniae</td>
|
||||
<td align="center">AMX</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">1537</td>
|
||||
<td align="center">1537</td>
|
||||
<td align="center">1570</td>
|
||||
<td align="center">1570</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">K. pneumoniae</td>
|
||||
<td align="center">AMC</td>
|
||||
<td align="center">1225</td>
|
||||
<td align="center">45</td>
|
||||
<td align="center">267</td>
|
||||
<td align="center">1537</td>
|
||||
<td align="center">1231</td>
|
||||
<td align="center">57</td>
|
||||
<td align="center">282</td>
|
||||
<td align="center">1570</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1086,34 +1086,34 @@ Longest: 24</p>
|
||||
<tr class="odd">
|
||||
<td align="center">E. coli</td>
|
||||
<td align="center">CIP</td>
|
||||
<td align="center">5934</td>
|
||||
<td align="center">5918</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">1881</td>
|
||||
<td align="center">7815</td>
|
||||
<td align="center">1910</td>
|
||||
<td align="center">7828</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">K. pneumoniae</td>
|
||||
<td align="center">CIP</td>
|
||||
<td align="center">1189</td>
|
||||
<td align="center">1191</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">348</td>
|
||||
<td align="center">1537</td>
|
||||
<td align="center">379</td>
|
||||
<td align="center">1570</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">S. aureus</td>
|
||||
<td align="center">CIP</td>
|
||||
<td align="center">3064</td>
|
||||
<td align="center">3045</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">937</td>
|
||||
<td align="center">4001</td>
|
||||
<td align="center">932</td>
|
||||
<td align="center">3977</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">S. pneumoniae</td>
|
||||
<td align="center">CIP</td>
|
||||
<td align="center">1780</td>
|
||||
<td align="center">1785</td>
|
||||
<td align="center">0</td>
|
||||
<td align="center">550</td>
|
||||
<td align="center">2330</td>
|
||||
<td align="center">535</td>
|
||||
<td align="center">2320</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1126,7 +1126,7 @@ Longest: 24</p>
|
||||
<p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
|
||||
<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%>%</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span>
|
||||
<span class="co"># [1] 0.5342728</span></code></pre></div>
|
||||
<span class="co"># [1] 0.536604</span></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="cb28"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%>%</span>
|
||||
@ -1141,19 +1141,19 @@ Longest: 24</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">0.5253802</td>
|
||||
<td align="center">0.5429950</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">0.5367779</td>
|
||||
<td align="center">0.5429998</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">0.5470814</td>
|
||||
<td align="center">0.5283993</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">0.5334627</td>
|
||||
<td align="center">0.5222153</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1173,23 +1173,23 @@ Longest: 24</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital A</td>
|
||||
<td align="center">0.5253802</td>
|
||||
<td align="center">4669</td>
|
||||
<td align="center">0.5429950</td>
|
||||
<td align="center">4768</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital B</td>
|
||||
<td align="center">0.5367779</td>
|
||||
<td align="center">5574</td>
|
||||
<td align="center">0.5429998</td>
|
||||
<td align="center">5407</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Hospital C</td>
|
||||
<td align="center">0.5470814</td>
|
||||
<td align="center">2347</td>
|
||||
<td align="center">0.5283993</td>
|
||||
<td align="center">2324</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Hospital D</td>
|
||||
<td align="center">0.5334627</td>
|
||||
<td align="center">3093</td>
|
||||
<td align="center">0.5222153</td>
|
||||
<td align="center">3196</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
@ -1211,27 +1211,27 @@ Longest: 24</p>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td align="center">Escherichia</td>
|
||||
<td align="center">0.8290467</td>
|
||||
<td align="center">0.8963532</td>
|
||||
<td align="center">0.9843890</td>
|
||||
<td align="center">0.8230710</td>
|
||||
<td align="center">0.9053398</td>
|
||||
<td align="center">0.9872253</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Klebsiella</td>
|
||||
<td align="center">0.8262850</td>
|
||||
<td align="center">0.9095641</td>
|
||||
<td align="center">0.9837345</td>
|
||||
<td align="center">0.8203822</td>
|
||||
<td align="center">0.9076433</td>
|
||||
<td align="center">0.9847134</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="center">Staphylococcus</td>
|
||||
<td align="center">0.8307923</td>
|
||||
<td align="center">0.9122719</td>
|
||||
<td align="center">0.9872532</td>
|
||||
<td align="center">0.8287654</td>
|
||||
<td align="center">0.9192859</td>
|
||||
<td align="center">0.9894393</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="center">Streptococcus</td>
|
||||
<td align="center">0.5351931</td>
|
||||
<td align="center">0.5379310</td>
|
||||
<td align="center">0.0000000</td>
|
||||
<td align="center">0.5351931</td>
|
||||
<td align="center">0.5379310</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
|
||||
Binary file not shown.
|
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|
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|
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@ -12,7 +12,7 @@
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<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
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@ -12,7 +12,7 @@
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|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
|
||||
@ -39,7 +39,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -311,17 +311,17 @@ Unique: 2</p>
|
||||
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span>
|
||||
<span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
|
||||
<span class="co"># 1 S S R I R S</span>
|
||||
<span class="co"># 2 I S R I I R</span>
|
||||
<span class="co"># 3 R R R S I R</span>
|
||||
<span class="co"># 4 I I R R S S</span>
|
||||
<span class="co"># 5 I R I S S R</span>
|
||||
<span class="co"># 6 I R I I S I</span>
|
||||
<span class="co"># 1 R I R S I S</span>
|
||||
<span class="co"># 2 I S I S S R</span>
|
||||
<span class="co"># 3 I I I R I R</span>
|
||||
<span class="co"># 4 S S I S R I</span>
|
||||
<span class="co"># 5 I R S R S R</span>
|
||||
<span class="co"># 6 I I I R S I</span>
|
||||
<span class="co"># kanamycin</span>
|
||||
<span class="co"># 1 R</span>
|
||||
<span class="co"># 2 S</span>
|
||||
<span class="co"># 1 S</span>
|
||||
<span class="co"># 2 I</span>
|
||||
<span class="co"># 3 I</span>
|
||||
<span class="co"># 4 I</span>
|
||||
<span class="co"># 4 S</span>
|
||||
<span class="co"># 5 I</span>
|
||||
<span class="co"># 6 R</span></code></pre></div>
|
||||
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
|
||||
@ -354,40 +354,40 @@ Unique: 5</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">Mono-resistant</td>
|
||||
<td align="right">3214</td>
|
||||
<td align="right">64.28%</td>
|
||||
<td align="right">3214</td>
|
||||
<td align="right">64.28%</td>
|
||||
<td align="right">3219</td>
|
||||
<td align="right">64.38%</td>
|
||||
<td align="right">3219</td>
|
||||
<td align="right">64.38%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">Negative</td>
|
||||
<td align="right">997</td>
|
||||
<td align="right">19.94%</td>
|
||||
<td align="right">4211</td>
|
||||
<td align="right">84.22%</td>
|
||||
<td align="right">982</td>
|
||||
<td align="right">19.64%</td>
|
||||
<td align="right">4201</td>
|
||||
<td align="right">84.02%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">3</td>
|
||||
<td align="left">Multi-drug-resistant</td>
|
||||
<td align="right">442</td>
|
||||
<td align="right">8.84%</td>
|
||||
<td align="right">4653</td>
|
||||
<td align="right">93.06%</td>
|
||||
<td align="right">434</td>
|
||||
<td align="right">8.68%</td>
|
||||
<td align="right">4635</td>
|
||||
<td align="right">92.70%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">4</td>
|
||||
<td align="left">Poly-resistant</td>
|
||||
<td align="right">239</td>
|
||||
<td align="right">4.78%</td>
|
||||
<td align="right">4892</td>
|
||||
<td align="right">97.84%</td>
|
||||
<td align="right">251</td>
|
||||
<td align="right">5.02%</td>
|
||||
<td align="right">4886</td>
|
||||
<td align="right">97.72%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">5</td>
|
||||
<td align="left">Extensively drug-resistant</td>
|
||||
<td align="right">108</td>
|
||||
<td align="right">2.16%</td>
|
||||
<td align="right">114</td>
|
||||
<td align="right">2.28%</td>
|
||||
<td align="right">5000</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
|
||||
@ -12,7 +12,7 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
|
||||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
|
||||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
|
||||
@ -39,7 +39,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -12,7 +12,7 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
|
||||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
|
||||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
|
||||
@ -39,7 +39,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -193,7 +193,7 @@
|
||||
<h1 data-toc-skip>How to import data from SPSS / SAS / Stata</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">24 December 2020</h4>
|
||||
<h4 class="date">26 December 2020</h4>
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/SPSS.Rmd"><code>vignettes/SPSS.Rmd</code></a></small>
|
||||
<div class="hidden name"><code>SPSS.Rmd</code></div>
|
||||
|
||||
@ -12,7 +12,7 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
|
||||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
|
||||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
|
||||
@ -39,7 +39,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -12,7 +12,7 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
|
||||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
|
||||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
|
||||
@ -39,7 +39,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -227,34 +227,20 @@
|
||||
