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(v0.7.0.9015) vignette fix

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dr. M.S. (Matthijs) Berends 2019-06-22 21:33:13 +02:00
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commit 278244140c
15 changed files with 29 additions and 27 deletions
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DESCRIPTION
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Package: AMR
Version: 0.7.0.9014
Version: 0.7.0.9015
Date: 2019-06-22
Title: Antimicrobial Resistance Analysis
Authors@R: c(

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NEWS.md
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# AMR 0.7.0.9014
# AMR 0.7.0.9015
#### New
* Function `rsi_df()` to transform a `data.frame` to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combination of the existing functions `count_df()` and `portion_df()` to immediately show resistance percentages and number of available isolates:

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docs/LICENSE-text.html
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</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">0.7.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9015</span>
</span>
</div>

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docs/articles/index.html
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</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">0.7.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9015</span>
</span>
</div>

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docs/articles/resistance_predict.html
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</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="Released version">0.7.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9015</span>
</span>
</div>
@ -125,13 +125,6 @@
Create frequency tables
</a>
</li>
<li>
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
</a>
</li>
<li>
<a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span>
@ -199,7 +192,7 @@
<h1>How to predict antimicrobial resistance</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">07 June 2019</h4>
<h4 class="date">22 June 2019</h4>
<div class="hidden name"><code>resistance_predict.Rmd</code></div>
@ -309,7 +302,7 @@
<a href="#choosing-the-right-model" class="anchor"></a>Choosing the right model</h3>
<p>Resistance is not easily predicted; if we look at vancomycin resistance in Gram positives, the spread (i.e. standard error) is enormous:</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb8-2" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(mo) <span class="op">==</span><span class="st"> "Gram positive"</span>) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb8-2" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(mo, <span class="dt">language =</span> <span class="ot">NULL</span>) <span class="op">==</span><span class="st"> "Gram-positive"</span>) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb8-3" title="3"><span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="dt">col_ab =</span> <span class="st">"VAN"</span>, <span class="dt">year_min =</span> <span class="dv">2010</span>, <span class="dt">info =</span> <span class="ot">FALSE</span>) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb8-4" title="4"><span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>()</a>
<a class="sourceLine" id="cb8-5" title="5"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `date` as input for `col_date`.</span></a></code></pre></div>
@ -354,7 +347,7 @@
</table>
<p>For the vancomycin resistance in Gram positive bacteria, a linear model might be more appropriate since no (left half of a) binomial distribution is to be expected based on the observed years:</p>
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb9-2" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(mo) <span class="op">==</span><span class="st"> "Gram positive"</span>) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb9-2" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(mo, <span class="dt">language =</span> <span class="ot">NULL</span>) <span class="op">==</span><span class="st"> "Gram-positive"</span>) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb9-3" title="3"><span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(<span class="dt">col_ab =</span> <span class="st">"VAN"</span>, <span class="dt">year_min =</span> <span class="dv">2010</span>, <span class="dt">info =</span> <span class="ot">FALSE</span>, <span class="dt">model =</span> <span class="st">"linear"</span>) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb9-4" title="4"><span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>()</a>
<a class="sourceLine" id="cb9-5" title="5"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `date` as input for `col_date`.</span></a></code></pre></div>

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docs/authors.html
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</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">0.7.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9015</span>
</span>
</div>

2
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">0.7.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9015</span>
</span>
</div>

8
docs/news/index.html
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@ -78,7 +78,7 @@
</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">0.7.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9015</span>
</span>
</div>
@ -232,9 +232,9 @@
</div>
<div id="amr-0709014" class="section level1">
<div id="amr-0709015" class="section level1">
<h1 class="page-header">
<a href="#amr-0709014" class="anchor"></a>AMR 0.7.0.9014<small> Unreleased </small>
<a href="#amr-0709015" class="anchor"></a>AMR 0.7.0.9015<small> Unreleased </small>
</h1>
<div id="new" class="section level4">
<h4 class="hasAnchor">
@ -1141,7 +1141,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0709014">0.7.0.9014</a></li>
<li><a href="#amr-0709015">0.7.0.9015</a></li>
<li><a href="#amr-070">0.7.0</a></li>
<li><a href="#amr-061">0.6.1</a></li>
<li><a href="#amr-060">0.6.0</a></li>

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docs/reference/index.html
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</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">0.7.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9015</span>
</span>
</div>

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git_premaster.sh
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@ -81,7 +81,16 @@ git commit -a -m "(v$new_version) $1" --quiet
git push --quiet
echo "Comparison:"
echo "https://gitlab.com/msberends/AMR/compare/master...premaster?view=inline"
echo "Check for all CRAN tests:"
echo "rhub::check_for_cran(devtools::build(args = c('--no-build-vignettes')))"
echo
echo "•••••••••"
echo "• Done •"
echo "••••••••"
echo
read -p "Upload to R-hub builder (y/N)? " choice
case "$choice" in
y|Y|j|J ) ;;
* ) exit 1;;
esac
Rscript -e "rhub::check_for_cran(devtools::build())"
echo
echo "Done."

4
vignettes/resistance_predict.Rmd
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@ -91,7 +91,7 @@ Resistance is not easily predicted; if we look at vancomycin resistance in Gram
```{r}
septic_patients %>%
filter(mo_gramstain(mo) == "Gram positive") %>%
filter(mo_gramstain(mo, language = NULL) == "Gram-positive") %>%
resistance_predict(col_ab = "VAN", year_min = 2010, info = FALSE) %>%
ggplot_rsi_predict()
```
@ -112,7 +112,7 @@ For the vancomycin resistance in Gram positive bacteria, a linear model might be
```{r}
septic_patients %>%
filter(mo_gramstain(mo) == "Gram positive") %>%
filter(mo_gramstain(mo, language = NULL) == "Gram-positive") %>%
resistance_predict(col_ab = "VAN", year_min = 2010, info = FALSE, model = "linear") %>%
ggplot_rsi_predict()
```