Fix inverse predictions for replicate measurements

For details, see NEWS.md

11 files changed, 517 insertions, 105 deletions

diff --git a/docs/reference/calplot.lm.html b/docs/reference/calplot.lm.html
index 7eda066..a5b3bbb 100644
--- a/docs/reference/calplot.lm.html
+++ b/docs/reference/calplot.lm.html
@@ -62,17 +62,26 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chemCal</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.1.37.9001</span>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.2.1</span>
       </span>
     </div>
 
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="../reference/index.html">Functions and data</a>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
 </li>
 <li>
-  <a href="../articles/chemCal.pdf">Short manual (pdf)</a>
+  <a href="../articles/chemCal.html">Get started</a>
+</li>
+<li>
+  <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+  <a href="../news/index.html">Changelog</a>
 </li>
       </ul>
       
@@ -134,7 +143,7 @@
       <th>alpha</th>
       <td><p>The error tolerance level for the confidence and prediction bands. Note that this 
     includes both tails of the Gaussian distribution, unlike the alpha and beta parameters
-    used in <code>lod</code> (see note below).</p></td>
+    used in <code><a href='lod.html'>lod</a></code> (see note below).</p></td>
     </tr>
     <tr>
       <th>varfunc</th>
@@ -157,7 +166,7 @@
   the internally used function <code>predict.lm</code>, therefore,
   <code>calplot</code> does not draw prediction bands for such models.</p>  
 <p>It is possible to compare the <code>calplot</code> prediction bands with the
-  <code>lod</code> values if the <code>lod()</code> alpha and beta parameters are
+  <code><a href='lod.html'>lod</a></code> values if the <code><a href='lod.html'>lod()</a></code> alpha and beta parameters are
   half the value of the <code>calplot()</code> alpha parameter.</p>
     
 
diff --git a/docs/reference/chemCal-package.html b/docs/reference/chemCal-package.html
index 8e6f39b..cadd357 100644
--- a/docs/reference/chemCal-package.html
+++ b/docs/reference/chemCal-package.html
@@ -61,17 +61,26 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chemCal</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.1.37.9001</span>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.2.1</span>
       </span>
     </div>
 
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="../reference/index.html">Functions and data</a>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
 </li>
 <li>
-  <a href="../articles/chemCal.pdf">Short manual (pdf)</a>
+  <a href="../articles/chemCal.html">Get started</a>
+</li>
+<li>
+  <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+  <a href="../news/index.html">Changelog</a>
 </li>
       </ul>
       
diff --git a/docs/reference/din32645.html b/docs/reference/din32645.html
index 03170e0..dbc9504 100644
--- a/docs/reference/din32645.html
+++ b/docs/reference/din32645.html
@@ -61,17 +61,26 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chemCal</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.1.37.9001</span>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.2.1</span>
       </span>
     </div>
 
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="../reference/index.html">Functions and data</a>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
 </li>
 <li>
-  <a href="../articles/chemCal.pdf">Short manual (pdf)</a>
+  <a href="../articles/chemCal.html">Get started</a>
+</li>
+<li>
+  <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+  <a href="../news/index.html">Changelog</a>
 </li>
       </ul>
       
