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(v0.8.0.9029) cleanup

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dr. M.S. (Matthijs) Berends
2019-11-10 15:50:18 +01:00
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2
docs/reference/AMR-deprecated.html
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@ -85,7 +85,7 @@
</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">0.8.0.9027</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9029</span>
</span>
</div>

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docs/reference/AMR.html
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@ -85,7 +85,7 @@
</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">0.8.0.9027</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9029</span>
</span>
</div>
@ -272,7 +272,8 @@ m.s.berends [at] umcg [dot] nl <br />
Department of Medical Microbiology, University of Groningen <br />
University Medical Center Groningen <br />
Post Office Box 30001 <br />
9700 RB Groningen</p>
9700 RB Groningen
The Netherlands</p>
<p>If you have found a bug, please file a new issue at: <br />
<a href='https://gitlab.com/msberends/AMR/issues'>https://gitlab.com/msberends/AMR/issues</a></p>

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docs/reference/as.rsi.html
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@ -85,7 +85,7 @@
</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">0.8.0.9027</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9029</span>
</span>
</div>
@ -306,7 +306,7 @@
</ul>
<p>Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.</p>
<p>This AMR package honours this new insight. Use <code><a href='proportion.html'>susceptibility</a></code> (equal to <code><a href='proportion.html'>proportion_SI</a></code>) to determine antimicrobial susceptibility and <code><a href='count.html'>count_susceptible</a></code> (equal to <code><a href='count.html'>count_SI</a></code>) to count susceptible isolates.</p>
<p>This AMR package honours this new insight. Use <code><a href='proportion.html'>susceptibility</a>()</code> (equal to <code><a href='proportion.html'>proportion_SI</a>()</code>) to determine antimicrobial susceptibility and <code><a href='count.html'>count_susceptible</a>()</code> (equal to <code><a href='count.html'>count_SI</a>()</code>) to count susceptible isolates.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>

2
docs/reference/availability.html
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@ -85,7 +85,7 @@
</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">0.8.0.9027</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9029</span>
</span>
</div>

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docs/reference/count.html
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@ -52,7 +52,7 @@
<meta property="og:title" content="Count isolates — count" />
<meta property="og:description" content="These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in dplyrs summarise and support grouped variables, see Examples.
count_resistant should be used to count resistant isolates, count_susceptible should be used to count susceptible isolates." />
count_resistant() should be used to count resistant isolates, count_susceptible() should be used to count susceptible isolates." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
<meta name="twitter:card" content="summary" />
@ -86,7 +86,7 @@ count_resistant should be used to count resistant isolates, count_susceptible sh
</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">0.8.0.9027</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9029</span>
</span>
</div>
@ -236,7 +236,7 @@ count_resistant should be used to count resistant isolates, count_susceptible sh
<div class="ref-description">
<p>These functions can be used to count resistant/susceptible microbial isolates. All functions support quasiquotation with pipes, can be used in <code>dplyr</code>s <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></code> and support grouped variables, see <em>Examples</em>.</p>
<p><code>count_resistant</code> should be used to count resistant isolates, <code>count_susceptible</code> should be used to count susceptible isolates.<br /></p>
<p><code>count_resistant()</code> should be used to count resistant isolates, <code>count_susceptible()</code> should be used to count susceptible isolates.<br /></p>
</div>
<pre class="usage"><span class='fu'>count_resistant</span>(<span class='no'>...</span>, <span class='kw'>only_all_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
@ -299,9 +299,9 @@ count_resistant should be used to count resistant isolates, count_susceptible sh
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>These functions are meant to count isolates. Use the <code><a href='proportion.html'>resistance</a></code>/<code><a href='proportion.html'>susceptibility</a></code> functions to calculate microbial resistance/susceptibility.</p>
<p>The function <code>count_resistant</code> is equal to the function <code>count_R</code>. The function <code>count_susceptible</code> is equal to the function <code>count_SI</code>.</p>
<p>The function <code>n_rsi</code> is an alias of <code>count_all</code>. They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to <code><a href='https://dplyr.tidyverse.org/reference/n_distinct.html'>n_distinct</a></code>. Their function is equal to <code>count_susceptible(...) + count_resistant(...)</code>.</p>
<p>The function <code>count_df</code> takes any variable from <code>data</code> that has an <code>"rsi"</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) and counts the number of S's, I's and R's. The function <code>rsi_df</code> works exactly like <code>count_df</code>, but adds the percentage of S, I and R.</p>
<p>The function <code>count_resistant()</code> is equal to the function <code>count_R()</code>. The function <code>count_susceptible()</code> is equal to the function <code>count_SI()</code>.</p>
<p>The function <code>n_rsi()</code> is an alias of <code>count_all()</code>. They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to <code><a href='https://dplyr.tidyverse.org/reference/n_distinct.html'>n_distinct</a>()</code>. Their function is equal to <code>count_susceptible(...) + count_resistant(...)</code>.</p>
<p>The function <code>count_df()</code> takes any variable from <code>data</code> that has an <code>"rsi"</code> class (created with <code><a href='as.rsi.html'>as.rsi</a>()</code>) and counts the number of S's, I's and R's. The function <code><a href='proportion.html'>rsi_df()</a></code> works exactly like <code>count_df()</code>, but adds the percentage of S, I and R.</p>
<h2 class="hasAnchor" id="interpretation-of-s-i-and-r"><a class="anchor" href="#interpretation-of-s-i-and-r"></a>Interpretation of S, I and R</h2>
@ -314,7 +314,7 @@ count_resistant should be used to count resistant isolates, count_susceptible sh
</ul>
<p>Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.</p>
<p>This AMR package honours this new insight. Use <code><a href='proportion.html'>susceptibility</a></code> (equal to <code><a href='proportion.html'>proportion_SI</a></code>) to determine antimicrobial susceptibility and <code>count_susceptible</code> (equal to <code>count_SI</code>) to count susceptible isolates.</p>
<p>This AMR package honours this new insight. Use <code><a href='proportion.html'>susceptibility</a>()</code> (equal to <code><a href='proportion.html'>proportion_SI</a>()</code>) to determine antimicrobial susceptibility and <code>count_susceptible()</code> (equal to <code>count_SI()</code>) to count susceptible isolates.</p>
<h2 class="hasAnchor" id="combination-therapy"><a class="anchor" href="#combination-therapy"></a>Combination therapy</h2>