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">S.aureus</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max</span>
|
||||
<span class="co"># as.mo("sau") 9.9 12.0 15.0 13.0 13.0 42.0</span>
|
||||
<span class="co"># as.mo("stau") 100.0 100.0 130.0 120.0 140.0 190.0</span>
|
||||
<span class="co"># as.mo("STAU") 110.0 110.0 130.0 130.0 140.0 150.0</span>
|
||||
<span class="co"># as.mo("staaur") 9.8 12.0 26.0 13.0 41.0 60.0</span>
|
||||
<span class="co"># as.mo("STAAUR") 11.0 11.0 15.0 13.0 13.0 41.0</span>
|
||||
<span class="co"># as.mo("S. aureus") 26.0 28.0 50.0 58.0 63.0 75.0</span>
|
||||
<span class="co"># as.mo("S aureus") 26.0 27.0 46.0 51.0 60.0 67.0</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus") 1.9 2.2 2.5 2.5 2.8 3.1</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 870.0 880.0 1100.0 910.0 1000.0 2400.0</span>
|
||||
<span class="co"># as.mo("Sthafilokkockus aaureuz") 360.0 370.0 400.0 380.0 420.0 540.0</span>
|
||||
<span class="co"># as.mo("MRSA") 9.7 11.0 17.0 12.0 13.0 66.0</span>
|
||||
<span class="co"># as.mo("VISA") 19.0 19.0 36.0 35.0 53.0 56.0</span>
|
||||
<span class="co"># as.mo("VRSA") 17.0 20.0 20.0 21.0 21.0 23.0</span>
|
||||
<span class="co"># neval</span>
|
||||
<span class="co"># 10</span>
|
||||
<span class="co"># 10</span>
|
||||
<span class="co"># 10</span>
|
||||
<span class="co"># 10</span>
|
||||
<span class="co"># 10</span>
|
||||
<span class="co"># 10</span>
|
||||
<span class="co"># 10</span>
|
||||
<span class="co"># 10</span>
|
||||
<span class="co"># 10</span>
|
||||
<span class="co"># 10</span>
|
||||
<span class="co"># 10</span>
|
||||
<span class="co"># 10</span>
|
||||
<span class="co"># 10</span></code></pre></div>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># as.mo("sau") 9.9 11 19.0 12.0 13.0 47.0 10</span>
|
||||
<span class="co"># as.mo("stau") 100.0 110 130.0 130.0 140.0 150.0 10</span>
|
||||
<span class="co"># as.mo("STAU") 110.0 110 130.0 140.0 140.0 150.0 10</span>
|
||||
<span class="co"># as.mo("staaur") 11.0 11 15.0 12.0 13.0 40.0 10</span>
|
||||
<span class="co"># as.mo("STAAUR") 12.0 12 21.0 13.0 40.0 46.0 10</span>
|
||||
<span class="co"># as.mo("S. aureus") 26.0 31 45.0 34.0 60.0 86.0 10</span>
|
||||
<span class="co"># as.mo("S aureus") 26.0 29 36.0 31.0 33.0 58.0 10</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus") 1.6 2 2.3 2.3 2.7 2.8 10</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 880.0 900 910.0 910.0 920.0 950.0 10</span>
|
||||
<span class="co"># as.mo("Sthafilokkockus aaureuz") 370.0 370 380.0 380.0 380.0 400.0 10</span>
|
||||
<span class="co"># as.mo("MRSA") 9.9 11 18.0 13.0 14.0 47.0 10</span>
|
||||
<span class="co"># as.mo("VISA") 17.0 19 29.0 21.0 48.0 50.0 10</span>
|
||||
<span class="co"># as.mo("VRSA") 16.0 19 29.0 20.0 47.0 55.0 10</span></code></pre></div>
|
||||
<p><img src="benchmarks_files/figure-html/unnamed-chunk-4-1.png" width="562.5"></p>
|
||||
<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. It is clear that accepted taxonomic names are extremely fast, but some variations can take up to 500-1000 times as much time.</p>
|
||||
<p>To improve performance, two important calculations take almost no time at all: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
|
||||
@ -284,8 +270,8 @@
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># mo_name(x) 134 167 201 179 207 310 10</span></code></pre></div>
|
||||
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.179 seconds. You only lose time on your unique input values.</p>
|
||||
<span class="co"># mo_name(x) 136 169 210 198 247 317 10</span></code></pre></div>
|
||||
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.198 seconds. You only lose time on your unique input values.</p>
|
||||
</div>
|
||||
<div id="precalculated-results" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
@ -299,10 +285,10 @@
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># A 7.59 7.93 8.24 8.09 8.66 9.06 10</span>
|
||||
<span class="co"># B 23.60 23.70 29.20 24.30 27.10 66.10 10</span>
|
||||
<span class="co"># C 1.84 2.13 2.22 2.19 2.35 2.62 10</span></code></pre></div>
|
||||
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0022 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>
|
||||
<span class="co"># A 7.21 7.32 7.92 7.69 8.49 9.43 10</span>
|
||||
<span class="co"># B 22.60 23.50 28.90 24.70 26.10 69.20 10</span>
|
||||
<span class="co"># C 1.87 1.92 2.10 2.08 2.27 2.34 10</span></code></pre></div>
|
||||
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0021 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="cb5"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">run_it</span> <span class="op"><-</span> <span class="fu">microbenchmark</span><span class="op">(</span>A <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span><span class="op">(</span><span class="st">"aureus"</span><span class="op">)</span>,
|
||||
B <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"Staphylococcus"</span><span class="op">)</span>,
|
||||
@ -316,14 +302,14 @@
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># A 1.69 1.77 1.82 1.83 1.86 1.92 10</span>
|
||||
<span class="co"># B 1.78 1.79 1.89 1.91 1.95 2.06 10</span>
|
||||
<span class="co"># C 1.74 1.79 1.88 1.87 1.94 2.06 10</span>
|
||||
<span class="co"># D 1.75 1.77 1.94 1.95 1.99 2.41 10</span>
|
||||
<span class="co"># E 1.70 1.75 1.84 1.81 1.87 2.08 10</span>
|
||||
<span class="co"># F 1.66 1.70 1.76 1.74 1.80 1.89 10</span>
|
||||
<span class="co"># G 1.68 1.70 1.82 1.75 1.93 2.09 10</span>
|
||||
<span class="co"># H 1.66 1.69 1.75 1.74 1.80 1.92 10</span></code></pre></div>
|
||||
<span class="co"># A 1.34 1.59 1.66 1.65 1.74 2.18 10</span>
|
||||
<span class="co"># B 1.34 1.63 1.73 1.72 1.85 2.31 10</span>
|
||||
<span class="co"># C 1.41 1.61 1.65 1.65 1.72 1.83 10</span>
|
||||
<span class="co"># D 1.59 1.63 1.77 1.77 1.89 2.03 10</span>
|
||||
<span class="co"># E 1.33 1.60 1.68 1.65 1.73 2.08 10</span>
|
||||
<span class="co"># F 1.31 1.34 1.56 1.52 1.71 2.11 10</span>
|
||||
<span class="co"># G 1.34 1.60 1.75 1.64 1.76 2.74 10</span>
|
||||
<span class="co"># H 1.32 1.38 1.57 1.63 1.71 1.78 10</span></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> anyway, 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">
|
||||
@ -350,14 +336,14 @@
|
||||
times <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">4</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># en 15.91 16.98 21.87 17.54 18.34 168.50 100</span>
|
||||
<span class="co"># de 18.98 20.14 26.30 20.74 22.64 66.68 100</span>
|
||||
<span class="co"># nl 31.02 32.71 37.56 33.84 35.81 82.77 100</span>
|
||||
<span class="co"># es 19.13 20.06 22.96 20.54 21.42 65.26 100</span>
|
||||
<span class="co"># it 18.90 19.84 24.26 20.59 22.80 60.30 100</span>
|
||||
<span class="co"># fr 18.89 19.92 23.46 20.49 21.72 62.85 100</span>
|
||||
<span class="co"># pt 18.90 19.99 23.80 20.70 22.17 61.42 100</span></code></pre></div>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># en 15.73 16.35 20.85 16.74 17.71 56.56 100</span>
|
||||
<span class="co"># de 18.96 19.62 22.32 19.86 20.46 59.58 100</span>
|
||||
<span class="co"># nl 31.06 31.91 37.31 32.78 34.57 75.58 100</span>
|
||||
<span class="co"># es 18.92 19.59 23.43 19.92 20.42 62.72 100</span>
|
||||
<span class="co"># it 18.80 19.36 22.59 19.74 20.54 62.72 100</span>
|
||||
<span class="co"># fr 18.88 19.53 23.89 19.85 20.91 61.56 100</span>
|
||||
<span class="co"># pt 18.89 19.51 21.46 19.87 20.29 59.12 100</span></code></pre></div>
|
||||
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 68 KiB After Width: | Height: | Size: 70 KiB |
@ -12,7 +12,7 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
|
||||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
|
||||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
|
||||
@ -39,7 +39,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9045</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -12,7 +12,7 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
|
||||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
|
||||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
|
||||
@ -39,7 +39,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -12,7 +12,7 @@
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
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<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
|
||||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
|
||||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
|
||||
@ -39,7 +39,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9045</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 55 KiB After Width: | Height: | Size: 60 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 1.1 MiB After Width: | Height: | Size: 1.5 MiB |
@ -12,7 +12,7 @@
|
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<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png">
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<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png">
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<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png">
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<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
|
||||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="bootstrap-toc.css">
|
||||
<script src="bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
|
||||
@ -43,7 +43,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9045</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -210,7 +210,7 @@ Since you are one of our users, we would like to know how you use the package an
|
||||
<p>This package is <a href="https://en.wikipedia.org/wiki/Dependency_hell">fully independent of any other R package</a> and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl">Certe Medical Diagnostics and Advice</a> and <a href="https://www.umcg.nl">University Medical Center Groningen</a>. This R package is <a href="./news">actively maintained</a> and is free software (see <a href="#copyright">Copyright</a>).</p>
|
||||
<div class="main-content" style="display: inline-block;">
|
||||
<p>
|
||||
<a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a> <strong>Used in 135 countries</strong><br> Since its first public release in early 2018, this package has been downloaded from 135 countries. Click the map to enlarge and to see the country names.
