mirror of https://github.com/msberends/AMR.git
(v1.6.0.9062) code consistency
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parent
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Package: AMR
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Version: 1.6.0.9061
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Date: 2021-05-23
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Version: 1.6.0.9062
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Date: 2021-05-24
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Title: Antimicrobial Resistance Data Analysis
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Authors@R: c(
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person(role = c("aut", "cre"),
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4
NEWS.md
4
NEWS.md
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@ -1,5 +1,5 @@
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# `AMR` 1.6.0.9061
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## <small>Last updated: 23 May 2021</small>
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# `AMR` 1.6.0.9062
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## <small>Last updated: 24 May 2021</small>
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### Breaking change
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* All antibiotic class selectors (such as `carbapenems()`, `aminoglycosides()`) can now be used for filtering as well, making all their accompanying `filter_*()` functions redundant (such as `filter_carbapenems()`, `filter_aminoglycosides()`). These functions are now deprecated and will be removed in a next release.
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@ -727,7 +727,7 @@ get_current_data <- function(arg_name, call) {
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}
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}
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if (current_R_older_than(3.2)) {
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if (getRversion() < "3.2") {
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# R-3.0 and R-3.1 do not have an `x` element in the call stack, rendering this function useless
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if (is.na(arg_name)) {
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# like in carbapenems() etc.
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@ -893,7 +893,7 @@ has_colour <- function() {
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if (Sys.getenv("RSTUDIO", "") == "") {
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return(FALSE)
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}
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if ((cols <- Sys.getenv("RSTUDIO_CONSOLE_COLOR", "")) != "" && !is.na(as.numeric(cols))) {
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if ((cols <- Sys.getenv("RSTUDIO_CONSOLE_COLOR", "")) != "" && !is.na(as.double(cols))) {
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return(TRUE)
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}
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tryCatch(get("isAvailable", envir = asNamespace("rstudioapi"))(), error = function(e) return(FALSE)) &&
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@ -1186,15 +1186,11 @@ percentage <- function(x, digits = NULL, ...) {
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}
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time_start_tracking <- function() {
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pkg_env$time_start <- round(as.numeric(Sys.time()) * 1000)
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pkg_env$time_start <- round(as.double(Sys.time()) * 1000)
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}
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time_track <- function(name = NULL) {
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paste("(until now:", trimws(round(as.numeric(Sys.time()) * 1000) - pkg_env$time_start), "ms)")
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}
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current_R_older_than <- function(version) {
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as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < version
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paste("(until now:", trimws(round(as.double(Sys.time()) * 1000) - pkg_env$time_start), "ms)")
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}
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# prevent dependency on package 'backports' ----
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@ -1245,7 +1241,7 @@ lengths <- function(x, use.names = TRUE) {
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vapply(x, length, FUN.VALUE = NA_integer_, USE.NAMES = use.names)
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}
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if (current_R_older_than(3.1)) {
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if (getRversion() < "3.1") {
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# R-3.0 does not contain these functions, set them here to prevent installation failure
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# (required for extension of the <mic> class)
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cospi <- function(...) 1
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@ -25,11 +25,11 @@
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#' Antibiotic Class Selectors
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#'
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#' These functions help to filter and select columns with antibiotic test results that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. \strong{\Sexpr{ifelse(as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2, paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}}
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#' These functions help to filter and select columns with antibiotic test results that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. \strong{\Sexpr{ifelse(getRversion() < "3.2", paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}}
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#' @inheritSection lifecycle Stable Lifecycle
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#' @param ab_class an antimicrobial class, such as `"carbapenems"`. The columns `group`, `atc_group1` and `atc_group2` of the [antibiotics] data set will be searched (case-insensitive) for this value.
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#' @param only_rsi_columns a [logical] to indicate whether only columns of class `<rsi>` must be selected (defaults to `FALSE`), see [as.rsi()]
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#' @details \strong{\Sexpr{ifelse(as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2, paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}}
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#' @details \strong{\Sexpr{ifelse(getRversion() < "3.2", paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}}
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#'
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#'
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#' These functions can be used in data set calls for selecting columns and filtering rows, see *Examples*. They support base R, but work more convenient in dplyr functions such as [`select()`][dplyr::select()], [`filter()`][dplyr::filter()] and [`summarise()`][dplyr::summarise()].