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docs/reference/first_isolate.html
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@ -85,7 +85,7 @@
</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">0.8.0.9028</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9029</span>
</span>
</div>

2
docs/reference/ggplot_rsi.html
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@ -85,7 +85,7 @@
</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">0.8.0.9027</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9029</span>
</span>
</div>

2
docs/reference/index.html
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@ -84,7 +84,7 @@
</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">0.8.0.9028</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9029</span>
</span>
</div>

8
docs/reference/mdro.html
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@ -51,7 +51,7 @@
<script src="../extra.js"></script>
<meta property="og:title" content="Determine multidrug-resistant organisms (MDRO) — mdro" />
<meta property="og:description" content="Determine which isolates are multidrug-resistant organisms (MDRO) according to (country-specific) guidelines." />
<meta property="og:description" content="Determine which isolates are multidrug-resistant organisms (MDRO) according to international and national guidelines." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
<meta name="twitter:card" content="summary" />
@ -85,7 +85,7 @@
</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">0.8.0.9027</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9029</span>
</span>
</div>
@ -234,7 +234,7 @@
</div>
<div class="ref-description">
<p>Determine which isolates are multidrug-resistant organisms (MDRO) according to (country-specific) guidelines.</p>
<p>Determine which isolates are multidrug-resistant organisms (MDRO) according to international and national guidelines.</p>
</div>
<pre class="usage"><span class='fu'>mdro</span>(<span class='no'>x</span>, <span class='kw'>guideline</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
@ -411,7 +411,7 @@
</ul>
<p>Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.</p>
<p>This AMR package honours this new insight. Use <code><a href='proportion.html'>susceptibility</a></code> (equal to <code><a href='proportion.html'>proportion_SI</a></code>) to determine antimicrobial susceptibility and <code><a href='count.html'>count_susceptible</a></code> (equal to <code><a href='count.html'>count_SI</a></code>) to count susceptible isolates.</p>
<p>This AMR package honours this new insight. Use <code><a href='proportion.html'>susceptibility</a>()</code> (equal to <code><a href='proportion.html'>proportion_SI</a>()</code>) to determine antimicrobial susceptibility and <code><a href='count.html'>count_susceptible</a>()</code> (equal to <code><a href='count.html'>count_SI</a>()</code>) to count susceptible isolates.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>