|
||||
<a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a> <strong>Used in 138 countries</strong><br> Since its first public release in early 2018, this package has been downloaded from 138 countries. Click the map to enlarge and to see the country names.
|
||||
</p>
|
||||
</div>
|
||||
<div id="with-amr-for-r-theres-always-a-knowledgeable-microbiologist-by-your-side" class="section level5">
|
||||
@ -222,9 +222,9 @@ Since you are one of our users, we would like to know how you use the package an
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
|
||||
|
||||
<span class="va">example_isolates</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="fu"><a href="reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="fu"><a href="reference/mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"cefotax"</span><span class="op">)</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="va">mo</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/dplyr/man/mutate.html">mutate</a></span><span class="op">(</span>mo <span class="op">=</span> <span class="fu"><a href="reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/dplyr/man/filter.html">filter</a></span><span class="op">(</span><span class="fu"><a href="reference/mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"cefotax"</span><span class="op">)</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/dplyr/man/select.html">select</a></span><span class="op">(</span><span class="va">mo</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>
|
||||
<span class="co">#> NOTE: Using column 'mo' as input for mo_is_gram_negative()</span>
|
||||
<span class="co">#> NOTE: Using column 'mo' as input for mo_is_intrinsic_resistant()</span>
|
||||
<span class="co">#> Selecting aminoglycosides: 'AMK' (amikacin), 'GEN' (gentamicin), </span>
|
||||
@ -411,7 +411,7 @@ Since you are one of our users, we would like to know how you use the package an
|
||||
<li>
|
||||
<p>It <strong>analyses the data</strong> with convenient functions that use well-known methods.</p>
|
||||
<ul>
|
||||
<li>Calculate the microbial susceptibility or resistance (and even co-resistance) with the <code><a href="reference/proportion.html">susceptibility()</a></code> and <code><a href="reference/proportion.html">resistance()</a></code> functions, or be even more specific with the <code><a href="reference/proportion.html">proportion_R()</a></code>, <code><a href="reference/proportion.html">proportion_IR()</a></code>, <code><a href="reference/proportion.html">proportion_I()</a></code>, <code><a href="reference/proportion.html">proportion_SI()</a></code> and <code><a href="reference/proportion.html">proportion_S()</a></code> functions. Similarly, the <em>number</em> of isolates can be determined with the <code><a href="reference/count.html">count_resistant()</a></code>, <code><a href="reference/count.html">count_susceptible()</a></code> and <code><a href="reference/count.html">count_all()</a></code> functions. All these functions can be used with the <code>dplyr</code> package (e.g. in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>)</li>
|
||||
<li>Calculate the microbial susceptibility or resistance (and even co-resistance) with the <code><a href="reference/proportion.html">susceptibility()</a></code> and <code><a href="reference/proportion.html">resistance()</a></code> functions, or be even more specific with the <code><a href="reference/proportion.html">proportion_R()</a></code>, <code><a href="reference/proportion.html">proportion_IR()</a></code>, <code><a href="reference/proportion.html">proportion_I()</a></code>, <code><a href="reference/proportion.html">proportion_SI()</a></code> and <code><a href="reference/proportion.html">proportion_S()</a></code> functions. Similarly, the <em>number</em> of isolates can be determined with the <code><a href="reference/count.html">count_resistant()</a></code>, <code><a href="reference/count.html">count_susceptible()</a></code> and <code><a href="reference/count.html">count_all()</a></code> functions. All these functions can be used with the <code>dplyr</code> package (e.g. in conjunction with <code><a href="https://rdrr.io/pkg/dplyr/man/summarise.html">summarise()</a></code>)</li>
|
||||
<li>Plot AMR results with <code><a href="reference/ggplot_rsi.html">geom_rsi()</a></code>, a function made for the <code>ggplot2</code> package</li>
|
||||
<li>Predict antimicrobial resistance for the nextcoming years using logistic regression models with the <code><a href="reference/resistance_predict.html">resistance_predict()</a></code> function</li>
|
||||
</ul>
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9045</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -236,26 +236,26 @@
|
||||
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
|
||||
</div>
|
||||
|
||||
<div id="amr-1409045" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="1.4.0.9045">
|
||||
<a href="#amr-1409045" class="anchor"></a>AMR 1.4.0.9045<small> Unreleased </small>
|
||||
<div id="amr-1409046" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="1.4.0.9046">
|
||||
<a href="#amr-1409046" class="anchor"></a>AMR 1.4.0.9046<small> Unreleased </small>
|
||||
</h1>
|
||||
<div id="last-updated-25-december-2020" class="section level2">
|
||||
<div id="last-updated-27-december-2020" class="section level2">
|
||||
<h2 class="hasAnchor">
|
||||
<a href="#last-updated-25-december-2020" class="anchor"></a><small>Last updated: 25 December 2020</small>
|
||||
<a href="#last-updated-27-december-2020" class="anchor"></a><small>Last updated: 27 December 2020</small>
|
||||
</h2>
|
||||
<div id="new" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
<a href="#new" class="anchor"></a>New</h3>
|
||||
<ul>
|
||||
<li>
|
||||
<p>Function <code><a href="../reference/is_new_episode.html">is_new_episode()</a></code> to determine patient episodes which are not necessarily based on microorganisms. It also supports grouped variables with e.g. <code><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate()</a></code>, <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code> of the <code>dplyr</code> package:</p>
|
||||
<p>Functions <code><a href="../reference/get_episode.html">get_episode()</a></code> and <code><a href="../reference/get_episode.html">is_new_episode()</a></code> to determine (patient) episodes which are not necessarily based on microorganisms. The <code><a href="../reference/get_episode.html">get_episode()</a></code> function returns the index number of the episode per group, while the <code><a href="../reference/get_episode.html">is_new_episode()</a></code> function returns values <code>TRUE</code>/<code>FALSE</code> to indicate whether an item in a vector is the start of a new episode. They also support <code>dplyr</code>s grouping (i.e. using <code><a href="https://rdrr.io/pkg/dplyr/man/group_by.html">group_by()</a></code>):</p>
|
||||
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R">
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
|
||||
<span class="va">example_isolates</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">patient_id</span>, <span class="va">hospital_id</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/is_new_episode.html">is_new_episode</a></span><span class="op">(</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span><span class="op">)</span></code></pre></div>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/dplyr/man/group_by.html">group_by</a></span><span class="op">(</span><span class="va">patient_id</span>, <span class="va">hospital_id</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/dplyr/man/filter.html">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/get_episode.html">is_new_episode</a></span><span class="op">(</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span><span class="op">)</span></code></pre></div>
|
||||
</li>
|
||||
<li><p>Functions <code><a href="../reference/mo_property.html">mo_is_gram_negative()</a></code> and <code><a href="../reference/mo_property.html">mo_is_gram_positive()</a></code> as wrappers around <code><a href="../reference/mo_property.html">mo_gramstain()</a></code>. They always return <code>TRUE</code> or <code>FALSE</code> (except when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>), thus always return <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p></li>
|
||||
<li><p>Function <code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> to test for intrinsic resistance, based on <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST Intrinsic Resistance and Unusual Phenotypes v3.2</a> from 2020.</p></li>
|
||||
@ -279,15 +279,15 @@
|
||||
</ul>
|
||||
</li>
|
||||
<li>
|
||||
<p>Some functions are now context-aware when used inside <code>dplyr</code> verbs, such as <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code>, <code><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>. This means that then the data argument does not need to be set anymore. This is the case for the new functions <code><a href="../reference/mo_property.html">mo_is_gram_negative()</a></code>, <code><a href="../reference/mo_property.html">mo_is_gram_positive()</a></code>, <code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> and for the existing functions <code><a href="../reference/first_isolate.html">first_isolate()</a></code>, <code><a href="../reference/key_antibiotics.html">key_antibiotics()</a></code>, <code><a href="../reference/mdro.html">mdro()</a></code>, <code><a href="../reference/mdro.html">brmo()</a></code>, <code><a href="../reference/mdro.html">mrgn()</a></code>, <code><a href="../reference/mdro.html">mdr_tb()</a></code>, <code><a href="../reference/mdro.html">mdr_cmi2012()</a></code>, <code><a href="../reference/mdro.html">eucast_exceptional_phenotypes()</a></code>. This was already the case for antibiotic selection functions (such as using <code><a href="../reference/antibiotic_class_selectors.html">penicillins()</a></code> in <code><a href="https://dplyr.tidyverse.org/reference/select.html">dplyr::select()</a></code>).</p>
|
||||
<p>Some functions are now context-aware when used inside <code>dplyr</code> verbs, such as <code><a href="https://rdrr.io/pkg/dplyr/man/filter.html">filter()</a></code>, <code><a href="https://rdrr.io/pkg/dplyr/man/mutate.html">mutate()</a></code> and <code><a href="https://rdrr.io/pkg/dplyr/man/summarise.html">summarise()</a></code>. This means that then the data argument does not need to be set anymore. This is the case for the new functions <code><a href="../reference/mo_property.html">mo_is_gram_negative()</a></code>, <code><a href="../reference/mo_property.html">mo_is_gram_positive()</a></code>, <code><a href="../reference/mo_property.html">mo_is_intrinsic_resistant()</a></code> and for the existing functions <code><a href="../reference/first_isolate.html">first_isolate()</a></code>, <code><a href="../reference/key_antibiotics.html">key_antibiotics()</a></code>, <code><a href="../reference/mdro.html">mdro()</a></code>, <code><a href="../reference/mdro.html">brmo()</a></code>, <code><a href="../reference/mdro.html">mrgn()</a></code>, <code><a href="../reference/mdro.html">mdr_tb()</a></code>, <code><a href="../reference/mdro.html">mdr_cmi2012()</a></code>, <code><a href="../reference/mdro.html">eucast_exceptional_phenotypes()</a></code>. This was already the case for antibiotic selection functions (such as using <code><a href="../reference/antibiotic_class_selectors.html">penicillins()</a></code> in <code><a href="https://rdrr.io/pkg/dplyr/man/select.html">dplyr::select()</a></code>).</p>
