Fix checks and tests

Static documentation rebuilt by pkgdown
author: Johannes Ranke <jranke@uni-bremen.de> 2019-10-26 22:52:53 +0200
committer: Johannes Ranke <jranke@uni-bremen.de> 2019-10-26 22:52:53 +0200
commit: 6e5630a0df7e857697ff2ce4730a5f7f45b67377 (patch)
tree: 1d65d0b5c0540b1ae1ab160ed3c6cd1c50a4446f /docs
parent: cb03bf1fb1e6326f06029969663f3399af96b05d (diff)
5 files changed, 477 insertions, 6 deletions
diff --git a/docs/news/index.html b/docs/news/index.html
index 67f64150..1322f75d 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -134,6 +134,7 @@
 <a href="#mkin-0-9-49-6-unreleased" class="anchor"></a>mkin 0.9.49.6 (unreleased)<small> Unreleased </small>
 </h1>
 <ul>
+<li><p>Add ‘parms’ and ‘confint’ methods for mkinfit objects. Confidence intervals based on the quadratic approximation as in the summary, and based on the profile likelihood</p></li>
 <li><p>Move long-running tests to tests/testthat/slow with a separate test log. They currently take around 7 minutes on my system</p></li>
 <li><p>‘mkinfit’: Clean the code and return functions to calculate the log-likelihood and the sum of squared residuals</p></li>
 <li><p>Vignette ‘twa.html’: Add the maximum time weighted average formulas for the hockey stick model</p></li>
diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html
new file mode 100644
index 00000000..64ea0d4c
--- /dev/null
+++ b/docs/reference/confint.mkinfit.html
@@ -0,0 +1,252 @@
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+      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
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+      <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
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+    <div class="page-header">
+    <h1>Confidence intervals for parameters of mkinfit objects</h1>
+    
+    <div class="hidden name"><code>confint.mkinfit.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>Confidence intervals for parameters of mkinfit objects</p>
+    </div>
+
+    <pre class="usage"><span class='co'># S3 method for mkinfit</span>
+<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>object</span>, <span class='no'>parm</span>, <span class='kw'>level</span> <span class='kw'>=</span> <span class='fl'>0.95</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>1</span> -
+  <span class='no'>level</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"profile"</span>, <span class='st'>"quadratic"</span>), <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+  <span class='kw'>backtransform</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>distribution</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"student_t"</span>, <span class='st'>"normal"</span>),
+  <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
+
+    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+    <table class="ref-arguments">
+    <colgroup><col class="name" /><col class="desc" /></colgroup>
+    <tr>
+      <th>object</th>
+      <td><p>An <code><a href='mkinfit.html'>mkinfit</a></code> object</p></td>
+    </tr>
+    <tr>
+      <th>parm</th>
+      <td><p>A vector of names of the parameters which are to be given
+confidence intervals. If missing, all parameters are considered.</p></td>
+    </tr>
+    <tr>
+      <th>level</th>
+      <td><p>The confidence level required</p></td>
+    </tr>
+    <tr>
+      <th>alpha</th>
+      <td><p>The allowed error probability, overrides 'level' if specified.</p></td>
+    </tr>
+    <tr>
+      <th>method</th>
+      <td><p>The 'profile' method searches the parameter space for the
+cutoff of the confidence intervals by means of a likelihood ratio test.
+The 'quadratic' method approximates the likelihood function at the
+optimised parameters using the second term of the Taylor expansion, using
+a second derivative (hessian) contained in the object.</p></td>
+    </tr>
+    <tr>
+      <th>transformed</th>
+      <td><p>If the quadratic approximation is used, should it be
+applied to the likelihood based on the transformed parameters?</p></td>
+    </tr>
+    <tr>
+      <th>backtransform</th>
+      <td><p>If we approximate the likelihood in terms of the
+transformed parameters, should we backtransform the parameters with
+their confidence intervals?</p></td>
+    </tr>
+    <tr>
+      <th>distribution</th>
+      <td><p>For the quadratic approximation, should we use
+the student t distribution or assume normal distribution for
+the parameter estimate</p></td>
+    </tr>
+    <tr>
+      <th>quiet</th>
+      <td><p>Should we suppress messages?</p></td>
+    </tr>
+    <tr>
+      <th>...</th>
+      <td><p>Not used</p></td>
+    </tr>
+    </table>
+
+    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+    <p>A matrix with columns giving lower and upper confidence limits for
+  each parameter.</p>
+    <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+
+    <p>Pawitan Y (2013) In all likelihood - Statistical modelling and
+  inference using likelihood. Clarendon Press, Oxford.</p>
+
+    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+    <pre class="examples"><div class='input'><span class='no'>f</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"SFO"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>)</div><div class='output co'>#&gt;                     2.5%      97.5%
+#&gt; parent_0      71.8242430 93.1600766
+#&gt; k_parent_sink  0.2109541  0.4440528
+#&gt; sigma          1.9778868  7.3681380</div><div class='input'><span class='co'># \dontrun{</span>
+  <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"profile"</span>)</div><div class='output co'>#&gt; <span class='message'>Profiling the likelihood</span></div><div class='output co'>#&gt;                     2.5%      97.5%
+#&gt; parent_0      71.3471007 93.9447024
+#&gt; k_parent_sink  0.2030765  0.4491067
+#&gt; sigma          2.9810656  8.8633278</div><div class='input'># }
+</div></pre>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+    <h2>Contents</h2>
+    <ul class="nav nav-pills nav-stacked">
+      <li><a href="#arguments">Arguments</a></li>
+      <li><a href="#value">Value</a></li>
+      <li><a href="#references">References</a></li>
+      <li><a href="#examples">Examples</a></li>
+    </ul>
+
+  </div>
+</div>
+
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diff --git a/docs/reference/index.html b/docs/reference/index.html
index 328f5aca..fa424060 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -185,12 +185,30 @@ more datasets</p></td>
       </tr><tr>
         
