mirror of
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(v1.6.0.9050) printing NA in custom_eucast_rules()
This commit is contained in:
parent
9a2879cba9
commit
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22
.github/workflows/check.yaml
vendored
22
.github/workflows/check.yaml
vendored
@ -96,7 +96,7 @@ jobs:
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- name: Install Linux dependencies
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if: runner.os == 'Linux'
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# update the below with sysreqs::sysreqs("DESCRIPTION") and check the "DEB" entries (for Ubuntu).
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# we don't want to depend on the sysreqs pkg here, as it requires a quite new R version
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# we don't want to depend on the sysreqs pkg here, as it requires quite a recent R version
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# as of May 2021: https://sysreqs.r-hub.io/pkg/AMR,R,cleaner,curl,dplyr,ggplot2,ggtext,knitr,microbenchmark,pillar,readxl,rmarkdown,rstudioapi,rvest,skimr,tidyr,tinytest,xml2,backports,crayon,rlang,vctrs,evaluate,highr,markdown,stringr,yaml,xfun,cli,ellipsis,fansi,lifecycle,utf8,glue,mime,magrittr,stringi,generics,R6,tibble,tidyselect,pkgconfig,purrr,digest,gtable,isoband,MASS,mgcv,scales,withr,nlme,Matrix,farver,labeling,munsell,RColorBrewer,viridisLite,lattice,colorspace,gridtext,Rcpp,RCurl,png,jpeg,bitops,cellranger,progress,rematch,hms,prettyunits,htmltools,jsonlite,tinytex,base64enc,httr,selectr,openssl,askpass,sys,repr,cpp11
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run: |
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sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev libpng-dev
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@ -109,29 +109,33 @@ jobs:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-v4
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- name: Install AMR and tinytest and update dependencies
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- name: Unpack AMR and install R dependencies
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if: always()
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run: |
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tar -xf data-raw/AMR_latest.tar.gz
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source("data-raw/_install_deps.R")
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shell: Rscript {0}
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- name: Show session info
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if: always()
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run: |
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options(width = 100)
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utils::sessionInfo()
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as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
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shell: Rscript {0}
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- name: Unpack shipped version and remove vignettes
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if: always()
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- name: Only keep vignettes on release version
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if: matrix.config.r != 'release'
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# writing to DESCRIPTION2 and then moving to DESCRIPTION is required for R < 3.3 as writeLines() cannot overwrite
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run: |
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tar -xf data-raw/AMR_latest.tar.gz
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rm -rf AMR/vignettes
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Rscript -e "writeLines(readLines('AMR/DESCRIPTION')[!grepl('VignetteBuilder', readLines('AMR/DESCRIPTION'))], 'AMR/DESCRIPTION')"
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Rscript -e "writeLines(readLines('AMR/DESCRIPTION')[gsub(' +', '', readLines('AMR/DESCRIPTION')) != ''], 'AMR/DESCRIPTION')"
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find AMR -name 'DESCRIPTION' -exec cat '{}' \; || true
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Rscript -e "writeLines(readLines('AMR/DESCRIPTION')[!grepl('VignetteBuilder', readLines('AMR/DESCRIPTION'))], 'AMR/DESCRIPTION2')"
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rm AMR/DESCRIPTION
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mv AMR/DESCRIPTION2 AMR/DESCRIPTION
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shell: bash
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- name: Run R CMD check
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if: always()
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env:
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_R_CHECK_CRAN_INCOMING_: false
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_R_CHECK_FORCE_SUGGESTS_: false
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@ -142,7 +146,7 @@ jobs:
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R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
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R_RUN_TINYTEST: true
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run: |
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R CMD check --no-manual --no-vignettes --no-build-vignettes --ignore-vignettes AMR
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R CMD check --no-manual AMR
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shell: bash
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- name: Show unit tests output
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 1.6.0.9049
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Date: 2021-05-19
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Version: 1.6.0.9050
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Date: 2021-05-20
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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
@ -1,5 +1,5 @@
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# `AMR` 1.6.0.9049
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## <small>Last updated: 19 May 2021</small>
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# `AMR` 1.6.0.9050
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## <small>Last updated: 20 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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@ -56,7 +56,7 @@
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#' - `"TU"` = thousand units
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#' - `"MU"` = million units
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#' - `"mmol"` = millimole
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#' - `"ml"` = milliliter (e.g. eyedrops)