|
||||
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R">
|
||||
<span class="co"># to select first isolates that are Gram-negative </span>
|
||||
<span class="co"># and view results of cephalosporins and aminoglycosides:</span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
|
||||
<span class="va">example_isolates</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="../reference/mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="va">mo</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">cephalosporins</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/dplyr/man/filter.html">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="../reference/mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/dplyr/man/select.html">select</a></span><span class="op">(</span><span class="va">mo</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">cephalosporins</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://tibble.tidyverse.org/reference/as_tibble.html">as_tibble</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
|
||||
</li>
|
||||
<li><p>For all function arguments in the code, it is now defined what the exact type of user input should be (inspired by the <a href="https://github.com/moodymudskipper/typed"><code>typed</code></a> package). If the user input for a certain function does not meet the requirements for a specific argument (such as the class or length), an informative error will be thrown. This makes the package more robust and the use of it more reproducible and reliable. In total, more than 420 arguments were defined.</p></li>
|
||||
@ -337,8 +337,8 @@
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
|
||||
<span class="va">intrinsic_resistant</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="va">antibiotic</span> <span class="op">==</span> <span class="st">"Vancomycin"</span>, <span class="va">microorganism</span> <span class="op">%like%</span> <span class="st">"Enterococcus"</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/pull.html">pull</a></span><span class="op">(</span><span class="va">microorganism</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/dplyr/man/filter.html">filter</a></span><span class="op">(</span><span class="va">antibiotic</span> <span class="op">==</span> <span class="st">"Vancomycin"</span>, <span class="va">microorganism</span> <span class="op">%like%</span> <span class="st">"Enterococcus"</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/dplyr/man/pull.html">pull</a></span><span class="op">(</span><span class="va">microorganism</span><span class="op">)</span>
|
||||
<span class="co">#> [1] "Enterococcus casseliflavus" "Enterococcus gallinarum" </span></code></pre></div>
|
||||
</li>
|
||||
<li><p>Support for veterinary ATC codes</p></li>
|
||||
@ -354,16 +354,16 @@
|
||||
<p>Improvements for <code><a href="../reference/as.rsi.html">as.rsi()</a></code>:</p>
|
||||
<ul>
|
||||
<li>
|
||||
<p>Support for using <code>dplyr</code>’s <code><a href="https://dplyr.tidyverse.org/reference/across.html">across()</a></code> to interpret MIC values or disk zone diameters, which also automatically determines the column with microorganism names or codes.</p>
|
||||
<p>Support for using <code>dplyr</code>’s <code><a href="https://rdrr.io/pkg/dplyr/man/across.html">across()</a></code> to interpret MIC values or disk zone diameters, which also automatically determines the column with microorganism names or codes.</p>
|
||||
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R">
|
||||
<span class="co"># until dplyr 1.0.0</span>
|
||||
<span class="va">your_data</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_if</a></span><span class="op">(</span><span class="va">is.mic</span>, <span class="va">as.rsi</span><span class="op">)</span>
|
||||
<span class="va">your_data</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_if</a></span><span class="op">(</span><span class="va">is.disk</span>, <span class="va">as.rsi</span><span class="op">)</span>
|
||||
<span class="va">your_data</span> <span class="op">%>%</span> <span class="fu"><a href="https://rdrr.io/pkg/dplyr/man/mutate_all.html">mutate_if</a></span><span class="op">(</span><span class="va">is.mic</span>, <span class="va">as.rsi</span><span class="op">)</span>
|
||||
<span class="va">your_data</span> <span class="op">%>%</span> <span class="fu"><a href="https://rdrr.io/pkg/dplyr/man/mutate_all.html">mutate_if</a></span><span class="op">(</span><span class="va">is.disk</span>, <span class="va">as.rsi</span><span class="op">)</span>
|
||||
|
||||
<span class="co"># since dplyr 1.0.0</span>
|
||||
<span class="va">your_data</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html">across</a></span><span class="op">(</span><span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span>, <span class="va">as.rsi</span><span class="op">)</span><span class="op">)</span>
|
||||
<span class="va">your_data</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html">across</a></span><span class="op">(</span><span class="fu">where</span><span class="op">(</span><span class="va">is.disk</span><span class="op">)</span>, <span class="va">as.rsi</span><span class="op">)</span><span class="op">)</span></code></pre></div>
|
||||
<span class="va">your_data</span> <span class="op">%>%</span> <span class="fu"><a href="https://rdrr.io/pkg/dplyr/man/mutate.html">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/pkg/dplyr/man/across.html">across</a></span><span class="op">(</span><span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span>, <span class="va">as.rsi</span><span class="op">)</span><span class="op">)</span>
|
||||
<span class="va">your_data</span> <span class="op">%>%</span> <span class="fu"><a href="https://rdrr.io/pkg/dplyr/man/mutate.html">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/pkg/dplyr/man/across.html">across</a></span><span class="op">(</span><span class="fu">where</span><span class="op">(</span><span class="va">is.disk</span><span class="op">)</span>, <span class="va">as.rsi</span><span class="op">)</span><span class="op">)</span></code></pre></div>
|
||||
</li>
|
||||
<li><p>Cleaning columns in a data.frame now allows you to specify those columns with tidy selection, e.g. <code><a href="../reference/as.rsi.html">as.rsi(df, col1:col9)</a></code></p></li>
|
||||
<li><p>Big speed improvement for interpreting MIC values and disk zone diameters. When interpreting 5,000 MIC values of two antibiotics (10,000 values in total), our benchmarks showed a total run time going from 80.7-85.1 seconds to 1.8-2.0 seconds.</p></li>
|
||||
@ -433,14 +433,14 @@
|
||||
<ul>
|
||||
<li><p>Function <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code> to retrieve antimicrobial drug names, doses and forms of administration from clinical texts in e.g. health care records, which also corrects for misspelling since it uses <code><a href="../reference/as.ab.html">as.ab()</a></code> internally</p></li>
|
||||
<li>
|
||||
<p><a href="https://tidyselect.r-lib.org/reference/language.html">Tidyverse selection helpers</a> for antibiotic classes, that help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. They can be used in any function that allows selection helpers, like <code><a href="https://dplyr.tidyverse.org/reference/select.html">dplyr::select()</a></code> and <code><a href="https://tidyr.tidyverse.org/reference/pivot_longer.html">tidyr::pivot_longer()</a></code>:</p>
|
||||
<p><a href="https://tidyselect.r-lib.org/reference/language.html">Tidyverse selection helpers</a> for antibiotic classes, that help to select the columns of antibiotics that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. They can be used in any function that allows selection helpers, like <code><a href="https://rdrr.io/pkg/dplyr/man/select.html">dplyr::select()</a></code> and <code><a href="https://tidyr.tidyverse.org/reference/pivot_longer.html">tidyr::pivot_longer()</a></code>:</p>
|
||||
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R">
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
|
||||
|
||||
<span class="co"># Columns 'IPM' and 'MEM' are in the example_isolates data set</span>
|
||||
<span class="va">example_isolates</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="fu"><a href="../reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/dplyr/man/select.html">select</a></span><span class="op">(</span><span class="fu"><a href="../reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>
|
||||
<span class="co">#> Selecting carbapenems: `IPM` (imipenem), `MEM` (meropenem)</span></code></pre></div>
|
||||
</li>
|
||||
<li><p>Added <code><a href="../reference/mo_property.html">mo_domain()</a></code> as an alias to <code><a href="../reference/mo_property.html">mo_kingdom()</a></code></p></li>
|
||||
@ -622,14 +622,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<ul>
|
||||
<li><p>Fixed important floating point error for some MIC comparisons in EUCAST 2020 guideline</p></li>
|
||||
<li>
|
||||
<p>Interpretation from MIC values (and disk zones) to R/SI can now be used with <code><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at()</a></code> of the <code>dplyr</code> package:</p>
|
||||
<p>Interpretation from MIC values (and disk zones) to R/SI can now be used with <code><a href="https://rdrr.io/pkg/dplyr/man/mutate_all.html">mutate_at()</a></code> of the <code>dplyr</code> package:</p>
|
||||
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R">
|
||||
<span class="va">yourdata</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span><span class="op">(</span><span class="va">antibiotic1</span><span class="op">:</span><span class="va">antibiotic25</span><span class="op">)</span>, <span class="va">as.rsi</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/dplyr/man/mutate_all.html">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/pkg/dplyr/man/vars.html">vars</a></span><span class="op">(</span><span class="va">antibiotic1</span><span class="op">:</span><span class="va">antibiotic25</span><span class="op">)</span>, <span class="va">as.rsi</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span><span class="op">)</span>
|
||||
|
||||
<span class="va">yourdata</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span><span class="op">(</span><span class="va">antibiotic1</span><span class="op">:</span><span class="va">antibiotic25</span><span class="op">)</span>, <span class="va">as.rsi</span>, mo <span class="op">=</span> <span class="va">.</span><span class="op">$</span><span class="va">mybacteria</span><span class="op">)</span></code></pre></div>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/dplyr/man/mutate_all.html">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/pkg/dplyr/man/vars.html">vars</a></span><span class="op">(</span><span class="va">antibiotic1</span><span class="op">:</span><span class="va">antibiotic25</span><span class="op">)</span>, <span class="va">as.rsi</span>, mo <span class="op">=</span> <span class="va">.</span><span class="op">$</span><span class="va">mybacteria</span><span class="op">)</span></code></pre></div>
|
||||
</li>
|
||||
<li><p>Added antibiotic abbreviations for a laboratory manufacturer (GLIMS) for cefuroxime, cefotaxime, ceftazidime, cefepime, cefoxitin and trimethoprim/sulfamethoxazole</p></li>
|
||||