@@ -118,33 +127,17 @@
     
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>din32645</span>)
-<span class='no'>m</span> <span class='kw'>&lt;-</span> <span class='fu'>lm</span>(<span class='no'>y</span> ~ <span class='no'>x</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='no'>din32645</span>)
-<span class='fu'>calplot</span>(<span class='no'>m</span>)</div><div class='img'><img src='din32645-1.png' alt='' width='700' height='433' /></div><div class='input'>
+    <pre class="examples"><div class='input'><span class='no'>m</span> <span class='kw'>&lt;-</span> <span class='fu'>lm</span>(<span class='no'>y</span> ~ <span class='no'>x</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='no'>din32645</span>)
+<span class='fu'><a href='calplot.lm.html'>calplot</a></span>(<span class='no'>m</span>)</div><div class='img'><img src='din32645-1.png' alt='' width='700' height='433' /></div><div class='input'>
 <span class='co'>## Prediction of x with confidence interval</span>
-(<span class='no'>prediction</span> <span class='kw'>&lt;-</span> <span class='fu'>inverse.predict</span>(<span class='no'>m</span>, <span class='fl'>3500</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.01</span>))</div><div class='output co'>#&gt; $Prediction
-#&gt; [1] 0.1054792
-#&gt; 
-#&gt; $`Standard Error`
-#&gt; [1] 0.02215619
-#&gt; 
-#&gt; $Confidence
-#&gt; [1] 0.07434261
-#&gt; 
-#&gt; $`Confidence Limits`
-#&gt; [1] 0.03113656 0.17982178
-#&gt; </div><div class='input'>
+<span class='no'>prediction</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='inverse.predict.html'>inverse.predict</a></span>(<span class='no'>m</span>, <span class='fl'>3500</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.01</span>)
+
 <span class='co'># This should give 0.07434 according to test data from Dintest, which </span>
 <span class='co'># was collected from Procontrol 3.1 (isomehr GmbH) in this case</span>
-<span class='fu'>round</span>(<span class='no'>prediction</span>$<span class='no'>Confidence</span>,<span class='fl'>5</span>)</div><div class='output co'>#&gt; [1] 0.07434</div><div class='input'>
+<span class='fu'>round</span>(<span class='no'>prediction</span>$<span class='no'>Confidence</span>, <span class='fl'>5</span>)</div><div class='output co'>#&gt; [1] 0.07434</div><div class='input'>
 <span class='co'>## Critical value:</span>
-(<span class='no'>crit</span> <span class='kw'>&lt;-</span> <span class='fu'>lod</span>(<span class='no'>m</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.01</span>, <span class='kw'>beta</span> <span class='kw'>=</span> <span class='fl'>0.5</span>))</div><div class='output co'>#&gt; $x
-#&gt; [1] 0.0698127
-#&gt; 
-#&gt; $y
-#&gt;        1 
-#&gt; 3155.393 
-#&gt; </div><div class='input'>
+<span class='no'>crit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='lod.html'>lod</a></span>(<span class='no'>m</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.01</span>, <span class='kw'>beta</span> <span class='kw'>=</span> <span class='fl'>0.5</span>)
+
 <span class='co'># According to DIN 32645, we should get 0.07 for the critical value</span>
 <span class='co'># (decision limit, "Nachweisgrenze")</span>
 <span class='fu'>round</span>(<span class='no'>crit</span>$<span class='no'>x</span>, <span class='fl'>2</span>)</div><div class='output co'>#&gt; [1] 0.07</div><div class='input'><span class='co'># and according to Dintest test data, we should get 0.0698 from</span>
@@ -153,21 +146,16 @@
 <span class='co'># In German, the smallest detectable value is the "Erfassungsgrenze", and we</span>
 <span class='co'># should get 0.14 according to DIN, which we achieve by using the method </span>
 <span class='co'># described in it:</span>
-<span class='no'>lod.din</span> <span class='kw'>&lt;-</span> <span class='fu'>lod</span>(<span class='no'>m</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.01</span>, <span class='kw'>beta</span> <span class='kw'>=</span> <span class='fl'>0.01</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"din"</span>)
+<span class='no'>lod.din</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='lod.html'>lod</a></span>(<span class='no'>m</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.01</span>, <span class='kw'>beta</span> <span class='kw'>=</span> <span class='fl'>0.01</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"din"</span>)
 <span class='fu'>round</span>(<span class='no'>lod.din</span>$<span class='no'>x</span>, <span class='fl'>2</span>)</div><div class='output co'>#&gt; [1] 0.14</div><div class='input'>
 <span class='co'>## Limit of quantification</span>
 <span class='co'># This accords to the test data coming with the test data from Dintest again, </span>
 <span class='co'># except for the last digits of the value cited for Procontrol 3.1 (0.2121)</span>
-(<span class='no'>loq</span> <span class='kw'>&lt;-</span> <span class='fu'>loq</span>(<span class='no'>m</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.01</span>))</div><div class='output co'>#&gt; $x
-#&gt; [1] 0.2119575
-#&gt; 
-#&gt; $y
-#&gt;        1 
-#&gt; 4528.787 
-#&gt; </div><div class='input'><span class='fu'>round</span>(<span class='no'>loq</span>$<span class='no'>x</span>,<span class='fl'>4</span>)</div><div class='output co'>#&gt; [1] 0.212</div><div class='input'>
+<span class='no'>loq</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='loq.html'>loq</a></span>(<span class='no'>m</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.01</span>)
+<span class='fu'>round</span>(<span class='no'>loq</span>$<span class='no'>x</span>, <span class='fl'>4</span>)</div><div class='output co'>#&gt; [1] 0.212</div><div class='input'>
 <span class='co'># A similar value is obtained using the approximation </span>
 <span class='co'># LQ = 3.04 * LC (Currie 1999, p. 120)</span>
-<span class='fl'>3.04</span> * <span class='fu'>lod</span>(<span class='no'>m</span>,<span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.01</span>, <span class='kw'>beta</span> <span class='kw'>=</span> <span class='fl'>0.5</span>)$<span class='no'>x</span></div><div class='output co'>#&gt; [1] 0.2122306</div></pre>
+<span class='fl'>3.04</span> * <span class='fu'><a href='lod.html'>lod</a></span>(<span class='no'>m</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.01</span>, <span class='kw'>beta</span> <span class='kw'>=</span> <span class='fl'>0.5</span>)$<span class='no'>x</span></div><div class='output co'>#&gt; [1] 0.2122306</div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index ce4f346..d314ec2 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -58,17 +58,26 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chemCal</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.1.37.9001</span>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.2.1</span>
       </span>
     </div>
 