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@ -220,7 +220,7 @@ ab_selector <- function(ab_class,
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meet_criteria(function_name, allow_class = "character", has_length = 1, .call_depth = 1)
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meet_criteria(only_rsi_columns, allow_class = "logical", has_length = 1, .call_depth = 1)
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if (current_R_older_than(3.2)) {
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if (getRversion() < "3.2") {
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warning_("antibiotic class selectors such as ", function_name,
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"() require R version 3.2 or later - you have ", R.version.string,
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call = FALSE)
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17
R/age.R
17
R/age.R
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@ -75,11 +75,16 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...) {
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# add decimals
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if (exact == TRUE) {
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# get dates of `x` when `x` would have the year of `reference`
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x_in_reference_year <- as.POSIXlt(paste0(format(as.Date(reference), "%Y"), format(as.Date(x), "-%m-%d")))
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x_in_reference_year <- as.POSIXlt(paste0(format(as.Date(reference), "%Y"),
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format(as.Date(x), "-%m-%d")),
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format = "%Y-%m-%d")
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# get differences in days
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n_days_x_rest <- as.double(difftime(as.Date(reference), as.Date(x_in_reference_year), units = "days"))
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n_days_x_rest <- as.double(difftime(as.Date(reference),
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as.Date(x_in_reference_year),
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units = "days"))
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# get numbers of days the years of `reference` has for a reliable denominator
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n_days_reference_year <- as.POSIXlt(paste0(format(as.Date(reference), "%Y"), "-12-31"))$yday + 1
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n_days_reference_year <- as.POSIXlt(paste0(format(as.Date(reference), "%Y"), "-12-31"),
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format = "%Y-%m-%d")$yday + 1
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# add decimal parts of year
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mod <- n_days_x_rest / n_days_reference_year
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# negative mods are cases where `x_in_reference_year` > `reference` - so 'add' a year
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@ -100,7 +105,11 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...) {
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ages <- ages[!is.na(ages)]
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}
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ages
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if (exact == TRUE) {
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as.double(ages)
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} else {
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as.integer(ages)
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}
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}
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#' Split Ages into Age Groups
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2
R/disk.R
2
R/disk.R
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@ -85,7 +85,7 @@ as.disk <- function(x, na.rm = FALSE) {
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fixed = TRUE)
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x_clean <- gsub(remove, "", x, ignore.case = TRUE, fixed = fixed)
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# remove everything that is not a number or dot
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as.numeric(gsub("[^0-9.]+", "", x_clean))
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as.double(gsub("[^0-9.]+", "", x_clean))
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}
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# round up and make it an integer
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2
R/pca.R
2
R/pca.R
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@ -120,7 +120,7 @@ pca <- function(x,
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message_("Columns selected for PCA: ", vector_and(font_bold(colnames(pca_data), collapse = NULL), quotes = TRUE),
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". Total observations available: ", nrow(pca_data), ".")
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if (current_R_older_than(3.4)) {
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if (getRversion() < "3.4.0") {
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# stats::prcomp prior to 3.4.0 does not have the 'rank.' argument
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pca_model <- prcomp(pca_data, retx = retx, center = center, scale. = scale., tol = tol)
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} else {
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Binary file not shown.