<li><p>Added <code>uti</code> (as abbreviation of urinary tract infections) as argument to <code><a href="../reference/as.rsi.html">as.rsi()</a></code>, so interpretation of MIC values and disk zones can be made dependent on isolates specifically from UTIs</p></li>
|
||||
@ -750,10 +750,10 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<code class="sourceCode R">
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
|
||||
<span class="va">example_isolates</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span>bug <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise</a></span><span class="op">(</span>amoxicillin <span class="op">=</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span>,
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/dplyr/man/group_by.html">group_by</a></span><span class="op">(</span>bug <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/dplyr/man/summarise.html">summarise</a></span><span class="op">(</span>amoxicillin <span class="op">=</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span>,
|
||||
amox_clav <span class="op">=</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMC</span><span class="op">)</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html">is.na</a></span><span class="op">(</span><span class="va">amoxicillin</span><span class="op">)</span> <span class="op">|</span> <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html">is.na</a></span><span class="op">(</span><span class="va">amox_clav</span><span class="op">)</span><span class="op">)</span></code></pre></div>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/dplyr/man/filter.html">filter</a></span><span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html">is.na</a></span><span class="op">(</span><span class="va">amoxicillin</span><span class="op">)</span> <span class="op">|</span> <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html">is.na</a></span><span class="op">(</span><span class="va">amox_clav</span><span class="op">)</span><span class="op">)</span></code></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Support for a new MDRO guideline: Magiorakos AP, Srinivasan A <em>et al.</em> “Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance.” Clinical Microbiology and Infection (2012).</p>
|
||||
@ -922,7 +922,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<span class="co"># (run this on your own console, as this page does not support colour printing)</span>
|
||||
<span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org">dplyr</a></span><span class="op">)</span>
|
||||
<span class="va">example_isolates</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="va">mo</span><span class="op">:</span><span class="va">AMC</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/dplyr/man/select.html">select</a></span><span class="op">(</span><span class="va">mo</span><span class="op">:</span><span class="va">AMC</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://tibble.tidyverse.org/reference/as_tibble.html">as_tibble</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
|
||||
</li>
|
||||
</ul>
|
||||
@ -1003,7 +1003,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R">
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="va">AMX</span>, <span class="va">CIP</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/dplyr/man/select.html">select</a></span><span class="op">(</span><span class="va">AMX</span>, <span class="va">CIP</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="../reference/proportion.html">rsi_df</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="co"># antibiotic interpretation value isolates</span>
|
||||
<span class="co"># 1 Amoxicillin SI 0.4442636 546</span>
|
||||
@ -1139,7 +1139,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="co"># grouped boxplots:</span>
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/dplyr/man/group_by.html">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
|
||||
</li>
|
||||
@ -1288,9 +1288,9 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R">
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>only_firsts <span class="op">=</span> <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span><span class="va">septic_patients</span>, <span class="va">...</span><span class="op">)</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="va">only_firsts</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="op">-</span><span class="va">only_firsts</span><span class="op">)</span></code></pre></div>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/dplyr/man/mutate.html">mutate</a></span><span class="op">(</span>only_firsts <span class="op">=</span> <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span><span class="va">septic_patients</span>, <span class="va">...</span><span class="op">)</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/dplyr/man/filter.html">filter</a></span><span class="op">(</span><span class="va">only_firsts</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/dplyr/man/select.html">select</a></span><span class="op">(</span><span class="op">-</span><span class="va">only_firsts</span><span class="op">)</span></code></pre></div>
|
||||
</li>
|
||||
<li><p>New function <code><a href="../reference/availability.html">availability()</a></code> to check the number of available (non-empty) results in a <code>data.frame</code></p></li>
|
||||
<li><p>New vignettes about how to conduct AMR analysis, predict antimicrobial resistance, use the <em>G</em>-test and more. These are also available (and even easier readable) on our website: <a href="https://msberends.gitlab.io/AMR" class="uri">https://msberends.gitlab.io/AMR</a>.</p></li>
|
||||
@ -1400,7 +1400,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span>
|
||||
<span class="co"># OLD WAY</span>
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>genus <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/dplyr/man/mutate.html">mutate</a></span><span class="op">(</span>genus <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu">freq</span><span class="op">(</span><span class="va">genus</span><span class="op">)</span>
|
||||
<span class="co"># NEW WAY</span>
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||
@ -1408,7 +1408,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
|
||||
<span class="co"># Even supports grouping variables:</span>
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/dplyr/man/group_by.html">group_by</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu">freq</span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span></code></pre></div>
|
||||
</li>
|
||||
<li><p>Header info is now available as a list, with the <code>header</code> function</p></li>
|
||||
@ -1419,7 +1419,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li><p>Fix for header text where all observations are <code>NA</code></p></li>
|
||||
<li><p>New argument <code>droplevels</code> to exclude empty factor levels when input is a factor</p></li>
|
||||
<li><p>Factor levels will be in header when present in input data (maximum of 5)</p></li>
|
||||
<li><p>Fix for using <code><a href="https://dplyr.tidyverse.org/reference/select.html">select()</a></code> on frequency tables</p></li>
|
||||
<li><p>Fix for using <code><a href="https://rdrr.io/pkg/dplyr/man/select.html">select()</a></code> on frequency tables</p></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>Function <code><a href="../reference/ggplot_rsi.html">scale_y_percent()</a></code> now contains the <code>limits</code> argument</li>
|
||||
@ -1499,7 +1499,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<div class="sourceCode" id="cb34"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R">
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/dplyr/man/group_by.html">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu">freq</span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
@ -1508,7 +1508,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<code class="sourceCode R">
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu">freq</span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="op">-</span><span class="va">count</span>, <span class="op">-</span><span class="va">cum_count</span><span class="op">)</span> <span class="co"># only get item, percent, cum_percent</span></code></pre></div>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/dplyr/man/select.html">select</a></span><span class="op">(</span><span class="op">-</span><span class="va">count</span>, <span class="op">-</span><span class="va">cum_count</span><span class="op">)</span> <span class="co"># only get item, percent, cum_percent</span></code></pre></div>
|
||||
</li>
|
||||
<li><p>Check for <code><a href="https://hms.tidyverse.org/reference/Deprecated.html">hms::is.hms</a></code></p></li>
|
||||
<li><p>Now prints in markdown at default in non-interactive sessions</p></li>
|
||||
@ -1672,7 +1672,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<p>Support for quasiquotation in the functions series <code>count_*</code> and <code>portions_*</code>, and <code>n_rsi</code>. This allows to check for more than 2 vectors or columns.</p>
|
||||
<div class="sourceCode" id="cb41"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R">
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="va">amox</span>, <span class="va">cipr</span><span class="op">)</span> <span class="op">%>%</span> <span class="fu"><a href="../reference/count.html">count_IR</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span> <span class="fu"><a href="https://rdrr.io/pkg/dplyr/man/select.html">select</a></span><span class="op">(</span><span class="va">amox</span>, <span class="va">cipr</span><span class="op">)</span> <span class="op">%>%</span> <span class="fu"><a href="../reference/count.html">count_IR</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="co"># which is the same as:</span>
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span> <span class="fu"><a href="../reference/count.html">count_IR</a></span><span class="op">(</span><span class="va">amox</span>, <span class="va">cipr</span><span class="op">)</span>
|
||||
|
||||
@ -1858,7 +1858,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<ul>
|
||||
<li>Full support for Windows, Linux and macOS</li>
|
||||
<li>Full support for old R versions, only R-3.0.0 (April 2013) or later is needed (needed packages may have other dependencies)</li>
|
||||
<li>Function <code>n_rsi</code> to count cases where antibiotic test results were available, to be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">dplyr::summarise</a></code>, see ?rsi</li>
|
||||
<li>Function <code>n_rsi</code> to count cases where antibiotic test results were available, to be used in conjunction with <code><a href="https://rdrr.io/pkg/dplyr/man/summarise.html">dplyr::summarise</a></code>, see ?rsi</li>
|
||||
<li>Function <code>guess_bactid</code> to <strong>determine the ID</strong> of a microorganism based on genus/species or known abbreviations like MRSA</li>
|
||||
<li>Function <code>guess_atc</code> to <strong>determine the ATC</strong> of an antibiotic based on name, trade name, or known abbreviations</li>
|
||||
<li>Function <code>freq</code> to create <strong>frequency tables</strong>, with additional info in a header</li>
|
||||
|
||||
@ -12,7 +12,7 @@ articles:
|
||||
datasets: datasets.html
|
||||
resistance_predict: resistance_predict.html
|
||||
welcome_to_AMR: welcome_to_AMR.html
|
||||
last_built: 2020-12-24T23:05Z
|
||||
last_built: 2020-12-26T23:05Z
|
||||
urls:
|
||||
reference: https://msberends.github.io/AMR//reference