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="../reference/index.html">Functions and data</a>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
 </li>
 <li>
-  <a href="../articles/chemCal.pdf">Short manual (pdf)</a>
+  <a href="../articles/chemCal.html">Get started</a>
+</li>
+<li>
+  <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+  <a href="../news/index.html">Changelog</a>
 </li>
       </ul>
       
@@ -152,6 +161,18 @@
           <p><code><a href="massart97ex3.html">massart97ex3</a></code> </p>
         </td>
         <td><p>Calibration data from Massart et al. (1997), example 3</p></td>
+      </tr><tr>
+        
+        <td>
+          <p><code><a href="rl95_toluene.html">rl95_toluene</a></code> </p>
+        </td>
+        <td><p>Toluene amounts by GC/MS as reported by Rocke and Lorenzato (1995)</p></td>
+      </tr><tr>
+        
+        <td>
+          <p><code><a href="utstats14.html">utstats14</a></code> </p>
+        </td>
+        <td><p>Example data for calibration with replicates from University of Toronto</p></td>
       </tr>
     </tbody>
     </table>
diff --git a/docs/reference/inverse.predict.html b/docs/reference/inverse.predict.html
index 672e322..b107154 100644
--- a/docs/reference/inverse.predict.html
+++ b/docs/reference/inverse.predict.html
@@ -70,17 +70,26 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chemCal</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.1.37.9001</span>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.2.1</span>
       </span>
     </div>
 
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="../reference/index.html">Functions and data</a>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
 </li>
 <li>
-  <a href="../articles/chemCal.pdf">Short manual (pdf)</a>
+  <a href="../articles/chemCal.html">Get started</a>
+</li>
+<li>
+  <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+  <a href="../news/index.html">Changelog</a>
 </li>
       </ul>
       
@@ -164,7 +173,11 @@
     
     <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
 
-    <p>The function was validated with examples 7 and 8 from Massart et al. (1997).</p>
+    <p>The function was validated with examples 7 and 8 from Massart et al. (1997). 
+  Note that the behaviour of inverse.predict changed with chemCal version
+  0.2.1. Confidence intervals for x values obtained from calibrations with
+  replicate measurements did not take the variation about the means into account.
+  Please refer to the vignette for details.</p>
     
