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AMR
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(v1.4.0.9022) small bugfix

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dr. M.S. (Matthijs) Berends 2020-11-16 20:02:20 +01:00
parent deefce9520
commit 93428415d0
13 changed files with 19 additions and 20 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 1.4.0.9021 Version: 1.4.0.9022
Date: 2020-11-16 Date: 2020-11-16
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.4.0.9021 # AMR 1.4.0.9022
## <small>Last updated: 16 November 2020</small> ## <small>Last updated: 16 November 2020</small>
### New ### New

3
R/aa_helper_functions.R
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@ -79,7 +79,6 @@ addin_insert_like <- function() {
modifyRange <- import_fn("insertText", "rstudioapi") modifyRange <- import_fn("insertText", "rstudioapi")
document_range <- import_fn("document_range", "rstudioapi") document_range <- import_fn("document_range", "rstudioapi")
document_position <- import_fn("document_position", "rstudioapi") document_position <- import_fn("document_position", "rstudioapi")
# setSelectionRanges <- import_fn("setSelectionRanges", "rstudioapi")
context <- getSourceEditorContext() context <- getSourceEditorContext()
current_row <- context$selection[[1]]$range$end[1] current_row <- context$selection[[1]]$range$end[1]
@ -688,7 +687,7 @@ set_clean_class <- function(x, new_class) {
lvls <- levels(x) lvls <- levels(x)
attributes(x) <- NULL attributes(x) <- NULL
levels(x) <- lvls levels(x) <- lvls
} else { } else if (!is.list(x) && !is.function(x)) {
attributes(x) <- NULL attributes(x) <- NULL
} }
class(x) <- new_class class(x) <- new_class

2
R/mo_property.R
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@ -598,7 +598,7 @@ mo_validate <- function(x, property, language, ...) {
} }
if (property == "mo") { if (property == "mo") {
return(to_class_mo(x)) return(set_clean_class(x, new_class = c("mo", "character")))
} else if (property == "snomed") { } else if (property == "snomed") {
return(as.double(eval(parse(text = x)))) return(as.double(eval(parse(text = x))))
} else { } else {

2
docs/404.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a> <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">1.4.0.9021</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9022</span>
</span> </span>
</div> </div>

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docs/LICENSE-text.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">1.4.0.9021</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9022</span>
</span> </span>
</div> </div>

2
docs/articles/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.4.0.9021</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9022</span>
</span> </span>
</div> </div>

2
docs/authors.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">1.4.0.9021</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9022</span>
</span> </span>
</div> </div>

2
docs/index.html
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@ -43,7 +43,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">1.4.0.9021</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9022</span>
</span> </span>
</div> </div>

12
docs/news/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.4.0.9021</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9022</span>
</span> </span>
</div> </div>
@ -236,9 +236,9 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small> <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div> </div>
<div id="amr-1409021" class="section level1"> <div id="amr-1409022" class="section level1">
<h1 class="page-header" data-toc-text="1.4.0.9021"> <h1 class="page-header" data-toc-text="1.4.0.9022">
<a href="#amr-1409021" class="anchor"></a>AMR 1.4.0.9021<small> Unreleased </small> <a href="#amr-1409022" class="anchor"></a>AMR 1.4.0.9022<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-16-november-2020" class="section level2"> <div id="last-updated-16-november-2020" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
@ -252,14 +252,14 @@
<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. If you have the <code>dplyr</code> package installed, they can even determine the column with microorganisms themselves when used inside <code>dplyr</code> verbs:</p> <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. If you have the <code>dplyr</code> package installed, they can even determine the column with microorganisms themselves when used inside <code>dplyr</code> verbs:</p>
<div class="sourceCode" id="cb1"><pre class="downlit"> <div class="sourceCode" id="cb1"><pre class="downlit">
<span class="va">example_isolates</span> <span class="op">%&gt;%</span> <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> <span class="co">#&gt; NOTE: Using column `mo` as input for mo_is_gram_positive()</span></pre></div>
</li> </li>
<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> <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="cb2"><pre class="downlit"> <div class="sourceCode" id="cb2"><pre class="downlit">
<span class="va">example_isolates</span> <span class="op">%&gt;%</span> <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> <span class="co">#&gt; NOTE: Using column `mo` as input for mo_is_intrinsic_resistant()</span></pre></div>
</li> </li>
<li><p>Functions <code><a href="../reference/like.html">%not_like%</a></code> and <code><a href="../reference/like.html">%not_like_case%</a></code> as wrappers around <code><a href="../reference/like.html">%like%</a></code> and <code><a href="../reference/like.html">%like_case%</a></code>. The RStudio addin to insert the text " %like% " as provided in this package now iterates over all like variants. So if you have defined the keyboard shortcut Ctrl/Cmd + L to this addin, it will first insert <code><a href="../reference/like.html">%like%</a></code> and by pressing it again it will be replaced with <code><a href="../reference/like.html">%not_like%</a></code>, etc.</p></li> <li><p>Functions <code><a href="../reference/like.html">%not_like%</a></code> and <code><a href="../reference/like.html">%not_like_case%</a></code> as wrappers around <code><a href="../reference/like.html">%like%</a></code> and <code><a href="../reference/like.html">%like_case%</a></code>. The RStudio addin to insert the text " %like% " as provided in this package now iterates over all like variants. So if you have defined the keyboard shortcut Ctrl/Cmd + L to this addin, it will first insert <code><a href="../reference/like.html">%like%</a></code> and by pressing it again it will be replaced with <code><a href="../reference/like.html">%not_like%</a></code>, etc.</p></li>

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docs/pkgdown.yml
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@ -12,7 +12,7 @@ articles:
datasets: datasets.html datasets: datasets.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html welcome_to_AMR: welcome_to_AMR.html
last_built: 2020-11-16T15:57Z last_built: 2020-11-16T18:55Z
urls: urls:
reference: https://msberends.github.io/AMR//reference reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles article: https://msberends.github.io/AMR//articles

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docs/reference/index.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">1.4.0.9021</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9022</span>
</span> </span>
</div> </div>

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docs/survey.html
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@ -81,7 +81,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <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">1.4.0.9021</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9022</span>
</span> </span>
</div> </div>