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#' - `"ml"` = millilitre (e.g. eyedrops)
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#'
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#' **N.B. This function requires an internet connection and only works if the following packages are installed: `curl`, `rvest`, `xml2`.**
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#' @export
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@ -150,7 +150,6 @@ custom_eucast_rules <- function(...) {
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result_group <- tryCatch(
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suppressWarnings(as.ab(result_group,
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fast_mode = TRUE,
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info = FALSE,
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flag_multiple_results = FALSE)),
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error = function(e) NA_character_)
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}
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@ -203,7 +202,9 @@ print.custom_eucast_rules <- function(x, ...) {
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for (i in seq_len(length(x))) {
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rule <- x[[i]]
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rule$query <- format_custom_query_rule(rule$query)
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if (rule$result_value == "R") {
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if (is.na(rule$result_value)) {
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val <- font_red("<NA>")
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} else if (rule$result_value == "R") {
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val <- font_rsi_R_bg(font_black(" R "))
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} else if (rule$result_value == "S") {
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val <- font_rsi_S_bg(font_black(" S "))
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Binary file not shown.
@ -23,32 +23,31 @@
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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install.packages("data-raw/AMR_latest.tar.gz", dependencies = FALSE)
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# some old R instances have trouble installing tinytest, so we ship it too
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install.packages("data-raw/tinytest_1.2.4.patched.tar.gz")
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pkg_suggests <- AMR:::trimws(unlist(strsplit(packageDescription("AMR")$Suggests, ",(\n)?")))
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descr <- readLines("AMR/DESCRIPTION")
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pkg_suggests <- gsub(".*Suggests: (.*)*?[A-Z].*", "\\1", paste0(descr, "*", collapse = ""), perl = FALSE)
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pkg_suggests <- unlist(strsplit(pkg_suggests, "[,* ]"))
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pkg_suggests <- pkg_suggests[pkg_suggests != ""]
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cat("Packages listed in Suggests:", paste(pkg_suggests, collapse = ", "), "\n")
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to_install <- pkg_suggests[!pkg_suggests %in% rownames(utils::installed.packages())]
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to_update <- as.data.frame(utils::old.packages(repos = "https://cran.rstudio.com/"), stringsAsFactors = FALSE)
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to_update <- to_update[which(to_update$Package %in% pkg_suggests), "Package", drop = TRUE]
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for (i in seq_len(length(to_install))) {
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if (isTRUE(is.character(to_install[i]))) {
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cat("Installing package", to_install[i], "\n")
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tryCatch(install.packages(to_install[i], repos = "https://cran.rstudio.com/", dependencies = TRUE, quiet = TRUE),
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# message = function(m) invisible(),
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warning = function(w) message(w$message),
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error = function(e) message(e$message))
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}
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}
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for (i in seq_len(length(to_update))) {
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if (isTRUE(is.character(to_update[i]))) {
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cat("Updating package", to_update[i], "\n")
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tryCatch(update.packages(to_update[i], repos = "https://cran.rstudio.com/", ask = FALSE),
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# message = function(m) invisible(),
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warning = function(w) message(w$message),
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error = function(e) message(e$message))
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}
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}
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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">1.6.0.9049</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9050</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">1.6.0.9049</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9050</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">1.6.0.9049</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9050</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">19 May 2021</h4>
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<h4 class="date">20 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">1.6.0.9049</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9050</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">1.6.0.9049</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9050</span>
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</span>
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</div>
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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">1.6.0.9049</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9050</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">1.6.0.9049</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9050</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-1609049" class="section level1">
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<h1 class="page-header" data-toc-text="1.6.0.9049">