     <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
 
@@ -175,7 +188,6 @@
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'><span class='co'># This is example 7 from Chapter 8 in Massart et al. (1997)</span>
-<span class='fu'>data</span>(<span class='no'>massart97ex1</span>)
 <span class='no'>m</span> <span class='kw'>&lt;-</span> <span class='fu'>lm</span>(<span class='no'>y</span> ~ <span class='no'>x</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='no'>massart97ex1</span>)
 <span class='fu'>inverse.predict</span>(<span class='no'>m</span>, <span class='fl'>15</span>)        <span class='co'>#  6.1 +- 4.9</span></div><div class='output co'>#&gt; $Prediction
 #&gt; [1] 6.09381
@@ -210,7 +222,44 @@
 #&gt; 
 #&gt; $`Confidence Limits`
 #&gt; [1] 40.77134 47.10832
-#&gt; </div></pre>
+#&gt; </div><div class='input'>
+<span class='co'># For reproducing the results for replicate standard measurements in example 8,</span>
+<span class='co'># we need to do the calibration on the means when using chemCal &gt; 0.2</span>
+<span class='no'>weights</span> <span class='kw'>&lt;-</span> <span class='fu'>with</span>(<span class='no'>massart97ex3</span>, {
+  <span class='no'>yx</span> <span class='kw'>&lt;-</span> <span class='fu'>split</span>(<span class='no'>y</span>, <span class='no'>x</span>)
+  <span class='no'>ybar</span> <span class='kw'>&lt;-</span> <span class='fu'>sapply</span>(<span class='no'>yx</span>, <span class='no'>mean</span>)
+  <span class='no'>s</span> <span class='kw'>&lt;-</span> <span class='fu'>round</span>(<span class='fu'>sapply</span>(<span class='no'>yx</span>, <span class='no'>sd</span>), <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>2</span>)
+  <span class='no'>w</span> <span class='kw'>&lt;-</span> <span class='fu'>round</span>(<span class='fl'>1</span> / (<span class='no'>s</span>^<span class='fl'>2</span>), <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>3</span>)
+})
+
+<span class='no'>massart97ex3.means</span> <span class='kw'>&lt;-</span> <span class='fu'>aggregate</span>(<span class='no'>y</span> ~ <span class='no'>x</span>, <span class='no'>massart97ex3</span>, <span class='no'>mean</span>)
+
+<span class='no'>m3.means</span> <span class='kw'>&lt;-</span> <span class='fu'>lm</span>(<span class='no'>y</span> ~ <span class='no'>x</span>, <span class='kw'>w</span> <span class='kw'>=</span> <span class='no'>weights</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='no'>massart97ex3.means</span>)
+
+<span class='fu'>inverse.predict</span>(<span class='no'>m3.means</span>, <span class='fl'>15</span>, <span class='kw'>ws</span> <span class='kw'>=</span> <span class='fl'>1.67</span>)  <span class='co'># 5.9 +- 2.5</span></div><div class='output co'>#&gt; $Prediction
+#&gt; [1] 5.865367
+#&gt; 
+#&gt; $`Standard Error`
+#&gt; [1] 0.8926109
+#&gt; 
+#&gt; $Confidence
+#&gt; [1] 2.478285
+#&gt; 
+#&gt; $`Confidence Limits`
+#&gt; [1] 3.387082 8.343652
+#&gt; </div><div class='input'><span class='fu'>inverse.predict</span>(<span class='no'>m3.means</span>, <span class='fl'>90</span>, <span class='kw'>ws</span> <span class='kw'>=</span> <span class='fl'>0.145</span>) <span class='co'># 44.1 +- 7.9</span></div><div class='output co'>#&gt; $Prediction
+#&gt; [1] 44.06025
+#&gt; 
+#&gt; $`Standard Error`
+#&gt; [1] 2.829162
+#&gt; 
+#&gt; $Confidence
+#&gt; [1] 7.855012
+#&gt; 
+#&gt; $`Confidence Limits`
+#&gt; [1] 36.20523 51.91526
+#&gt; </div><div class='input'>
+</div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
diff --git a/docs/reference/lod.html b/docs/reference/lod.html
index 7519f19..b3d9574 100644
--- a/docs/reference/lod.html
+++ b/docs/reference/lod.html
@@ -68,17 +68,26 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chemCal</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.1.37.9001</span>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.2.1</span>
       </span>
     </div>
 
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="../reference/index.html">Functions and data</a>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
 </li>
 <li>
-  <a href="../articles/chemCal.pdf">Short manual (pdf)</a>
+  <a href="../articles/chemCal.html">Get started</a>
+</li>
+<li>
+  <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+  <a href="../news/index.html">Changelog</a>
 </li>
       </ul>
       
@@ -184,18 +193,16 @@
     
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
-    <div class='dont-index'><p>Examples for <code>din32645</code></p></div>
+    <div class='dont-index'><p>Examples for <code><a href='din32645.html'>din32645</a></code></p></div>
     
