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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9231</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9232</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> containing isolates. Can be left blank for automatic determination, see <em>Examples</em>.</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> containing isolates. Can be left blank for automatic determination, see <em>Examples</em>.</p></dd>
<dt id="arg-col-ab">col_ab<a class="anchor" aria-label="anchor" href="#arg-col-ab"></a></dt>
<dd><p>column name of <code>x</code> containing antimicrobial interpretations (<code>"R"</code>, <code>"I"</code> and <code>"S"</code>)</p></dd>
<dd><p>Column name of <code>x</code> containing antimicrobial interpretations (<code>"R"</code>, <code>"I"</code> and <code>"S"</code>)</p></dd>
<dt id="arg-col-date">col_date<a class="anchor" aria-label="anchor" href="#arg-col-date"></a></dt>
<dd><p>column name of the date, will be used to calculate years if this column doesn't consist of years already - the default is the first column of with a date class</p></dd>
<dd><p>Column name of the date, will be used to calculate years if this column doesn't consist of years already - the default is the first column of with a date class</p></dd>
<dt id="arg-year-min">year_min<a class="anchor" aria-label="anchor" href="#arg-year-min"></a></dt>
<dd><p>lowest year to use in the prediction model, dafaults to the lowest year in <code>col_date</code></p></dd>
<dd><p>Lowest year to use in the prediction model, dafaults to the lowest year in <code>col_date</code></p></dd>
<dt id="arg-year-max">year_max<a class="anchor" aria-label="anchor" href="#arg-year-max"></a></dt>
<dd><p>highest year to use in the prediction model - the default is 10 years after today</p></dd>
<dd><p>Highest year to use in the prediction model - the default is 10 years after today</p></dd>
<dt id="arg-year-every">year_every<a class="anchor" aria-label="anchor" href="#arg-year-every"></a></dt>
<dd><p>unit of sequence between lowest year found in the data and <code>year_max</code></p></dd>
<dd><p>Unit of sequence between lowest year found in the data and <code>year_max</code></p></dd>
<dt id="arg-minimum">minimum<a class="anchor" aria-label="anchor" href="#arg-minimum"></a></dt>
<dd><p>minimal amount of available isolates per year to include. Years containing less observations will be estimated by the model.</p></dd>
<dd><p>Minimal amount of available isolates per year to include. Years containing less observations will be estimated by the model.</p></dd>
<dt id="arg-model">model<a class="anchor" aria-label="anchor" href="#arg-model"></a></dt>
<dd><p>the statistical model of choice. This could be a generalised linear regression model with binomial distribution (i.e. using <code>glm(..., family = binomial)</code>, assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance. See <em>Details</em> for all valid options.</p></dd>
<dd><p>The statistical model of choice. This could be a generalised linear regression model with binomial distribution (i.e. using <code>glm(..., family = binomial)</code>, assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance. See <em>Details</em> for all valid options.</p></dd>
<dt id="arg-i-as-s">I_as_S<a class="anchor" aria-label="anchor" href="#arg-i-as-s"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether values <code>"I"</code> should be treated as <code>"S"</code> (will otherwise be treated as <code>"R"</code>). The default, <code>TRUE</code>, follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section <em>Interpretation of S, I and R</em> below.</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether values <code>"I"</code> should be treated as <code>"S"</code> (will otherwise be treated as <code>"R"</code>). The default, <code>TRUE</code>, follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section <em>Interpretation of S, I and R</em> below.</p></dd>
<dt id="arg-preserve-measurements">preserve_measurements<a class="anchor" aria-label="anchor" href="#arg-preserve-measurements"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> 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></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> 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></dd>
<dt id="arg-info">info<a class="anchor" aria-label="anchor" href="#arg-info"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether textual analysis should be printed with the name and <code><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary()</a></code> of the statistical model.</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether textual analysis should be printed with the name and <code><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary()</a></code> of the statistical model.</p></dd>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>arguments passed on to functions</p></dd>
<dd><p>Arguments passed on to functions</p></dd>
<dt id="arg-main">main<a class="anchor" aria-label="anchor" href="#arg-main"></a></dt>
<dd><p>title of the plot</p></dd>
<dd><p>Title of the plot</p></dd>
<dt id="arg-ribbon">ribbon<a class="anchor" aria-label="anchor" href="#arg-ribbon"></a></dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a ribbon should be shown (default) or error bars</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a ribbon should be shown (default) or error bars</p></dd>
<dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
<dd><p>model data to be plotted</p></dd>
<dd><p>Model data to be plotted</p></dd>
</dl></div>
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