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<a href="#amr-1609049" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9049</h1>
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<div id="last-updated-19-may-2021" class="section level2">
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<div id="amr-1609050" class="section level1">
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<h1 class="page-header" data-toc-text="1.6.0.9050">
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<a href="#amr-1609050" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9050</h1>
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<div id="last-updated-20-may-2021" class="section level2">
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<h2 class="hasAnchor">
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<a href="#last-updated-19-may-2021" class="anchor"></a><small>Last updated: 19 May 2021</small>
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<a href="#last-updated-20-may-2021" class="anchor"></a><small>Last updated: 20 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: 2021-05-19T21:58Z
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last_built: 2021-05-20T08:10Z
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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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@ -82,7 +82,7 @@
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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">1.6.0.9021</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9050</span>
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</span>
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</div>
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@ -309,7 +309,7 @@
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<li><p><code>"TU"</code> = thousand units</p></li>
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<li><p><code>"MU"</code> = million units</p></li>
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<li><p><code>"mmol"</code> = millimole</p></li>
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<li><p><code>"ml"</code> = milliliter (e.g. eyedrops)</p></li>
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<li><p><code>"ml"</code> = millilitre (e.g. eyedrops)</p></li>
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</ul>
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<p><strong>N.B. This function requires an internet connection and only works if the following packages are installed: <code>curl</code>, <code>rvest</code>, <code>xml2</code>.</strong></p>
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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">1.6.0.9049</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9050</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">1.6.0.9049</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9050</span>
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</span>
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</div>
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@ -23,7 +23,10 @@
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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if (tryCatch(curl::has_internet(), error = function(e) FALSE)) {
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if (pkg_is_available("curl", also_load = FALSE) &&
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pkg_is_available("rvest", also_load = FALSE) &&
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pkg_is_available("xml2", also_load = FALSE) &&
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tryCatch(curl::has_internet(), error = function(e) FALSE)) {
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expect_true(length(atc_online_groups(ab_atc("AMX"))) >= 1)
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expect_equal(atc_online_ddd(ab_atc("AMX"), administration = "O"), 1.5)
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expect_equal(atc_online_ddd(ab_atc("AMX"), administration = "P"), 3)
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@ -35,17 +35,17 @@ expect_equal(proportion_R(example_isolates$AMX) + proportion_I(example_isolates$
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expect_equal(proportion_S(example_isolates$AMX) + proportion_I(example_isolates$AMX),
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proportion_SI(example_isolates$AMX))
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expect_equal(example_isolates %>% proportion_SI(AMC),
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if (pkg_is_available("dplyr")) {
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expect_equal(example_isolates %>% proportion_SI(AMC),
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0.7626397,
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tolerance = 0.0001)
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expect_equal(example_isolates %>% proportion_SI(AMC, GEN),
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expect_equal(example_isolates %>% proportion_SI(AMC, GEN),
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0.9408,
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tolerance = 0.0001)
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expect_equal(example_isolates %>% proportion_SI(AMC, GEN, only_all_tested = TRUE),
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expect_equal(example_isolates %>% proportion_SI(AMC, GEN, only_all_tested = TRUE),
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0.9382647,
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tolerance = 0.0001)
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if (pkg_is_available("dplyr")) {
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# percentages
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expect_equal(example_isolates %>%
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group_by(hospital_id) %>%
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@ -61,7 +61,7 @@ Abbreviations of return values when using \code{property = "U"} (unit):
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\item \code{"TU"} = thousand units
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\item \code{"MU"} = million units
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\item \code{"mmol"} = millimole
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\item \code{"ml"} = milliliter (e.g. eyedrops)
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\item \code{"ml"} = millilitre (e.g. eyedrops)
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}
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\strong{N.B. This function requires an internet connection and only works if the following packages are installed: \code{curl}, \code{rvest}, \code{xml2}.}
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