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(v1.0.1.9000) first PCA implementation
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@ -78,7 +78,7 @@
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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">1.0.1</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.0.1.9000</span>
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</span>
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</div>
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Predict antimicrobial resistance
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</a>
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</li>
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<li>
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<a href="../articles/PCA.html">
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<span class="fa fa-compress"></span>
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Conduct principal component analysis for AMR
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</a>
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</li>
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<li>
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<a href="../articles/MDR.html">
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<span class="fa fa-skull-crossbones"></span>
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@ -287,12 +294,6 @@
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<p><code><a href="read.4D.html">read.4D()</a></code> </p>
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</td>
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<td><p>Read data from 4D database</p></td>
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</tr><tr>
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<td>
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<p><code><a href="rsi_translation.html">rsi_translation</a></code> </p>
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</td>
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<td><p>Data set for R/SI interpretation</p></td>
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</tr>
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</tbody><tbody>
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<tr>
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@ -371,6 +372,18 @@
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</tr>
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<tr>
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<td>
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<p><code><a href="proportion.html">resistance()</a></code> <code><a href="proportion.html">susceptibility()</a></code> <code><a href="proportion.html">proportion_R()</a></code> <code><a href="proportion.html">proportion_IR()</a></code> <code><a href="proportion.html">proportion_I()</a></code> <code><a href="proportion.html">proportion_SI()</a></code> <code><a href="proportion.html">proportion_S()</a></code> <code><a href="proportion.html">proportion_df()</a></code> <code><a href="proportion.html">rsi_df()</a></code> </p>
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</td>
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<td><p>Calculate microbial resistance</p></td>
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</tr><tr>
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<td>
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<p><code><a href="count.html">count_resistant()</a></code> <code><a href="count.html">count_susceptible()</a></code> <code><a href="count.html">count_R()</a></code> <code><a href="count.html">count_IR()</a></code> <code><a href="count.html">count_I()</a></code> <code><a href="count.html">count_SI()</a></code> <code><a href="count.html">count_S()</a></code> <code><a href="count.html">count_all()</a></code> <code><a href="count.html">n_rsi()</a></code> <code><a href="count.html">count_df()</a></code> </p>
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</td>
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<td><p>Count available isolates</p></td>
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</tr><tr>
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<td>
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<p><code><a href="availability.html">availability()</a></code> </p>
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</td>
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@ -384,9 +397,15 @@
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</tr><tr>
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<td>
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<p><code><a href="count.html">count_resistant()</a></code> <code><a href="count.html">count_susceptible()</a></code> <code><a href="count.html">count_R()</a></code> <code><a href="count.html">count_IR()</a></code> <code><a href="count.html">count_I()</a></code> <code><a href="count.html">count_SI()</a></code> <code><a href="count.html">count_S()</a></code> <code><a href="count.html">count_all()</a></code> <code><a href="count.html">n_rsi()</a></code> <code><a href="count.html">count_df()</a></code> </p>
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<p><code><a href="resistance_predict.html">resistance_predict()</a></code> <code><a href="resistance_predict.html">rsi_predict()</a></code> <code><a href="resistance_predict.html">plot(<i><resistance_predict></i>)</a></code> <code><a href="resistance_predict.html">ggplot_rsi_predict()</a></code> </p>
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</td>
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<td><p>Count available isolates</p></td>
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<td><p>Predict antimicrobial resistance</p></td>
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</tr><tr>
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<td>
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<p><code><a href="pca.html">prcomp(<i><data.frame></i>)</a></code> <code><a href="pca.html">pca()</a></code> </p>
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</td>
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<td><p>Principal Component Analysis (for AMR)</p></td>
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</tr><tr>
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<td>
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<td><p>AMR plots with <code>ggplot2</code></p></td>
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</tr><tr>
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<td>
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<p><code><a href="ggplot_pca.html">ggplot_pca()</a></code> </p>
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</td>
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<td><p>PCA biplot with <code>ggplot2</code></p></td>
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</tr><tr>
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<td>
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<p><code><a href="kurtosis.html">kurtosis()</a></code> </p>
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</td>
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<td><p>Kurtosis of the sample</p></td>
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</tr><tr>
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<td>
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<p><code><a href="proportion.html">resistance()</a></code> <code><a href="proportion.html">susceptibility()</a></code> <code><a href="proportion.html">proportion_R()</a></code> <code><a href="proportion.html">proportion_IR()</a></code> <code><a href="proportion.html">proportion_I()</a></code> <code><a href="proportion.html">proportion_SI()</a></code> <code><a href="proportion.html">proportion_S()</a></code> <code><a href="proportion.html">proportion_df()</a></code> <code><a href="proportion.html">rsi_df()</a></code> </p>
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</td>
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<td><p>Calculate microbial resistance</p></td>
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</tr><tr>
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<td>
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<p><code><a href="resistance_predict.html">resistance_predict()</a></code> <code><a href="resistance_predict.html">rsi_predict()</a></code> <code><a href="resistance_predict.html">plot(<i><resistance_predict></i>)</a></code> <code><a href="resistance_predict.html">ggplot_rsi_predict()</a></code> </p>
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</td>
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<td><p>Predict antimicrobial resistance</p></td>
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</tr><tr>
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<td>
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<p><code><a href="skewness.html">skewness()</a></code> </p>
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</td>
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</tr>
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<tr>
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<td>
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<p><code><a href="microorganisms.html">microorganisms</a></code> </p>
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</td>
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<td><p>Data set with ~70,000 microorganisms</p></td>
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</tr><tr>
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<td>
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<p><code><a href="antibiotics.html">antibiotics</a></code> <code><a href="antibiotics.html">antivirals</a></code> </p>
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</td>
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<td><p>Data set with unclean data</p></td>
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</tr><tr>
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<td>
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<p><code><a href="rsi_translation.html">rsi_translation</a></code> </p>
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</td>
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<td><p>Data set for R/SI interpretation</p></td>
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</tr><tr>
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<td>
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<p><code><a href="microorganisms.codes.html">microorganisms.codes</a></code> </p>
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</td>
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@ -469,12 +494,6 @@
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<td><p>Data set with previously accepted taxonomic names</p></td>
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</tr><tr>
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<td>
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<p><code><a href="microorganisms.html">microorganisms</a></code> </p>
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</td>
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<td><p>Data set with ~70,000 microorganisms</p></td>
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</tr><tr>
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<td>
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<p><code><a href="WHONET.html">WHONET</a></code> </p>
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</td>
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