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>din32645</span>)
-<span class='no'>m</span> <span class='kw'>&lt;-</span> <span class='fu'>lm</span>(<span class='no'>y</span> ~ <span class='no'>x</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='no'>din32645</span>)
+    <pre class="examples"><div class='input'><span class='no'>m</span> <span class='kw'>&lt;-</span> <span class='fu'>lm</span>(<span class='no'>y</span> ~ <span class='no'>x</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='no'>din32645</span>)
 <span class='fu'>lod</span>(<span class='no'>m</span>)</div><div class='output co'>#&gt; $x
 #&gt; [1] 0.08655484
 #&gt; 
 #&gt; $y
-#&gt;        1 
-#&gt; 3317.154 
+#&gt; [1] 3317.154
 #&gt; </div><div class='input'>
 <span class='co'># The critical value (decision limit, German Nachweisgrenze) can be obtained</span>
 <span class='co'># by using beta = 0.5:</span>
@@ -203,8 +210,7 @@
 #&gt; [1] 0.0698127
 #&gt; 
 #&gt; $y
-#&gt;        1 
-#&gt; 3155.393 
+#&gt; [1] 3155.393
 #&gt; </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
diff --git a/docs/reference/loq.html b/docs/reference/loq.html
index 09567db..eee0925 100644
--- a/docs/reference/loq.html
+++ b/docs/reference/loq.html
@@ -67,17 +67,26 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chemCal</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.1.37.9001</span>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.2.1</span>
       </span>
     </div>
 
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="../reference/index.html">Functions and data</a>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
 </li>
 <li>
-  <a href="../articles/chemCal.pdf">Short manual (pdf)</a>
+  <a href="../articles/chemCal.html">Get started</a>
+</li>
+<li>
+  <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+  <a href="../news/index.html">Changelog</a>
 </li>
       </ul>
       
@@ -108,7 +117,7 @@
     $$L = k c(L)$$
   where c(L) is half of the length of the confidence interval at the limit L
   (DIN 32645, equivalent to ISO 11843). c(L) is internally estimated by
-  <code>inverse.predict</code>, and L is obtained by iteration.</p>
+  <code><a href='inverse.predict.html'>inverse.predict</a></code>, and L is obtained by iteration.</p>
     
     </div>
 
@@ -150,7 +159,7 @@
       <th>w.loq</th>
       <td><p>The weight that should be attributed to the LOQ. Defaults
     to one for unweighted regression, and to the mean of the weights
-    for weighted regression. See <code>massart97ex3</code> for 
+    for weighted regression. See <code><a href='massart97ex3.html'>massart97ex3</a></code> for 
     an example how to take advantage of knowledge about the 
     variance function.</p></td>
     </tr>
@@ -180,27 +189,23 @@
     
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
-    <div class='dont-index'><p>Examples for <code>din32645</code></p></div>
+    <div class='dont-index'><p>Examples for <code><a href='din32645.html'>din32645</a></code></p></div>
     
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>massart97ex3</span>)
-<span class='fu'>attach</span>(<span class='no'>massart97ex3</span>)
-<span class='no'>m</span> <span class='kw'>&lt;-</span> <span class='fu'>lm</span>(<span class='no'>y</span> ~ <span class='no'>x</span>)
+    <pre class="examples"><div class='input'><span class='no'>m</span> <span class='kw'>&lt;-</span> <span class='fu'>lm</span>(<span class='no'>y</span> ~ <span class='no'>x</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='no'>massart97ex1</span>)
 <span class='fu'>loq</span>(<span class='no'>m</span>)</div><div class='output co'>#&gt; $x
 #&gt; [1] 13.97764
 #&gt; 
 #&gt; $y
-#&gt;       1 
-#&gt; 30.6235 
+#&gt; [1] 30.6235
 #&gt; </div><div class='input'>
 <span class='co'># We can get better by using replicate measurements</span>
 <span class='fu'>loq</span>(<span class='no'>m</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>3</span>)</div><div class='output co'>#&gt; $x
 #&gt; [1] 9.971963
 #&gt; 
 #&gt; $y
-#&gt;        1 
-#&gt; 22.68539 
+#&gt; [1] 22.68539
 #&gt; </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
diff --git a/docs/reference/massart97ex1.html b/docs/reference/massart97ex1.html
index ddd1ce1..844023f 100644
--- a/docs/reference/massart97ex1.html
+++ b/docs/reference/massart97ex1.html
@@ -61,17 +61,26 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chemCal</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.1.37.9001</span>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.2.1</span>
       </span>
     </div>
 