|
||||
article: https://msberends.github.io/AMR//articles
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -83,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
378
docs/reference/get_episode.html
Normal file
378
docs/reference/get_episode.html
Normal file
@ -0,0 +1,378 @@
|
||||
<!-- Generated by pkgdown: do not edit by hand -->
|
||||
<!DOCTYPE html>
|
||||
<html lang="en">
|
||||
<head>
|
||||
<meta charset="utf-8">
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<title>Determine (new) episodes for patients — get_episode • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
|
||||
<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png" />
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png" />
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png" />
|
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<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png" />
|
||||
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
|
||||
<!-- Font Awesome icons -->
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
|
||||
|
||||
<!-- clipboard.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- headroom.js -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- pkgdown -->
|
||||
<link href="../pkgdown.css" rel="stylesheet">
|
||||
<script src="../pkgdown.js"></script>
|
||||
|
||||
|
||||
|
||||
<link href="../extra.css" rel="stylesheet">
|
||||
<script src="../extra.js"></script>
|
||||
|
||||
<meta property="og:title" content="Determine (new) episodes for patients — get_episode" />
|
||||
<meta property="og:description" content="These functions determine which items in a vector can be considered (the start of) a new episode, based on the argument episode_days. This can be used to determine clinical episodes for any epidemiological analysis. The get_episode() function returns the index number of the episode per group, while the is_new_episode() function returns values TRUE/FALSE to indicate whether an item in a vector is the start of a new episode." />
|
||||
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
|
||||
|
||||
|
||||
|
||||
|
||||
<!-- mathjax -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
<![endif]-->
|
||||
|
||||
|
||||
|
||||
</head>
|
||||
|
||||
<body data-spy="scroll" data-target="#toc">
|
||||
<div class="container template-reference-topic">
|
||||
<header>
|
||||
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
|
||||
<div class="container">
|
||||
<div class="navbar-header">
|
||||
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
|
||||
<span class="sr-only">Toggle navigation</span>
|
||||
<span class="icon-bar"></span>
|
||||
<span class="icon-bar"></span>
|
||||
<span class="icon-bar"></span>
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
<div id="navbar" class="navbar-collapse collapse">
|
||||
<ul class="nav navbar-nav">
|
||||
<li>
|
||||
<a href="../index.html">
|
||||
<span class="fas fa-home"></span>
|
||||
|
||||
Home
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-question-circle"></span>
|
||||
|
||||
How to
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="../articles/AMR.html">
|
||||
<span class="fas fa-directions"></span>
|
||||
|
||||
Conduct AMR analysis
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/resistance_predict.html">
|
||||
<span class="fas fa-dice"></span>
|
||||
|
||||
Predict antimicrobial resistance
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/datasets.html">
|
||||
<span class="fas fa-database"></span>
|
||||
|
||||
Data sets for download / own use
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/PCA.html">
|
||||
<span class="fas fa-compress"></span>
|
||||
|
||||
Conduct principal component analysis for AMR
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/MDR.html">
|
||||
<span class="fas fa-skull-crossbones"></span>
|
||||
|
||||
Determine multi-drug resistance (MDR)
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/WHONET.html">
|
||||
<span class="fas fa-globe-americas"></span>
|
||||
|
||||
Work with WHONET data
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/SPSS.html">
|
||||
<span class="fas fa-file-upload"></span>
|
||||
|
||||
Import data from SPSS/SAS/Stata
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/EUCAST.html">
|
||||
<span class="fas fa-exchange-alt"></span>
|
||||
|
||||
Apply EUCAST rules
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/mo_property.html">
|
||||
<span class="fas fa-bug"></span>
|
||||
|
||||
Get properties of a microorganism
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/ab_property.html">
|
||||
<span class="fas fa-capsules"></span>
|
||||
|
||||
Get properties of an antibiotic
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../articles/benchmarks.html">
|
||||
<span class="fas fa-shipping-fast"></span>
|
||||
|
||||
Other: benchmarks
|
||||
</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../reference/index.html">
|
||||
<span class="fas fa-book-open"></span>
|
||||
|
||||
Manual
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../authors.html">
|
||||
<span class="fas fa-users"></span>
|
||||
|
||||
Authors
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../news/index.html">
|
||||
<span class="far fa-newspaper"></span>
|
||||
|
||||
Changelog
|
||||
</a>
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
|
||||
Source Code
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="../survey.html">
|
||||
<span class="fas fa-clipboard-list"></span>
|
||||
|
||||
Survey
|
||||
</a>
|
||||
</li>
|
||||
</ul>
|
||||
|
||||
</div><!--/.nav-collapse -->
|
||||
</div><!--/.container -->
|
||||
</div><!--/.navbar -->
|
||||
|
||||
|
||||
|
||||
</header>
|
||||
|
||||
<div class="row">
|
||||
<div class="col-md-9 contents">
|
||||
<div class="page-header">
|
||||
<h1>Determine (new) episodes for patients</h1>
|
||||
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/episode.R'><code>R/episode.R</code></a></small>
|
||||
<div class="hidden name"><code>get_episode.Rd</code></div>
|
||||
</div>
|
||||
|
||||
<div class="ref-description">
|
||||
<p>These functions determine which items in a vector can be considered (the start of) a new episode, based on the argument <code>episode_days</code>. This can be used to determine clinical episodes for any epidemiological analysis. The <code>get_episode()</code> function returns the index number of the episode per group, while the <code>is_new_episode()</code> function returns values <code>TRUE</code>/<code>FALSE</code> to indicate whether an item in a vector is the start of a new episode.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>get_episode</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>episode_days</span>, <span class='va'>...</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'>is_new_episode</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>episode_days</span>, <span class='va'>...</span><span class='op'>)</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>x</th>
|
||||
<td><p>vector of dates (class <code>Date</code> or <code>POSIXt</code>)</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>episode_days</th>
|
||||
<td><p>length of the required episode in days, please see <em>Details</em></p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>...</th>
|
||||
<td><p>arguments passed on to <code><a href='https://rdrr.io/r/base/as.Date.html'>as.Date()</a></code></p></td>
|
||||
</tr>
|
||||
</table>
|
||||
|
||||
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
|
||||
|
||||
|
||||
<ul>
|
||||
<li><p><code>get_episode()</code>: a <a href='https://rdrr.io/r/base/double.html'>double</a> vector</p></li>
|
||||
<li><p><code>is_new_episode()</code>: a <a href='https://rdrr.io/r/base/logical.html'>logical</a> vector</p></li>
|
||||
</ul>
|
||||
|
||||
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
|
||||
|
||||
<p>Dates are first sorted from old to new. The oldest date will mark the start of the first episode. After this date, the next date will be marked that is at least <code>episode_days</code> days later than the start of the first episode. From that second marked date on, the next date will be marked that is at least <code>episode_days</code> days later than the start of the second episode which will be the start of the third episode, and so on. Before the vector is being returned, the original order will be restored.</p>
|
||||
<p>The <code><a href='first_isolate.html'>first_isolate()</a></code> function is a wrapper around the <code>is_new_episode()</code> function, but is more efficient for data sets containing microorganism codes or names.</p>
|
||||
<p>The <code>dplyr</code> package is not required for these functions to work, but these functions support <a href='https://rdrr.io/pkg/dplyr/man/group_by.html'>variable grouping</a> and work conveniently inside <code>dplyr</code> verbs such as <code><a href='https://rdrr.io/pkg/dplyr/man/filter.html'>filter()</a></code>, <code><a href='https://rdrr.io/pkg/dplyr/man/mutate.html'>mutate()</a></code> and <code><a href='https://rdrr.io/pkg/dplyr/man/summarise.html'>summarise()</a></code>.</p>
|
||||
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
|
||||
|
||||
|
||||
|
||||
<p><img src='figures/lifecycle_stable.svg' style=margin-bottom:5px /> <br />
|
||||
The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
|
||||
<p>If the unlying code needs breaking changes, they will occur gradually. For example, a argument will be deprecated and first continue to work, but will emit an message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
|
||||
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
|
||||
|
||||
|
||||
|
||||
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>. As we would like to better understand the backgrounds and needs of our users, please <a href='https://msberends.github.io/AMR/survey.html'>participate in our survey</a>!</p>
|
||||
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
|
||||
|
||||
<div class='dont-index'><p><code><a href='first_isolate.html'>first_isolate()</a></code></p></div>
|
||||
|
||||
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
|
||||
<pre class="examples"><span class='co'># `example_isolates` is a dataset available in the AMR package.</span>
|
||||
<span class='co'># See ?example_isolates.</span>
|
||||
|
||||
<span class='fu'>get_episode</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>date</span>, episode_days <span class='op'>=</span> <span class='fl'>60</span><span class='op'>)</span>
|
||||
<span class='fu'>is_new_episode</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>date</span>, episode_days <span class='op'>=</span> <span class='fl'>60</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># filter on results from the third 60-day episode using base R</span>
|
||||
<span class='va'>example_isolates</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/which.html'>which</a></span><span class='op'>(</span><span class='fu'>get_episode</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>date</span>, <span class='fl'>60</span><span class='op'>)</span> <span class='op'>==</span> <span class='fl'>3</span><span class='op'>)</span>, <span class='op'>]</span>
|
||||
|
||||
<span class='co'># \donttest{</span>
|
||||
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
|
||||
<span class='co'># is_new_episode() can also be used in dplyr verbs to determine patient</span>
|
||||
<span class='co'># episodes based on any (combination of) grouping variables:</span>