12
docs/reference/proportion.html
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@ -52,7 +52,7 @@
<meta property="og:title" content="Calculate microbial resistance — proportion" />
<meta property="og:description" content="These functions can be used to calculate the (co-)resistance or susceptibility of microbial isolates (i.e. percentage of S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in dplyrs summarise and support grouped variables, see Examples.
resistance should be used to calculate resistance, susceptibility should be used to calculate susceptibility." />
resistance() should be used to calculate resistance, susceptibility() should be used to calculate susceptibility." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
<meta name="twitter:card" content="summary" />
@ -86,7 +86,7 @@ resistance should be used to calculate resistance, susceptibility should be used
</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">0.8.0.9027</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9029</span>
</span>
</div>
@ -236,7 +236,7 @@ resistance should be used to calculate resistance, susceptibility should be used
<div class="ref-description">
<p>These functions can be used to calculate the (co-)resistance or susceptibility of microbial isolates (i.e. percentage of S, SI, I, IR or R). All functions support quasiquotation with pipes, can be used in <code>dplyr</code>s <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></code> and support grouped variables, see <em>Examples</em>.</p>
<p><code>resistance</code> should be used to calculate resistance, <code>susceptibility</code> should be used to calculate susceptibility.<br /></p>
<p><code>resistance()</code> should be used to calculate resistance, <code>susceptibility()</code> should be used to calculate susceptibility.<br /></p>
</div>
<pre class="usage"><span class='fu'>resistance</span>(<span class='no'>...</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
@ -317,10 +317,10 @@ resistance should be used to calculate resistance, susceptibility should be used
<p>Double or, when <code>as_percent = TRUE</code>, a character.</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The function <code>resistance</code> is equal to the function <code>proportion_R</code>. The function <code>susceptibility</code> is equal to the function <code>proportion_SI</code>.</p>
<p>The function <code>resistance()</code> is equal to the function <code>proportion_R()</code>. The function <code>susceptibility()</code> is equal to the function <code>proportion_SI()</code>.</p>
<p><strong>Remember that you should filter your table to let it contain only first isolates!</strong> This is needed to exclude duplicates and to reduce selection bias. Use <code><a href='first_isolate.html'>first_isolate</a></code> to determine them in your data set.</p>
<p>These functions are not meant to count isolates, but to calculate the proportion of resistance/susceptibility. Use the <code><a href='count.html'>count</a></code> functions to count isolates. The function <code>susceptibility()</code> is essentially equal to <code>count_susceptible() / count_all()</code>. <em>Low counts can infuence the outcome - the <code>proportion</code> functions may camouflage this, since they only return the proportion (albeit being dependent on the <code>minimum</code> parameter).</em></p>
<p>The function <code>proportion_df</code> takes any variable from <code>data</code> that has an <code>"rsi"</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) and calculates the proportions R, I and S. The function <code>rsi_df</code> works exactly like <code>proportion_df</code>, but adds the number of isolates.</p>
<p>The function <code>proportion_df()</code> takes any variable from <code>data</code> that has an <code>"rsi"</code> class (created with <code><a href='as.rsi.html'>as.rsi</a>()</code>) and calculates the proportions R, I and S. The function <code>rsi_df()</code> works exactly like <code>proportion_df()</code>, but adds the number of isolates.</p>
<h2 class="hasAnchor" id="combination-therapy"><a class="anchor" href="#combination-therapy"></a>Combination therapy</h2>
@ -366,7 +366,7 @@ resistance should be used to calculate resistance, susceptibility should be used
</ul>
<p>Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.</p>
<p>This AMR package honours this new insight. Use <code>susceptibility</code> (equal to <code>proportion_SI</code>) to determine antimicrobial susceptibility and <code><a href='count.html'>count_susceptible</a></code> (equal to <code><a href='count.html'>count_SI</a></code>) to count susceptible isolates.</p>
<p>This AMR package honours this new insight. Use <code>susceptibility()</code> (equal to <code>proportion_SI()</code>) to determine antimicrobial susceptibility and <code><a href='count.html'>count_susceptible</a>()</code> (equal to <code><a href='count.html'>count_SI</a>()</code>) to count susceptible isolates.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>