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="../reference/index.html">Functions and data</a>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
 </li>
 <li>
-  <a href="../articles/chemCal.pdf">Short manual (pdf)</a>
+  <a href="../articles/chemCal.html">Get started</a>
+</li>
+<li>
+  <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+  <a href="../news/index.html">Changelog</a>
 </li>
       </ul>
       
diff --git a/docs/reference/massart97ex3.html b/docs/reference/massart97ex3.html
index 434fc7b..e9fa06a 100644
--- a/docs/reference/massart97ex3.html
+++ b/docs/reference/massart97ex3.html
@@ -61,17 +61,26 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">chemCal</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.1.37.9001</span>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.2.1</span>
       </span>
     </div>
 
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="../reference/index.html">Functions and data</a>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
 </li>
 <li>
-  <a href="../articles/chemCal.pdf">Short manual (pdf)</a>
+  <a href="../articles/chemCal.html">Get started</a>
+</li>
+<li>
+  <a href="../reference/index.html">Reference</a>
+</li>
+<li>
+  <a href="../news/index.html">Changelog</a>
 </li>
       </ul>
       
@@ -100,7 +109,7 @@
     
     </div>
 
-    <pre class="usage"><span class='fu'>data</span>(<span class='no'>massart97ex3</span>)</pre>
+    <pre class="usage"><span class='no'>massart97ex3</span></pre>
         
