mirror of https://github.com/msberends/AMR.git
(v1.6.0.9018) unit tests
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Package: AMR
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Version: 1.6.0.9017
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Version: 1.6.0.9018
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Date: 2021-05-04
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Title: Antimicrobial Resistance Data Analysis
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Authors@R: c(
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2
NEWS.md
2
NEWS.md
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# `AMR` 1.6.0.9017
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# `AMR` 1.6.0.9018
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## <small>Last updated: 4 May 2021</small>
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### New
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@ -841,6 +841,14 @@ message_not_thrown_before <- function(fn, entire_session = FALSE) {
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is.null(pkg_env[[paste0("thrown_msg.", fn)]]) || !identical(pkg_env[[paste0("thrown_msg.", fn)]], unique_call_id(entire_session))
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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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# can be found in tests/testthat/*.R
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pkg_env_contents <- ls(envir = pkg_env)
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rm(list = pkg_env_contents[pkg_env_contents %like% "^thrown_msg."],
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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, but disables colours on emacs
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20
R/rsi.R
20
R/rsi.R
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@ -259,12 +259,22 @@ as.rsi.default <- function(x, ...) {
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}
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if (inherits(x, c("integer", "numeric", "double")) && all(x %in% c(1:3, NA))) {
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x <- as.character(x) # this is needed to prevent the vctrs pkg to throw an error
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x[x == "1"] <- "S"
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x[x == "2"] <- "I"
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x[x == "3"] <- "R"
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x.bak <- x
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x <- as.character(x) # this is needed to prevent the vctrs pkg from throwing an error
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} else if (!all(is.na(x)) && !identical(levels(x), c("S", "I", "R")) && !all(x %in% c("R", "S", "I", NA))) {
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# support haven package for importing e.g., from SPSS - it adds the 'labels' attribute
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lbls <- attributes(x)$labels
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if (!is.null(lbls) && all(c("R", "S", "I") %in% names(lbls)) && all(c(1:3) %in% lbls)) {
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x[x.bak == 1] <- names(lbls[lbls == 1])
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x[x.bak == 2] <- names(lbls[lbls == 2])
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x[x.bak == 3] <- names(lbls[lbls == 3])
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} else {
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x[x.bak == 1] <- "S"
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x[x.bak == 2] <- "I"
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x[x.bak == 3] <- "R"
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}
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} else if (!all(is.na(x)) && !identical(levels(x), c("R", "S", "I")) && !all(x %in% c("R", "S", "I", NA))) {
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if (all(x %unlike% "(R|S|I)", na.rm = TRUE)) {
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# check if they are actually MICs or disks
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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">1.6.0.9017</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9018</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">1.6.0.9017</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9018</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">1.6.0.9017</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9018</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">1.6.0.9017</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9018</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">1.6.0.9017</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9018</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">1.6.0.9017</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9018</span>
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</span>
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</div>
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@ -236,9 +236,9 @@
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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-1609017" class="section level1">
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<h1 class="page-header" data-toc-text="1.6.0.9017">
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<a href="#amr-1609017" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9017</h1>
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<div id="amr-1609018" class="section level1">
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<h1 class="page-header" data-toc-text="1.6.0.9018">
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<a href="#amr-1609018" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9018</h1>
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<div id="last-updated-4-may-2021" class="section level2">
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<h2 class="hasAnchor">
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<a href="#last-updated-4-may-2021" class="anchor"></a><small>Last updated: 4 May 2021</small>
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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: 2021-05-04T10:36Z
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last_built: 2021-05-04T13:19Z
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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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@ -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">1.6.0.9017</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9018</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">1.6.0.9017</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9018</span>
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</span>
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</div>
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