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(v1.4.0.9060) ab class selector fix
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Package: AMR
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Version: 1.4.0.9059
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Version: 1.4.0.9060
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Date: 2021-01-04
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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2
NEWS.md
2
NEWS.md
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# AMR 1.4.0.9059
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# AMR 1.4.0.9060
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## <small>Last updated: 4 January 2021</small>
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### New
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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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@ -527,7 +527,7 @@ meet_criteria <- function(object,
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}
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get_current_data <- function(arg_name, call) {
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if (as.double(R.Version()$major) + (as.double(R.Version()$minor) / 100) < 3.2) {
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if (as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2) {
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if (is.na(arg_name)) {
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warning_("this function can only be used in R >= 3.2", call = call)
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return(data.frame())
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@ -164,7 +164,7 @@ ab_selector <- function(ab_class, function_name) {
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meet_criteria(ab_class, allow_class = "character", has_length = 1, .call_depth = 1)
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meet_criteria(function_name, allow_class = "character", has_length = 1, .call_depth = 1)
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if (as.double(R.Version()$major) + (as.double(R.Version()$minor) / 100) < 3.2) {
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if (as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) < 3.2) {
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warning_(function_name, "() can only be used in R >= 3.2", call = FALSE)
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return(NULL)
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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">1.4.0.9059</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9060</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">1.4.0.9059</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9060</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">1.4.0.9059</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9060</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">1.4.0.9059</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9060</span>
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</span>
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</div>
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@ -43,7 +43,7 @@
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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">1.4.0.9059</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9060</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">1.4.0.9059</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9060</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-1409059" class="section level1">
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<h1 class="page-header" data-toc-text="1.4.0.9059">
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<a href="#amr-1409059" class="anchor"></a>AMR 1.4.0.9059<small> Unreleased </small>
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<div id="amr-1409060" class="section level1">
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<h1 class="page-header" data-toc-text="1.4.0.9060">
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<a href="#amr-1409060" class="anchor"></a>AMR 1.4.0.9060<small> Unreleased </small>
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</h1>
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<div id="last-updated-4-january-2021" class="section level2">
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<h2 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: 2021-01-04T11:28Z
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last_built: 2021-01-04T12:36Z
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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">1.4.0.9059</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9060</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">1.4.0.9059</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9060</span>
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</span>
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</div>
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@ -105,12 +105,13 @@ test_that("imports work", {
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import_functions <- c(import_functions, call_functions)
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# check if all are in Suggests field
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expect_true(all(unique(import_functions) %in% strsplit(packageDescription("AMR")$Suggests, ",\n")[[1]]))
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for (i in seq_len(length(import_functions))) {
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fn <- names(import_functions)[i]
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pkg <- unname(import_functions[i])
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# package should be in Suggests field of DESCRIPTION
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expect(pkg %in% strsplit(packageDescription("AMR")$Suggests, ",\n")[[1]],
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failure_message = paste0("Package ", pkg, " is not in Suggests field"))
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# function should exist in foreign pkg namespace
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expect(!is.null(import_fn(name = fn, pkg = pkg, error_on_fail = FALSE)),
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failure_message = paste0("Function ", pkg, "::", fn, "() does not exist anymore"))
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}
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