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(v1.7.1.9003) unit test

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dr. M.S. (Matthijs) Berends 2021-06-14 22:37:05 +02:00
parent 99be4c7e7e
commit 556bf0014d
15 changed files with 24 additions and 24 deletions
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DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 1.7.1.9002
Version: 1.7.1.9003
Date: 2021-06-14
Title: Antimicrobial Resistance Data Analysis
Authors@R: c(

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NEWS.md
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# `AMR` 1.7.1.9002
# `AMR` 1.7.1.9003
## <small>Last updated: 14 June 2021</small>
### Changed

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R/aa_helper_functions.R
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@ -713,9 +713,9 @@ meet_criteria <- function(object,
return(invisible())
}
get_current_data <- function(arg_name, call, reuse_equal_call = TRUE) {
get_current_data <- function(arg_name, call, reuse_from_1st_call = TRUE) {
# check if retrieved before, then get it from package environment to improve speed
if (reuse_equal_call == TRUE &&
if (reuse_from_1st_call == TRUE &&
identical(unique_call_id(entire_session = FALSE), pkg_env$get_current_data.call)) {
return(pkg_env$get_current_data.out)
}

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data-raw/AMR_latest.tar.gz
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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">1.7.1.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9003</span>
</span>
</div>

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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">1.7.1.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9003</span>
</span>
</div>

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docs/articles/datasets.html
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@ -39,7 +39,7 @@
</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">1.7.1.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9003</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">1.7.1.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9003</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">1.7.1.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9003</span>
</span>
</div>

6
docs/index.html
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@ -42,7 +42,7 @@
</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">1.7.1.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9003</span>
</span>
</div>
@ -223,9 +223,9 @@
<span class="co">#&gt; ℹ Using column 'mo' as input for `mo_is_gram_negative()`</span>
<span class="co">#&gt; ℹ Using column 'mo' as input for `mo_is_intrinsic_resistant()`</span>
<span class="co">#&gt; ℹ Determining intrinsic resistance based on 'EUCAST Expert Rules' and 'EUCAST Intrinsic</span>
<span class="co">#&gt; Resistance and Unusual Phenotypes' v3.2 (2020)</span>
<span class="co">#&gt; Resistance and Unusual Phenotypes' v3.2 (2020)</span>
<span class="co">#&gt; ℹ For `aminoglycosides()` using columns: 'AMK' (amikacin), 'GEN' (gentamicin), 'KAN'</span>
<span class="co">#&gt; (kanamycin) and 'TOB' (tobramycin)</span>
<span class="co">#&gt; (kanamycin) and 'TOB' (tobramycin)</span>
<span class="co">#&gt; ℹ For `carbapenems()` using columns: 'IPM' (imipenem) and 'MEM' (meropenem)</span></code></pre></div>
<p>With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (<code><a href="reference/mo_property.html">mo_is_gram_negative()</a></code> and <code><a href="reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>) and a column selection on two antibiotic groups (<code><a href="reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> and <code><a href="reference/antibiotic_class_selectors.html">carbapenems()</a></code>), the reference data about <a href="./reference/microorganisms.html">all microorganisms</a> and <a href="./reference/antibiotics.html">all antibiotics</a> in the <code>AMR</code> package make sure you get what you meant:</p>
<table class="table">

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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">1.7.1.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9003</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-1719002" class="section level1">
<h1 class="page-header" data-toc-text="1.7.1.9002">
<a href="#amr-1719002" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9002</h1>
<div id="amr-1719003" class="section level1">
<h1 class="page-header" data-toc-text="1.7.1.9003">
<a href="#amr-1719003" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9003</h1>
<div id="last-updated-14-june-2021" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-14-june-2021" class="anchor"></a><small>Last updated: 14 June 2021</small>
@ -307,7 +307,7 @@
</ul>
</li>
<li>Function <code><a href="../reference/antibiotic_class_selectors.html">betalactams()</a></code> as additional antbiotic column selector and function <code><a href="../reference/AMR-deprecated.html">filter_betalactams()</a></code> as additional antbiotic column filter. The group of betalactams consists of all carbapenems, cephalosporins and penicillins.</li>
<li>A <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> method for <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
<li>A <code>ggplot()</code> method for <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
</li>
</ul>
</div>
@ -408,7 +408,7 @@
<span class="co">#&gt; Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"</span></code></pre></div>
</li>
<li><p>Support for custom MDRO guidelines, using the new <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function, please see <code><a href="../reference/mdro.html">mdro()</a></code> for additional info</p></li>
<li><p><code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
<li><p><code>ggplot()</code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
<li>
<p>Function <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
@ -465,7 +465,7 @@
<li>Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent</li>
<li>All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)</li>
<li>Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see <code>translate</code>)</li>
<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> on any vector of MIC and disk diffusion values</li>
<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code>ggplot()</code> on any vector of MIC and disk diffusion values</li>
</ul>
</li>
<li>Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the <code>microorganisms</code> data set</li>

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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: 2021-06-14T20:03Z
last_built: 2021-06-14T20:36Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles

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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">1.7.1.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9003</span>
</span>
</div>

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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">1.7.1.9002</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9003</span>
</span>
</div>

4
index.md
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@ -31,9 +31,9 @@ example_isolates %>%
#> ℹ Using column 'mo' as input for `mo_is_gram_negative()`
#> ℹ Using column 'mo' as input for `mo_is_intrinsic_resistant()`
#> ℹ Determining intrinsic resistance based on 'EUCAST Expert Rules' and 'EUCAST Intrinsic
#> Resistance and Unusual Phenotypes' v3.2 (2020)
#> Resistance and Unusual Phenotypes' v3.2 (2020)
#> ℹ For `aminoglycosides()` using columns: 'AMK' (amikacin), 'GEN' (gentamicin), 'KAN'
#> (kanamycin) and 'TOB' (tobramycin)
#> (kanamycin) and 'TOB' (tobramycin)
#> ℹ For `carbapenems()` using columns: 'IPM' (imipenem) and 'MEM' (meropenem)
```