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website update

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dr. M.S. (Matthijs) Berends
2019-01-12 19:31:30 +01:00
parent 3661df7365
commit cda7087722
8 changed files with 57 additions and 39 deletions
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4
docs/reference/guess_ab_col.html
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@ -47,7 +47,7 @@
<script src="../extra.js"></script>
<meta property="og:title" content="Guess antibiotic column — guess_ab_col" />
<meta property="og:description" content="This tries to find a column name in a data set based on information from the antibiotics data set. You can look for an antibiotic (trade) of abbreviation and it will search the data for any column containing a name or ATC code of that antibiotic." />
<meta property="og:description" content="This tries to find a column name in a data set based on information from the antibiotics data set. You can look for an antibiotic (trade) name or abbreviation and it will search the data.frame for any column containing a name or ATC code of that antibiotic." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
<meta name="twitter:card" content="summary" />
@ -223,7 +223,7 @@
<div class="ref-description">
<p>This tries to find a column name in a data set based on information from the <code><a href='antibiotics.html'>antibiotics</a></code> data set. You can look for an antibiotic (trade) of abbreviation and it will search the data for any column containing a name or ATC code of that antibiotic.</p>
<p>This tries to find a column name in a data set based on information from the <code><a href='antibiotics.html'>antibiotics</a></code> data set. You can look for an antibiotic (trade) name or abbreviation and it will search the <code>data.frame</code> for any column containing a name or ATC code of that antibiotic.</p>
</div>

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docs/reference/resistance_predict.html
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@ -253,11 +253,11 @@
</tr>
<tr>
<th>year_min</th>
<td><p>lowest year to use in the prediction model, dafaults the lowest year in <code>col_date</code></p></td>
<td><p>lowest year to use in the prediction model, dafaults to the lowest year in <code>col_date</code></p></td>
</tr>
<tr>
<th>year_max</th>
<td><p>highest year to use in the prediction model, defaults to 15 years after today</p></td>
<td><p>highest year to use in the prediction model, defaults to 10 years after today</p></td>
</tr>
<tr>
<th>year_every</th>
@ -273,15 +273,15 @@
</tr>
<tr>
<th>I_as_R</th>
<td><p>treat <code>I</code> as <code>R</code></p></td>
<td><p>a logical to indicate whether values <code>I</code> should be treated as <code>R</code></p></td>
</tr>
<tr>
<th>preserve_measurements</th>
<td><p>logical to indicate whether predictions of years that are actually available in the data should be overwritten with the original data. The standard errors of those years will be <code>NA</code>.</p></td>
<td><p>a logical to indicate whether predictions of years that are actually available in the data should be overwritten by the original data. The standard errors of those years will be <code>NA</code>.</p></td>
</tr>
<tr>
<th>info</th>
<td><p>print textual analysis with the name and <code><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></code> of the model.</p></td>
<td><p>a logical to indicate whether textual analysis should be printed with the name and <code><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></code> of the statistical model.</p></td>
</tr>
</table>
@ -290,11 +290,11 @@
<p><code>data.frame</code> with columns:</p><ul>
<li><p><code>year</code></p></li>
<li><p><code>value</code>, the same as <code>estimated</code> when <code>preserve_measurements = FALSE</code>, and a combination of <code>observed</code> and <code>estimated</code> otherwise</p></li>
<li><p><code>se_min</code>, the lower bound of the standard error with a minimum of <code>0</code></p></li>
<li><p><code>se_max</code> the upper bound of the standard error with a maximum of <code>1</code></p></li>
<li><p><code>observations</code>, the total number of observations, i.e. S + I + R</p></li>
<li><p><code>observed</code>, the original observed values</p></li>
<li><p><code>estimated</code>, the estimated values, calculated by the model</p></li>
<li><p><code>se_min</code>, the lower bound of the standard error with a minimum of <code>0</code> (so the standard error will never go below 0%)</p></li>
<li><p><code>se_max</code> the upper bound of the standard error with a maximum of <code>1</code> (so the standard error will never go above 100%)</p></li>
<li><p><code>observations</code>, the total number of available observations in that year, i.e. S + I + R</p></li>
<li><p><code>observed</code>, the original observed resistant percentages</p></li>
<li><p><code>estimated</code>, the estimated resistant percentages, calculated by the model</p></li>
</ul>