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://rdrr.io/pkg/dplyr/man/mutate.html'>mutate</a></span><span class='op'>(</span>condition <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/sample.html'>sample</a></span><span class='op'>(</span>x <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"A"</span>, <span class='st'>"B"</span>, <span class='st'>"C"</span><span class='op'>)</span>,
|
||||
size <span class='op'>=</span> <span class='fl'>2000</span>,
|
||||
replace <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://rdrr.io/pkg/dplyr/man/group_by.html'>group_by</a></span><span class='op'>(</span><span class='va'>condition</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://rdrr.io/pkg/dplyr/man/mutate.html'>mutate</a></span><span class='op'>(</span>new_episode <span class='op'>=</span> <span class='fu'>is_new_episode</span><span class='op'>(</span><span class='va'>date</span>, <span class='fl'>365</span><span class='op'>)</span><span class='op'>)</span>
|
||||
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://rdrr.io/pkg/dplyr/man/group_by.html'>group_by</a></span><span class='op'>(</span><span class='va'>hospital_id</span>, <span class='va'>patient_id</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://rdrr.io/pkg/dplyr/man/mutate.html'>transmute</a></span><span class='op'>(</span><span class='va'>date</span>,
|
||||
<span class='va'>patient_id</span>,
|
||||
new_index <span class='op'>=</span> <span class='fu'>get_episode</span><span class='op'>(</span><span class='va'>date</span>, <span class='fl'>60</span><span class='op'>)</span>,
|
||||
new_logical <span class='op'>=</span> <span class='fu'>is_new_episode</span><span class='op'>(</span><span class='va'>date</span>, <span class='fl'>60</span><span class='op'>)</span><span class='op'>)</span>
|
||||
|
||||
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://rdrr.io/pkg/dplyr/man/group_by.html'>group_by</a></span><span class='op'>(</span><span class='va'>hospital_id</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://rdrr.io/pkg/dplyr/man/summarise.html'>summarise</a></span><span class='op'>(</span>patients <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/dplyr/man/n_distinct.html'>n_distinct</a></span><span class='op'>(</span><span class='va'>patient_id</span><span class='op'>)</span>,
|
||||
n_episodes_365 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span><span class='op'>(</span><span class='fu'>is_new_episode</span><span class='op'>(</span><span class='va'>date</span>, episode_days <span class='op'>=</span> <span class='fl'>365</span><span class='op'>)</span><span class='op'>)</span>,
|
||||
n_episodes_60 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span><span class='op'>(</span><span class='fu'>is_new_episode</span><span class='op'>(</span><span class='va'>date</span>, episode_days <span class='op'>=</span> <span class='fl'>60</span><span class='op'>)</span><span class='op'>)</span>,
|
||||
n_episodes_30 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span><span class='op'>(</span><span class='fu'>is_new_episode</span><span class='op'>(</span><span class='va'>date</span>, episode_days <span class='op'>=</span> <span class='fl'>30</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>
|
||||
|
||||
|
||||
<span class='co'># grouping on patients and microorganisms leads to the same results</span>
|
||||
<span class='co'># as first_isolate():</span>
|
||||
<span class='va'>x</span> <span class='op'><-</span> <span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://rdrr.io/pkg/dplyr/man/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'><a href='first_isolate.html'>first_isolate</a></span><span class='op'>(</span><span class='va'>.</span>, include_unknown <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span><span class='op'>)</span>
|
||||
|
||||
<span class='va'>y</span> <span class='op'><-</span> <span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://rdrr.io/pkg/dplyr/man/group_by.html'>group_by</a></span><span class='op'>(</span><span class='va'>patient_id</span>, <span class='va'>mo</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://rdrr.io/pkg/dplyr/man/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'>is_new_episode</span><span class='op'>(</span><span class='va'>date</span>, <span class='fl'>365</span><span class='op'>)</span><span class='op'>)</span>
|
||||
|
||||
<span class='fu'><a href='https://rdrr.io/r/base/identical.html'>identical</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>patient_id</span>, <span class='va'>y</span><span class='op'>$</span><span class='va'>patient_id</span><span class='op'>)</span>
|
||||
|
||||
<span class='co'># but is_new_episode() has a lot more flexibility than first_isolate(),</span>
|
||||
<span class='co'># since you can now group on anything that seems relevant:</span>
|
||||
<span class='va'>example_isolates</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://rdrr.io/pkg/dplyr/man/group_by.html'>group_by</a></span><span class='op'>(</span><span class='va'>patient_id</span>, <span class='va'>mo</span>, <span class='va'>hospital_id</span>, <span class='va'>ward_icu</span><span class='op'>)</span> <span class='op'>%>%</span>
|
||||
<span class='fu'><a href='https://rdrr.io/pkg/dplyr/man/mutate.html'>mutate</a></span><span class='op'>(</span>flag_episode <span class='op'>=</span> <span class='fu'>is_new_episode</span><span class='op'>(</span><span class='va'>date</span>, <span class='fl'>365</span><span class='op'>)</span><span class='op'>)</span>
|
||||
<span class='op'>}</span>
|
||||
<span class='co'># }</span>
|
||||
</pre>
|
||||
</div>
|
||||
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
|
||||
<nav id="toc" data-toggle="toc" class="sticky-top">
|
||||
<h2 data-toc-skip>Contents</h2>
|
||||
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|
||||
</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/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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||||
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||||
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||||
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||||
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|
||||
</html>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<!-- Bootstrap -->
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<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
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||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
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</div>
|
||||
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|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<!-- Bootstrap -->
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<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
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|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<!-- Bootstrap -->
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<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
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|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
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|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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<!-- Bootstrap -->
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<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
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||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9045</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@ -455,7 +455,7 @@
|
||||
<tr>
|
||||
<th colspan="2">
|
||||
<h2 id="section-analysing-data-antimicrobial-resistance" class="hasAnchor"><a href="#section-analysing-data-antimicrobial-resistance" class="anchor"></a>Analysing data: antimicrobial resistance</h2>
|
||||
<p class="section-desc"><p>Use these function for the analysis part. You can use <code><a href="../reference/proportion.html">susceptibility()</a></code> or <code><a href="../reference/proportion.html">resistance()</a></code> on any antibiotic column. Be sure to first select the isolates that are appropiate for analysis, by using <code><a href="../reference/first_isolate.html">first_isolate()</a></code> or <code><a href="../reference/is_new_episode.html">is_new_episode()</a></code>. You can also filter your data on certain resistance in certain antibiotic classes (<code><a href="../reference/filter_ab_class.html">filter_ab_class()</a></code>), or determine multi-drug resistant microorganisms (MDRO, <code><a href="../reference/mdro.html">mdro()</a></code>).</p></p>
|
||||
<p class="section-desc"><p>Use these function for the analysis part. You can use <code><a href="../reference/proportion.html">susceptibility()</a></code> or <code><a href="../reference/proportion.html">resistance()</a></code> on any antibiotic column. Be sure to first select the isolates that are appropiate for analysis, by using <code><a href="../reference/first_isolate.html">first_isolate()</a></code> or <code><a href="../reference/get_episode.html">is_new_episode()</a></code>. You can also filter your data on certain resistance in certain antibiotic classes (<code><a href="../reference/filter_ab_class.html">filter_ab_class()</a></code>), or determine multi-drug resistant microorganisms (MDRO, <code><a href="../reference/mdro.html">mdro()</a></code>).</p></p>
|
||||
</th>
|
||||
</tr>
|
||||
|
||||
@ -478,7 +478,7 @@
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
<p><code><a href="is_new_episode.html">is_new_episode()</a></code> </p>
|
||||
<p><code><a href="get_episode.html">get_episode()</a></code> <code><a href="get_episode.html">is_new_episode()</a></code> </p>
|
||||
</td>
|
||||
<td><p>Determine (new) episodes for patients</p></td>
|
||||
</tr><tr>
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -84,7 +84,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -83,7 +83,7 @@ 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="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -83,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -83,7 +83,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -82,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
@ -84,6 +84,9 @@
|
||||
<url>
|
||||
<loc>https://msberends.github.io/AMR//reference/g.test.html</loc>
|
||||
</url>
|
||||
<url>
|
||||
<loc>https://msberends.github.io/AMR//reference/get_episode.html</loc>
|
||||
</url>
|
||||
<url>
|
||||
<loc>https://msberends.github.io/AMR//reference/ggplot_pca.html</loc>
|
||||
</url>
|
||||
@ -96,9 +99,6 @@
|
||||
<url>
|
||||
<loc>https://msberends.github.io/AMR//reference/intrinsic_resistant.html</loc>
|
||||
</url>
|
||||
<url>
|
||||
<loc>https://msberends.github.io/AMR//reference/is_new_episode.html</loc>
|
||||
</url>
|
||||
<url>
|
||||
<loc>https://msberends.github.io/AMR//reference/join.html</loc>
|
||||
</url>
|
||||
|
||||
@ -19,8 +19,8 @@
|
||||
<!-- jquery -->
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
<link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous" />
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
@ -81,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9045</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9046</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
||||
4
index.md
4
index.md
@ -18,8 +18,8 @@ This package is [fully independent of any other R package](https://en.wikipedia.
