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(v1.4.0.9031) as.ab() fix
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Package: AMR
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Version: 1.4.0.9030
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Version: 1.4.0.9031
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Date: 2020-12-03
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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3
NEWS.md
3
NEWS.md
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# AMR 1.4.0.9030
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# AMR 1.4.0.9031
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## <small>Last updated: 3 December 2020</small>
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### New
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@ -32,6 +32,7 @@
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* `as.rsi()` on a data.frame will not print a message anymore if the values are already clean R/SI values
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* Fixed a bug where `mo_uncertainties()` would not return the results based on the MO matching score
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* Fixed a bug where `as.mo()` would not return results for known laboratory codes for microorganisms
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* Fixed a bug where `as.ab()` would sometimes fail
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### Other
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* All messages and warnings thrown by this package now break sentences on whole words
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6
R/ab.R
6
R/ab.R
@ -153,7 +153,8 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
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}
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if (isTRUE(flag_multiple_results) & x[i] %like% "[ ]") {
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from_text <- suppressWarnings(ab_from_text(x[i], initial_search = FALSE, translate_ab = FALSE)[[1]])
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from_text <- tryCatch(suppressWarnings(ab_from_text(x[i], initial_search = FALSE, translate_ab = FALSE)[[1]]),
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error = function(e) character(0))
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} else {
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from_text <- character(0)
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}
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@ -345,7 +346,8 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
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if (isTRUE(flag_multiple_results)) {
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found <- from_text[1L]
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} else {
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found <- suppressWarnings(ab_from_text(x[i], initial_search = FALSE, translate_ab = FALSE)[[1]][1L])
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found <- tryCatch(suppressWarnings(ab_from_text(x[i], initial_search = FALSE, translate_ab = FALSE)[[1]][1L]),
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error = function(e) NA_character_)
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}
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if (!is.na(found)) {
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x_new[i] <- note_if_more_than_one_found(found, i, from_text)
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@ -38,12 +38,17 @@ EUCAST_VERSION_EXPERT_RULES <- list("3.1" = list(version_txt = "v3.1",
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title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'",
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url = "https://www.eucast.org/expert_rules_and_intrinsic_resistance/"))
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format_eucast_version_nr <- function(version) {
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format_eucast_version_nr <- function(version, markdown = TRUE) {
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# for documentation - adds title, version number, year and url in markdown language
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lst <- c(EUCAST_VERSION_BREAKPOINTS, EUCAST_VERSION_EXPERT_RULES)
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version <- format(version, nsmall = 1)
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paste0("[", lst[[version]]$title, " ", lst[[version]]$version_txt, "](", lst[[version]]$url, ")",
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" from ", lst[[version]]$year)
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if (markdown == TRUE) {
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paste0("[", lst[[version]]$title, " ", lst[[version]]$version_txt, "](", lst[[version]]$url, ")",
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" from ", lst[[version]]$year)
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} else {
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paste0(lst[[version]]$title, " ", lst[[version]]$version_txt,
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" from ", lst[[version]]$year)
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}
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}
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#' Apply EUCAST rules
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@ -386,6 +386,14 @@ mo_is_intrinsic_resistant <- function(x, ab, language = get_locale(), ...) {
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stop_("length of `x` and `ab` must be equal, or one of them must be of length 1.")
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}
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# show used version number once per session
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if (is.null(getOption("AMR_intrinsic_resistance_note", NULL))) {
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message_("Determining intrinsic resistance based on ",
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AMR:::format_eucast_version_nr(3.2, FALSE), ". ",
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font_bold("This message is shown once per session."))
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options(AMR_intrinsic_resistance_note = "shown")
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}
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# this saves about 50% in calculation time
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intrinsic_to_check <- intrinsic_resistant[which(intrinsic_resistant$microorganism %in% x |
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intrinsic_resistant$antibiotic %in% ab), , drop = FALSE]
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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">1.4.0.9030</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9031</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">1.4.0.9030</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9031</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">1.4.0.9030</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9031</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">1.4.0.9030</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9031</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">1.4.0.9030</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9031</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">1.4.0.9030</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9031</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-1409030" class="section level1">
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<h1 class="page-header" data-toc-text="1.4.0.9030">
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<a href="#amr-1409030" class="anchor"></a>AMR 1.4.0.9030<small> Unreleased </small>
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<div id="amr-1409031" class="section level1">
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<h1 class="page-header" data-toc-text="1.4.0.9031">
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<a href="#amr-1409031" class="anchor"></a>AMR 1.4.0.9031<small> Unreleased </small>
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</h1>
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<div id="last-updated-3-december-2020" class="section level2">
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<h2 class="hasAnchor">
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@ -252,21 +252,21 @@
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<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>
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<div class="sourceCode" id="cb1"><pre class="downlit">
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<span class="va">example_isolates</span> <span class="op">%>%</span>
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<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>
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<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></pre></div>
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<span class="fu">group_by</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>
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<span class="fu"><a href="https://rdrr.io/r/stats/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></pre></div>
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</li>
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<li>
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<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. They can even determine the column with microorganisms themselves when used inside <code>dplyr</code> verbs:</p>
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<div class="sourceCode" id="cb2"><pre class="downlit">
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<span class="va">example_isolates</span> <span class="op">%>%</span>
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<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_positive</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>
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<span class="fu"><a href="https://rdrr.io/r/stats/filter.html">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_is_gram_positive</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>
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<span class="co">#> NOTE: Using column `mo` as input for mo_is_gram_positive()</span></pre></div>
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</li>
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<li>
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<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. As with the new <code>mo_is_gram_*()</code> functions, if you have the <code>dplyr</code> package installed the column with microorganisms will be automatically determined when used inside <code>dplyr</code> verbs:</p>
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<div class="sourceCode" id="cb3"><pre class="downlit">
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<span class="va">example_isolates</span> <span class="op">%>%</span>
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<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_intrinsic_resistant</a></span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"Vancomycin"</span><span class="op">)</span><span class="op">)</span>
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<span class="fu"><a href="https://rdrr.io/r/stats/filter.html">filter</a></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">"Vancomycin"</span><span class="op">)</span><span class="op">)</span>
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<span class="co">#> NOTE: Using column `mo` as input for mo_is_intrinsic_resistant()</span></pre></div>
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</li>
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</ul>
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@ -286,6 +286,7 @@
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<code><a href="../reference/as.rsi.html">as.rsi()</a></code> on a data.frame will not print a message anymore if the values are already clean R/SI values</li>
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<li>Fixed a bug where <code><a href="../reference/as.mo.html">mo_uncertainties()</a></code> would not return the results based on the MO matching score</li>
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<li>Fixed a bug where <code><a href="../reference/as.mo.html">as.mo()</a></code> would not return results for known laboratory codes for microorganisms</li>
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<li>Fixed a bug where <code><a href="../reference/as.ab.html">as.ab()</a></code> would sometimes fail</li>
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</ul>
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</div>
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<div id="other" class="section level3">
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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: 2020-12-03T15:56Z
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last_built: 2020-12-03T21:21Z
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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">1.4.0.9030</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9031</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">1.4.0.9030</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9031</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">1.4.0.9030</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9031</span>
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</span>
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</div>
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