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
@@ -115,18 +124,21 @@
     
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>massart97ex3</span>)
-<span class='fu'>attach</span>(<span class='no'>massart97ex3</span>)</div><div class='output co'>#&gt; <span class='message'>The following objects are masked from massart97ex3 (pos = 3):</span>
-#&gt; <span class='message'></span>
-#&gt; <span class='message'>    x, y</span></div><div class='input'><span class='no'>yx</span> <span class='kw'>&lt;-</span> <span class='fu'>split</span>(<span class='no'>y</span>, <span class='no'>x</span>)
-<span class='no'>ybar</span> <span class='kw'>&lt;-</span> <span class='fu'>sapply</span>(<span class='no'>yx</span>, <span class='no'>mean</span>)
-<span class='no'>s</span> <span class='kw'>&lt;-</span> <span class='fu'>round</span>(<span class='fu'>sapply</span>(<span class='no'>yx</span>, <span class='no'>sd</span>), <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>2</span>)
-<span class='no'>w</span> <span class='kw'>&lt;-</span> <span class='fu'>round</span>(<span class='fl'>1</span> / (<span class='no'>s</span>^<span class='fl'>2</span>), <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>3</span>)
-<span class='no'>weights</span> <span class='kw'>&lt;-</span> <span class='no'>w</span>[<span class='fu'>factor</span>(<span class='no'>x</span>)]
-<span class='no'>m</span> <span class='kw'>&lt;-</span> <span class='fu'>lm</span>(<span class='no'>y</span> ~ <span class='no'>x</span>, <span class='kw'>w</span> <span class='kw'>=</span> <span class='no'>weights</span>)
-<span class='fu'>calplot</span>(<span class='no'>m</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Assuming constant prediction variance even though model fit is weighted</span></div><div class='img'><img src='massart97ex3-1.png' alt='' width='700' height='433' /></div><div class='input'>
+    <pre class="examples"><div class='input'><span class='co'># For reproducing the results for replicate standard measurements in example 8,</span>
+<span class='co'># we need to do the calibration on the means when using chemCal &gt; 0.2</span>
+<span class='no'>weights</span> <span class='kw'>&lt;-</span> <span class='fu'>with</span>(<span class='no'>massart97ex3</span>, {
+  <span class='no'>yx</span> <span class='kw'>&lt;-</span> <span class='fu'>split</span>(<span class='no'>y</span>, <span class='no'>x</span>)
+  <span class='no'>ybar</span> <span class='kw'>&lt;-</span> <span class='fu'>sapply</span>(<span class='no'>yx</span>, <span class='no'>mean</span>)
+  <span class='no'>s</span> <span class='kw'>&lt;-</span> <span class='fu'>round</span>(<span class='fu'>sapply</span>(<span class='no'>yx</span>, <span class='no'>sd</span>), <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>2</span>)
+  <span class='no'>w</span> <span class='kw'>&lt;-</span> <span class='fu'>round</span>(<span class='fl'>1</span> / (<span class='no'>s</span>^<span class='fl'>2</span>), <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>3</span>)
+})
+
+<span class='no'>massart97ex3.means</span> <span class='kw'>&lt;-</span> <span class='fu'>aggregate</span>(<span class='no'>y</span> ~ <span class='no'>x</span>, <span class='no'>massart97ex3</span>, <span class='no'>mean</span>)
+
+<span class='no'>m3.means</span> <span class='kw'>&lt;-</span> <span class='fu'>lm</span>(<span class='no'>y</span> ~ <span class='no'>x</span>, <span class='kw'>w</span> <span class='kw'>=</span> <span class='no'>weights</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='no'>massart97ex3.means</span>)
+
 <span class='co'># The following concords with the book p. 200</span>
-<span class='fu'>inverse.predict</span>(<span class='no'>m</span>, <span class='fl'>15</span>, <span class='kw'>ws</span> <span class='kw'>=</span> <span class='fl'>1.67</span>)  <span class='co'># 5.9 +- 2.5</span></div><div class='output co'>#&gt; $Prediction
+<span class='fu'><a href='inverse.predict.html'>inverse.predict</a></span>(<span class='no'>m3.means</span>, <span class='fl'>15</span>, <span class='kw'>ws</span> <span class='kw'>=</span> <span class='fl'>1.67</span>)  <span class='co'># 5.9 +- 2.5</span></div><div class='output co'>#&gt; $Prediction
 #&gt; [1] 5.865367
 #&gt; 
 #&gt; $`Standard Error`
@@ -137,7 +149,7 @@
 #&gt; 
 #&gt; $`Confidence Limits`
 #&gt; [1] 3.387082 8.343652
-#&gt; </div><div class='input'><span class='fu'>inverse.predict</span>(<span class='no'>m</span>, <span class='fl'>90</span>, <span class='kw'>ws</span> <span class='kw'>=</span> <span class='fl'>0.145</span>) <span class='co'># 44.1 +- 7.9</span></div><div class='output co'>#&gt; $Prediction
+#&gt; </div><div class='input'><span class='fu'><a href='inverse.predict.html'>inverse.predict</a></span>(<span class='no'>m3.means</span>, <span class='fl'>90</span>, <span class='kw'>ws</span> <span class='kw'>=</span> <span class='fl'>0.145</span>) <span class='co'># 44.1 +- 7.9</span></div><div class='output co'>#&gt; $Prediction
 #&gt; [1] 44.06025
 #&gt; 
 #&gt; $`Standard Error`
@@ -151,33 +163,30 @@
 #&gt; </div><div class='input'>
 <span class='co'># The LOD is only calculated for models from unweighted regression</span>
 <span class='co'># with this version of chemCal</span>
-<span class='no'>m0</span> <span class='kw'>&lt;-</span> <span class='fu'>lm</span>(<span class='no'>y</span> ~ <span class='no'>x</span>)
-<span class='fu'>lod</span>(<span class='no'>m0</span>)</div><div class='output co'>#&gt; $x
+<span class='no'>m0</span> <span class='kw'>&lt;-</span> <span class='fu'>lm</span>(<span class='no'>y</span> ~ <span class='no'>x</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='no'>massart97ex3</span>)
+<span class='fu'><a href='lod.html'>lod</a></span>(<span class='no'>m0</span>)</div><div class='output co'>#&gt; $x
 #&gt; [1] 5.407085
 #&gt; 
 #&gt; $y
-#&gt;        1 
-#&gt; 13.63911 
+#&gt; [1] 13.63911
 #&gt; </div><div class='input'>