         <td>
+          <p><code><a href="parms.html">parms()</a></code> </p>
+        </td>
+        <td><p>Extract model parameters from mkinfit models</p></td>
+      </tr><tr>
+        
+        <td>
+          <p><code><a href="confint.mkinfit.html">confint(<i>&lt;mkinfit&gt;</i>)</a></code> </p>
+        </td>
+        <td><p>Confidence intervals for parameters of mkinfit objects</p></td>
+      </tr><tr>
+        
+        <td>
           <p><code><a href="summary.mkinfit.html">summary(<i>&lt;mkinfit&gt;</i>)</a></code> <code><a href="summary.mkinfit.html">print(<i>&lt;summary.mkinfit&gt;</i>)</a></code> </p>
         </td>
         <td><p>Summary method for class "mkinfit"</p></td>
       </tr><tr>
         
         <td>
+          <p><code><a href="logLik.mkinfit.html">logLik(<i>&lt;mkinfit&gt;</i>)</a></code> </p>
+        </td>
+        <td><p>Calculated the log-likelihood of a fitted mkinfit object</p></td>
+      </tr><tr>
+        
+        <td>
           <p><code><a href="mkinresplot.html">mkinresplot()</a></code> </p>
         </td>
         <td><p>Function to plot residuals stored in an mkin object</p></td>
@@ -219,12 +237,6 @@ with mkinfit</p></td>
           <p><code><a href="mkinerrmin.html">mkinerrmin()</a></code> </p>
         </td>
         <td><p>Calculate the minimum error to assume in order to pass the variance test</p></td>
-      </tr><tr>
-        
-        <td>
-          <p><code><a href="logLik.mkinfit.html">logLik(<i>&lt;mkinfit&gt;</i>)</a></code> </p>
-        </td>
-        <td><p>Calculated the log-likelihood of a fitted mkinfit object</p></td>
       </tr>
     </tbody><tbody>
       <tr>
diff --git a/docs/reference/parms.html b/docs/reference/parms.html
new file mode 100644
index 00000000..8ab26240
--- /dev/null
+++ b/docs/reference/parms.html
@@ -0,0 +1,200 @@
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+    </li>
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+    </li>
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+      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+    </li>
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+      <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+    </li>
+    <li>
+      <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
+    </li>
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+    <div class="page-header">
+    <h1>Extract model parameters from mkinfit models</h1>
+    
+    <div class="hidden name"><code>parms.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>This function always returns degradation model parameters as well as error
+model parameters, in order to avoid working with a fitted model without
+considering the error structure that was assumed for the fit.</p>
+    </div>
+
+    <pre class="usage"><span class='fu'>parms</span>(<span class='no'>object</span>, <span class='no'>...</span>)
+
+<span class='co'># S3 method for mkinfit</span>
+<span class='fu'>parms</span>(<span class='no'>object</span>, <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
+
+    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+    <table class="ref-arguments">
+    <colgroup><col class="name" /><col class="desc" /></colgroup>
+    <tr>
+      <th>object</th>
+      <td><p>A fitted model object</p></td>
+    </tr>
+    <tr>
+      <th>...</th>
+      <td><p>Not used</p></td>
+    </tr>
+    <tr>
+      <th>transformed</th>
+      <td><p>Should the parameters be returned
+as used internally during the optimisation?</p></td>
+    </tr>
+    </table>
+
+    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+    <p>A numeric vector of fitted model parameters</p>
+
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+    <h2>Contents</h2>
+    <ul class="nav nav-pills nav-stacked">
+      <li><a href="#arguments">Arguments</a></li>
+      <li><a href="#value">Value</a></li>
+    </ul>
+
+  </div>
+</div>
+
+
+      <footer>
+      <div class="copyright">
+  <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+</div>
+
+      </footer>
+   </div>
+
+  
+
+
+  </body>
+</html>
+
+
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index b62b9a44..9e3363ba 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -55,6 +55,9 @@
     <loc>https://pkgdown.jrwb.de/mkin/reference/add_err.html</loc>
   </url>
   <url>
+    <loc>https://pkgdown.jrwb.de/mkin/reference/confint.mkinfit.html</loc>
+  </url>
+  <url>
     <loc>https://pkgdown.jrwb.de/mkin/reference/endpoints.html</loc>
   </url>
   <url>
@@ -118,6 +121,9 @@
     <loc>https://pkgdown.jrwb.de/mkin/reference/nafta.html</loc>
   </url>
   <url>
+    <loc>https://pkgdown.jrwb.de/mkin/reference/parms.html</loc>
+  </url>
+  <url>
     <loc>https://pkgdown.jrwb.de/mkin/reference/plot.mkinfit.html</loc>
   </url>
   <url>
author	Johannes Ranke <jranke@uni-bremen.de>	2019-10-26 22:52:53 +0200
committer	Johannes Ranke <jranke@uni-bremen.de>	2019-10-26 22:52:53 +0200
commit	6e5630a0df7e857697ff2ce4730a5f7f45b67377 (patch)
tree	1d65d0b5c0540b1ae1ab160ed3c6cd1c50a4446f /docs
parent	cb03bf1fb1e6326f06029969663f3399af96b05d (diff)