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AMR
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(v1.4.0.9031) as.ab() fix

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dr. M.S. (Matthijs) Berends 2020-12-03 22:30:14 +01:00
parent e03b3c96d3
commit fdf29e6c5b
15 changed files with 41 additions and 24 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 1.4.0.9030
Version: 1.4.0.9031
Date: 2020-12-03
Title: Antimicrobial Resistance Analysis
Authors@R: c(

3
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.4.0.9030
# AMR 1.4.0.9031
## <small>Last updated: 3 December 2020</small>
### New
@ -32,6 +32,7 @@
* `as.rsi()` on a data.frame will not print a message anymore if the values are already clean R/SI values
* Fixed a bug where `mo_uncertainties()` would not return the results based on the MO matching score
* Fixed a bug where `as.mo()` would not return results for known laboratory codes for microorganisms
* Fixed a bug where `as.ab()` would sometimes fail
### Other
* All messages and warnings thrown by this package now break sentences on whole words

6
R/ab.R
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@ -153,7 +153,8 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
}
if (isTRUE(flag_multiple_results) & x[i] %like% "[ ]") {
from_text <- suppressWarnings(ab_from_text(x[i], initial_search = FALSE, translate_ab = FALSE)[[1]])
from_text <- tryCatch(suppressWarnings(ab_from_text(x[i], initial_search = FALSE, translate_ab = FALSE)[[1]]),
error = function(e) character(0))
} else {
from_text <- character(0)
}
@ -345,7 +346,8 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
if (isTRUE(flag_multiple_results)) {
found <- from_text[1L]
} else {
found <- suppressWarnings(ab_from_text(x[i], initial_search = FALSE, translate_ab = FALSE)[[1]][1L])
found <- tryCatch(suppressWarnings(ab_from_text(x[i], initial_search = FALSE, translate_ab = FALSE)[[1]][1L]),
error = function(e) NA_character_)
}
if (!is.na(found)) {
x_new[i] <- note_if_more_than_one_found(found, i, from_text)

11
R/eucast_rules.R
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@ -38,12 +38,17 @@ EUCAST_VERSION_EXPERT_RULES <- list("3.1" = list(version_txt = "v3.1",
title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'",
url = "https://www.eucast.org/expert_rules_and_intrinsic_resistance/"))
format_eucast_version_nr <- function(version) {
format_eucast_version_nr <- function(version, markdown = TRUE) {
# for documentation - adds title, version number, year and url in markdown language
lst <- c(EUCAST_VERSION_BREAKPOINTS, EUCAST_VERSION_EXPERT_RULES)
version <- format(version, nsmall = 1)
paste0("[", lst[[version]]$title, " ", lst[[version]]$version_txt, "](", lst[[version]]$url, ")",
" from ", lst[[version]]$year)
if (markdown == TRUE) {
paste0("[", lst[[version]]$title, " ", lst[[version]]$version_txt, "](", lst[[version]]$url, ")",
" from ", lst[[version]]$year)
} else {
paste0(lst[[version]]$title, " ", lst[[version]]$version_txt,
" from ", lst[[version]]$year)
}
}
#' Apply EUCAST rules

8
R/mo_property.R
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@ -386,6 +386,14 @@ mo_is_intrinsic_resistant <- function(x, ab, language = get_locale(), ...) {
stop_("length of `x` and `ab` must be equal, or one of them must be of length 1.")
}
# show used version number once per session
if (is.null(getOption("AMR_intrinsic_resistance_note", NULL))) {
message_("Determining intrinsic resistance based on ",
AMR:::format_eucast_version_nr(3.2, FALSE), ". ",
font_bold("This message is shown once per session."))
options(AMR_intrinsic_resistance_note = "shown")
}
# this saves about 50% in calculation time
intrinsic_to_check <- intrinsic_resistant[which(intrinsic_resistant$microorganism %in% x |
intrinsic_resistant$antibiotic %in% ab), , drop = FALSE]

2
docs/404.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9031</span>
</span>
</div>

2
docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</button>
<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">1.4.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9031</span>
</span>
</div>

2
docs/articles/index.html
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@ -81,7 +81,7 @@
</button>
<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">1.4.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9031</span>
</span>
</div>

2
docs/authors.html
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@ -81,7 +81,7 @@
</button>
<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">1.4.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9031</span>
</span>
</div>

2
docs/index.html
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@ -43,7 +43,7 @@
</button>
<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">1.4.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9031</span>
</span>
</div>

17
docs/news/index.html
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@ -81,7 +81,7 @@
</button>
<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">1.4.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9031</span>
</span>
</div>
@ -236,9 +236,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1409030" class="section level1">
<h1 class="page-header" data-toc-text="1.4.0.9030">
<a href="#amr-1409030" class="anchor"></a>AMR 1.4.0.9030<small> Unreleased </small>
<div id="amr-1409031" class="section level1">
<h1 class="page-header" data-toc-text="1.4.0.9031">
<a href="#amr-1409031" class="anchor"></a>AMR 1.4.0.9031<small> Unreleased </small>
</h1>
<div id="last-updated-3-december-2020" class="section level2">
<h2 class="hasAnchor">
@ -252,21 +252,21 @@
<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>
<div class="sourceCode" id="cb1"><pre class="downlit">
<span class="va">example_isolates</span> <span class="op">%&gt;%</span>
<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">%&gt;%</span>
<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>
<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">%&gt;%</span>
<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>
</li>
<li>
<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>
<div class="sourceCode" id="cb2"><pre class="downlit">
<span class="va">example_isolates</span> <span class="op">%&gt;%</span>
<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>
<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>
<span class="co">#&gt; NOTE: Using column `mo` as input for mo_is_gram_positive()</span></pre></div>
</li>
<li>
<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>
<div class="sourceCode" id="cb3"><pre class="downlit">
<span class="va">example_isolates</span> <span class="op">%&gt;%</span>
<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>
<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>
<span class="co">#&gt; NOTE: Using column `mo` as input for mo_is_intrinsic_resistant()</span></pre></div>
</li>
</ul>
@ -286,6 +286,7 @@
<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>
<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>
<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>
<li>Fixed a bug where <code><a href="../reference/as.ab.html">as.ab()</a></code> would sometimes fail</li>
</ul>
</div>
<div id="other" class="section level3">

2
docs/pkgdown.yml
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@ -12,7 +12,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2020-12-03T15:56Z
last_built: 2020-12-03T21:21Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles

2
docs/reference/guess_ab_col.html
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@ -82,7 +82,7 @@
</button>
<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">1.4.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9031</span>
</span>
</div>

2
docs/reference/index.html
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@ -81,7 +81,7 @@
</button>
<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">1.4.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9031</span>
</span>
</div>

2
docs/survey.html
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@ -81,7 +81,7 @@
</button>
<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">1.4.0.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9031</span>
</span>
</div>