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="https://msberends.github.io/AMR//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">1.6.0.9061</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9062</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9061</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9062</span>
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</span>
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</div>
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@ -39,7 +39,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9061</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9062</span>
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</span>
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</div>
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@ -192,7 +192,7 @@
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<div class="page-header toc-ignore">
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<h1 data-toc-skip>Data sets for download / own use</h1>
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<h4 class="date">23 May 2021</h4>
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<h4 class="date">24 May 2021</h4>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd"><code>vignettes/datasets.Rmd</code></a></small>
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<div class="hidden name"><code>datasets.Rmd</code></div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9061</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9062</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9061</span>
|
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9062</span>
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</span>
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</div>
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|
|
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@ -42,7 +42,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
|
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9061</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9062</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9061</span>
|
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9062</span>
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</span>
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</div>
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@ -236,12 +236,12 @@
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<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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</div>
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<div id="amr-1609061" class="section level1">
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<h1 class="page-header" data-toc-text="1.6.0.9061">
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<a href="#amr-1609061" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9061</h1>
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<div id="last-updated-23-may-2021" class="section level2">
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<div id="amr-1609062" class="section level1">
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<h1 class="page-header" data-toc-text="1.6.0.9062">
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<a href="#amr-1609062" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9062</h1>
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<div id="last-updated-24-may-2021" class="section level2">
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<h2 class="hasAnchor">
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<a href="#last-updated-23-may-2021" class="anchor"></a><small>Last updated: 23 May 2021</small>
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<a href="#last-updated-24-may-2021" class="anchor"></a><small>Last updated: 24 May 2021</small>
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</h2>
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<div id="breaking-change" class="section level3">
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<h3 class="hasAnchor">
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@ -12,7 +12,7 @@ articles:
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datasets: datasets.html
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resistance_predict: resistance_predict.html
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welcome_to_AMR: welcome_to_AMR.html
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last_built: 2021-05-23T20:10Z
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last_built: 2021-05-23T22:05Z
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urls:
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reference: https://msberends.github.io/AMR//reference
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article: https://msberends.github.io/AMR//articles
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@ -83,7 +83,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9061</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9062</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9061</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9062</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9061</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9062</span>
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</span>
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</div>
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@ -23,7 +23,7 @@
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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if (!AMR:::current_R_older_than(3.2)) {
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if (getRversion() >= "3.2") {
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# antibiotic class selectors require at least R-3.2
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expect_true(ncol(example_isolates[, aminoglycosides(), drop = FALSE]) < ncol(example_isolates))
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expect_true(ncol(example_isolates[, betalactams(), drop = FALSE]) < ncol(example_isolates))
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@ -85,7 +85,7 @@ suppressWarnings(expect_identical(log1p(x), log1p(x_double)))
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suppressWarnings(expect_identical(cos(x), cos(x_double)))
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suppressWarnings(expect_identical(sin(x), sin(x_double)))
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suppressWarnings(expect_identical(tan(x), tan(x_double)))
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if (!AMR:::current_R_older_than(3.1)) {
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if (getRversion() >= "3.1") {
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suppressWarnings(expect_identical(cospi(x), cospi(x_double)))
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suppressWarnings(expect_identical(sinpi(x), sinpi(x_double)))
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suppressWarnings(expect_identical(tanpi(x), tanpi(x_double)))
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@ -58,10 +58,10 @@ tetracyclines(only_rsi_columns = FALSE)
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\item{only_rsi_columns}{a \link{logical} to indicate whether only columns of class \verb{<rsi>} must be selected (defaults to \code{FALSE}), see \code{\link[=as.rsi]{as.rsi()}}}
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}
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\description{
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These functions help to filter and select columns with antibiotic test results that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. \strong{\Sexpr{ifelse(as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2, paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}}
|
||||
These functions help to filter and select columns with antibiotic test results that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations. \strong{\Sexpr{ifelse(getRversion() < "3.2", paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}}
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}
|
||||
\details{
|
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\strong{\Sexpr{ifelse(as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2, paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}}
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\strong{\Sexpr{ifelse(getRversion() < "3.2", paste0("NOTE: THESE FUNCTIONS DO NOT WORK ON YOUR CURRENT R VERSION. These functions require R version 3.2 or later - you have ", R.version.string, "."), "")}}
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These functions can be used in data set calls for selecting columns and filtering rows, see \emph{Examples}. They support base R, but work more convenient in dplyr functions such as \code{\link[dplyr:select]{select()}}, \code{\link[dplyr:filter]{filter()}} and \code{\link[dplyr:summarise]{summarise()}}.
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@ -27,9 +27,7 @@
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if (identical(Sys.getenv("R_RUN_TINYTEST"), "true")) {
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# env var 'R_LIBS_USER' got overwritten during 'R CMD check' in GitHub Actions, so:
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.libPaths(c(Sys.getenv("R_LIBS_USER_GH_ACTIONS"), .libPaths()))
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print("here")
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if (AMR:::pkg_is_available("tinytest")) {
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print("here2")
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library(AMR)
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out <- test_package("AMR",
|
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testdir = ifelse(AMR:::dir.exists("inst/tinytest"),
|
||||
|
|
|
|||
Loading…
Reference in New Issue