|
||||
<div class="main-content" style="display: inline-block;">
|
||||
<p>
|
||||
<a href="./countries_large.png" target="_blank"><img src="./countries.png" class="countries_map"></a>
|
||||
<strong>Used in 135 countries</strong><br>
|
||||
Since its first public release in early 2018, this package has been downloaded from 135 countries. Click the map to enlarge and to see the country names.</p>
|
||||
<strong>Used in 138 countries</strong><br>
|
||||
Since its first public release in early 2018, this package has been downloaded from 138 countries. Click the map to enlarge and to see the country names.</p>
|
||||
</div>
|
||||
|
||||
##### With `AMR` (for R), there's always a knowledgeable microbiologist by your side!
|
||||
|
||||
@ -1,30 +1,36 @@
|
||||
% Generated by roxygen2: do not edit by hand
|
||||
% Please edit documentation in R/is_new_episode.R
|
||||
\name{is_new_episode}
|
||||
% Please edit documentation in R/episode.R
|
||||
\name{get_episode}
|
||||
\alias{get_episode}
|
||||
\alias{is_new_episode}
|
||||
\title{Determine (new) episodes for patients}
|
||||
\usage{
|
||||
is_new_episode(x, episode_days = 365, ...)
|
||||
get_episode(x, episode_days, ...)
|
||||
|
||||
is_new_episode(x, episode_days, ...)
|
||||
}
|
||||
\arguments{
|
||||
\item{x}{vector of dates (class \code{Date} or \code{POSIXt})}
|
||||
|
||||
\item{episode_days}{length of the required episode in days, defaults to 365. Every element in the input will return \code{TRUE} after this number of days has passed since the last included date, independent of calendar years. Please see \emph{Details}.}
|
||||
\item{episode_days}{length of the required episode in days, please see \emph{Details}}
|
||||
|
||||
\item{...}{arguments passed on to \code{\link[=as.Date]{as.Date()}}}
|
||||
}
|
||||
\value{
|
||||
a \link{logical} vector
|
||||
\itemize{
|
||||
\item \code{\link[=get_episode]{get_episode()}}: a \link{double} vector
|
||||
\item \code{\link[=is_new_episode]{is_new_episode()}}: a \link{logical} vector
|
||||
}
|
||||
}
|
||||
\description{
|
||||
This function determines which items in a vector can be considered (the start of) a new episode, based on the argument \code{episode_days}. This can be used to determine clinical episodes for any epidemiological analysis.
|
||||
These functions determine which items in a vector can be considered (the start of) a new episode, based on the argument \code{episode_days}. This can be used to determine clinical episodes for any epidemiological analysis. The \code{\link[=get_episode]{get_episode()}} function returns the index number of the episode per group, while the \code{\link[=is_new_episode]{is_new_episode()}} function returns values \code{TRUE}/\code{FALSE} to indicate whether an item in a vector is the start of a new episode.
|
||||
}
|
||||
\details{
|
||||
Dates are first sorted from old to new. The oldest date will mark the start of the first episode. After this date, the next date will be marked that is at least \code{episode_days} days later than the start of the first episode. From that second marked date on, the next date will be marked that is at least \code{episode_days} days later than the start of the second episode which will be the start of the third episode, and so on. Before the vector is being returned, the original order will be restored.
|
||||
|
||||
The \code{\link[=first_isolate]{first_isolate()}} function is a wrapper around the \code{\link[=is_new_episode]{is_new_episode()}} function, but more efficient for data sets containing microorganism codes or names.
|
||||
The \code{\link[=first_isolate]{first_isolate()}} function is a wrapper around the \code{\link[=is_new_episode]{is_new_episode()}} function, but is more efficient for data sets containing microorganism codes or names.
|
||||
|
||||
The \code{dplyr} package is not required for this function to work, but this function works conveniently inside \code{dplyr} verbs such as \code{\link[dplyr:filter]{filter()}}, \code{\link[dplyr:mutate]{mutate()}} and \code{\link[dplyr:summarise]{summarise()}}.
|
||||
The \code{dplyr} package is not required for these functions to work, but these functions support \link[dplyr:group_by]{variable grouping} and work conveniently inside \code{dplyr} verbs such as \code{\link[dplyr:filter]{filter()}}, \code{\link[dplyr:mutate]{mutate()}} and \code{\link[dplyr:summarise]{summarise()}}.
|
||||
}
|
||||
\section{Stable lifecycle}{
|
||||
|
||||
@ -43,8 +49,12 @@ On our website \url{https://msberends.github.io/AMR/} you can find \href{https:/
|
||||
# `example_isolates` is a dataset available in the AMR package.
|
||||
# See ?example_isolates.
|
||||
|
||||
is_new_episode(example_isolates$date)
|
||||
get_episode(example_isolates$date, episode_days = 60)
|
||||
is_new_episode(example_isolates$date, episode_days = 60)
|
||||
|
||||
# filter on results from the third 60-day episode using base R
|
||||
example_isolates[which(get_episode(example_isolates$date, 60) == 3), ]
|
||||
|
||||
\donttest{
|
||||
if (require("dplyr")) {
|
||||
# is_new_episode() can also be used in dplyr verbs to determine patient
|
||||
@ -54,7 +64,15 @@ if (require("dplyr")) {
|
||||
size = 2000,
|
||||
replace = TRUE)) \%>\%
|
||||
group_by(condition) \%>\%
|
||||
mutate(new_episode = is_new_episode(date))
|
||||
mutate(new_episode = is_new_episode(date, 365))
|
||||
|
||||
example_isolates \%>\%
|
||||
group_by(hospital_id, patient_id) \%>\%
|
||||
transmute(date,
|
||||
patient_id,
|
||||
new_index = get_episode(date, 60),
|
||||
new_logical = is_new_episode(date, 60))
|
||||
|
||||
|
||||
example_isolates \%>\%
|
||||
group_by(hospital_id) \%>\%
|
||||
@ -71,7 +89,7 @@ if (require("dplyr")) {
|
||||
|
||||
y <- example_isolates \%>\%
|
||||
group_by(patient_id, mo) \%>\%
|
||||
filter(is_new_episode(date))
|
||||
filter(is_new_episode(date, 365))
|
||||
|
||||
identical(x$patient_id, y$patient_id)
|
||||
|
||||
@ -79,7 +97,10 @@ if (require("dplyr")) {
|
||||
# since you can now group on anything that seems relevant:
|
||||
example_isolates \%>\%
|
||||
group_by(patient_id, mo, hospital_id, ward_icu) \%>\%
|
||||
mutate(flag_episode = is_new_episode(date))
|
||||
mutate(flag_episode = is_new_episode(date, 365))
|
||||
}
|
||||
}
|
||||
}
|
||||
\seealso{
|
||||
\code{\link[=first_isolate]{first_isolate()}}
|
||||
}
|
||||
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@ -79,7 +79,9 @@ test_that("counts work", {
|
||||
)
|
||||
|
||||
# warning for speed loss
|
||||
reset_all_thrown_messages()
|
||||
expect_warning(count_resistant(as.character(example_isolates$AMC)))
|
||||
reset_all_thrown_messages()
|
||||
expect_warning(count_resistant(example_isolates$AMC,
|
||||
as.character(example_isolates$GEN)))
|
||||
|
||||
|
||||
@ -23,7 +23,7 @@
|
||||
# how to conduct AMR analysis: https://msberends.github.io/AMR/ #
|
||||
# ==================================================================== #
|
||||
|
||||
context("is_new_episode.R")
|
||||
context("episode.R")
|
||||
|
||||
test_that("new episodes work", {
|
||||
skip_on_cran()
|
||||
@ -28,6 +28,7 @@ context("filter_ab_class.R")
|
||||
test_that("ATC-group filtering works", {
|
||||
skip_on_cran()
|
||||
|
||||
library(dplyr)
|
||||
expect_gt(example_isolates %>% filter_ab_class("carbapenem") %>% nrow(), 0)
|
||||
expect_gt(example_isolates %>% filter_aminoglycosides() %>% nrow(), 0)
|
||||
expect_gt(example_isolates %>% filter_carbapenems() %>% nrow(), 0)
|
||||
|
||||
@ -77,10 +77,14 @@ test_that("proportions works", {
|
||||
pull(combination_n),
|
||||
c(305, 617, 241, 711))
|
||||
|
||||
reset_all_thrown_messages()
|
||||
expect_warning(proportion_R(as.character(example_isolates$AMC)))
|
||||
reset_all_thrown_messages()
|
||||
expect_warning(proportion_S(as.character(example_isolates$AMC)))
|
||||
reset_all_thrown_messages()
|
||||
expect_warning(proportion_S(as.character(example_isolates$AMC,
|
||||
example_isolates$GEN)))
|
||||
reset_all_thrown_messages()
|
||||
expect_warning(n_rsi(as.character(example_isolates$AMC,
|
||||
example_isolates$GEN)))
|
||||
expect_equal(suppressWarnings(n_rsi(as.character(example_isolates$AMC,
|
||||
@ -105,8 +109,11 @@ test_that("proportions works", {
|
||||
NA_real_)
|
||||
|
||||
# warning for speed loss
|
||||
reset_all_thrown_messages()
|
||||
expect_warning(proportion_R(as.character(example_isolates$GEN)))
|
||||
reset_all_thrown_messages()
|
||||
expect_warning(proportion_I(as.character(example_isolates$GEN)))
|
||||
reset_all_thrown_messages()
|
||||
expect_warning(proportion_S(example_isolates$AMC, as.character(example_isolates$GEN)))
|
||||
|
||||
# proportion_df
|
||||
|
||||
Loading…
Reference in New Issue
Block a user