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(v1.1.0.9004) lose dependencies
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@ -83,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9004</span>
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</span>
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</div>
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@ -304,7 +304,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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<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>
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<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>
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<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>
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<p>The function <code>count_df()</code> takes any variable from <code>data</code> that has an <code><a href='as.rsi.html'>rsi</a></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>
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<p>The function <code>count_df()</code> takes any variable from <code>data</code> that has an <code><a href='as.rsi.html'>rsi</a></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. It also supports grouped variables. 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>
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<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
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@ -338,21 +338,21 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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-------- -------- ---------- ----------- ---------- -----------
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S or I S or I X X X X
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R S or I X X X X
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<NA> S or I X X - -
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&lt;NA&gt; S or I X X - -
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S or I R X X X X
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R R - X - X
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<NA> R - - - -
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S or I <NA> X X - -
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R <NA> - - - -
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<NA> <NA> - - - -
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&lt;NA&gt; R - - - -
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S or I &lt;NA&gt; X X - -
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R &lt;NA&gt; - - - -
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&lt;NA&gt; &lt;NA&gt; - - - -
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--------------------------------------------------------------------
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</pre>
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<p>Please note that, in combination therapies, for <code>only_all_tested = TRUE</code> applies that:</p><pre> <span class='fu'>count_S</span>() + <span class='fu'>count_I</span>() + <span class='fu'>count_R</span>() <span class='kw'>=</span> <span class='fu'>count_all</span>()
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<span class='fu'><a href='proportion.html'>proportion_S</a></span>() + <span class='fu'><a href='proportion.html'>proportion_I</a></span>() + <span class='fu'><a href='proportion.html'>proportion_R</a></span>() <span class='kw'>=</span> <span class='fl'>1</span></pre>
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<p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p><pre> count_S() + count_I() + count_R() >= count_all()
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proportion_S() + proportion_I() + proportion_R() >= 1
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<p>and that, in combination therapies, for <code>only_all_tested = FALSE</code> applies that:</p><pre> count_S() + count_I() + count_R() &gt;= count_all()
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proportion_S() + proportion_I() + proportion_R() &gt;= 1
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</pre>
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<p>Using <code>only_all_tested</code> has no impact when only using one antibiotic as input.</p>
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@ -399,7 +399,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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<span class='kw'>S</span> <span class='kw'>=</span> <span class='fu'>count_S</span>(<span class='no'>CIP</span>),
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<span class='kw'>n1</span> <span class='kw'>=</span> <span class='fu'>count_all</span>(<span class='no'>CIP</span>), <span class='co'># the actual total; sum of all three</span>
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<span class='kw'>n2</span> <span class='kw'>=</span> <span class='fu'>n_rsi</span>(<span class='no'>CIP</span>), <span class='co'># same - analogous to n_distinct</span>
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<span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/context.html'>n</a></span>()) <span class='co'># NOT the number of tested isolates!</span>
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<span class='kw'>total</span> <span class='kw'>=</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/n.html'>n</a></span>()) <span class='co'># NOT the number of tested isolates!</span>
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<span class='co'># Count co-resistance between amoxicillin/clav acid and gentamicin,</span>
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<span class='co'># so we can see that combination therapy does a lot more than mono therapy.</span>
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@ -437,7 +437,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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</div>
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<div class="pkgdown">
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.0.</p>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
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</div>
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</footer>
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