 <span class='co'># Limit of quantification from unweighted regression</span>
-<span class='fu'>loq</span>(<span class='no'>m0</span>)</div><div class='output co'>#&gt; $x
-#&gt; [1] 13.97764
+<span class='fu'><a href='loq.html'>loq</a></span>(<span class='no'>m0</span>)</div><div class='output co'>#&gt; $x
+#&gt; [1] 9.627349
 #&gt; 
 #&gt; $y
-#&gt;       1 
-#&gt; 30.6235 
+#&gt; [1] 22.00246
 #&gt; </div><div class='input'>
 <span class='co'># For calculating the limit of quantification from a model from weighted</span>
 <span class='co'># regression, we need to supply weights, internally used for inverse.predict</span>
 <span class='co'># If we are not using a variance function, we can use the weight from</span>
 <span class='co'># the above example as a first approximation (x = 15 is close to our</span>
 <span class='co'># loq approx 14 from above).</span>
-<span class='fu'>loq</span>(<span class='no'>m</span>, <span class='kw'>w.loq</span> <span class='kw'>=</span> <span class='fl'>1.67</span>)</div><div class='output co'>#&gt; $x
+<span class='fu'><a href='loq.html'>loq</a></span>(<span class='no'>m3.means</span>, <span class='kw'>w.loq</span> <span class='kw'>=</span> <span class='fl'>1.67</span>)</div><div class='output co'>#&gt; $x
 #&gt; [1] 7.346195
 #&gt; 
 #&gt; $y
-#&gt;        1 
-#&gt; 17.90777 
+#&gt; [1] 17.90777
 #&gt; </div><div class='input'># The weight for the loq should therefore be derived at x = 7.3 instead
 # of 15, but the graphical procedure of Massart (p. 201) to derive the 
 # variances on which the weights are based is quite inaccurate anyway. 
diff --git a/docs/reference/rl95_toluene.html b/docs/reference/rl95_toluene.html
new file mode 100644
index 0000000..b252760
--- /dev/null
+++ b/docs/reference/rl95_toluene.html
@@ -0,0 +1,153 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+  <head>
+  <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Toluene amounts by GC/MS as reported by Rocke and Lorenzato (1995) — rl95_toluene • chemCal</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
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+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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+<!-- Font Awesome icons -->
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+
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+
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+
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+<script src="../pkgdown.js"></script>
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+<meta property="og:title" content="Toluene amounts by GC/MS as reported by Rocke and Lorenzato (1995) — rl95_toluene" />
+
+<meta property="og:description" content="Dataset reproduced from Table 4 in Rocke and Lorenzato (1995)." />
+<meta name="twitter:card" content="summary" />
+
+
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+<!-- mathjax -->
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
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+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
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+  </head>
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+    <div class="container template-reference-topic">
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+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
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+        <a class="navbar-link" href="../index.html">chemCal</a>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.2.1</span>
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+    </div>
+
+    <div id="navbar" class="navbar-collapse collapse">
+      <ul class="nav navbar-nav">
+        <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
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+</li>
+      </ul>
+      
+      <ul class="nav navbar-nav navbar-right">
+        
+      </ul>
+      
+    </div><!--/.nav-collapse -->
+  </div><!--/.container -->
+</div><!--/.navbar -->
+
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+      </header>
+
+<div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Toluene amounts by GC/MS as reported by Rocke and Lorenzato (1995)</h1>
+    
+    <div class="hidden name"><code>rl95_toluene.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    
+    <p>Dataset reproduced from Table 4 in Rocke and Lorenzato (1995).</p>
+    
+    </div>
+
+        
+    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+
+    <p>A dataframe containing four replicate observations for each 
+  of the six calibration standards.</p>
+    
+    <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
+
+    <p>Rocke, David M. und Lorenzato, Stefan (1995) A two-component model for
+  measurement error in analytical chemistry. Technometrics 37(2), 176-184.</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="#format">Format</a></li>
+
+      <li><a href="#source">Source</a></li>
+          </ul>
+
+  </div>
+</div>
+
+      <footer>
+      <div class="copyright">
+  <p>Developed by Johannes Ranke.</p>
+</div>
+
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diff --git a/docs/reference/utstats14.html b/docs/reference/utstats14.html
new file mode 100644
index 0000000..c16955f
--- /dev/null
+++ b/docs/reference/utstats14.html
@@ -0,0 +1,154 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+  <head>
+  <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+<title>Example data for calibration with replicates from University of Toronto — utstats14 • chemCal</title>
+
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+    <h1>Example data for calibration with replicates from University of Toronto</h1>
+    
+    <div class="hidden name"><code>utstats14.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    
+    <p>Dataset read into R from <a href='http://www.chem.utoronto.ca/coursenotes/analsci/stats/files/example14.xls'>http://www.chem.utoronto.ca/coursenotes/analsci/stats/files/example14.xls</a>.</p>
+    
+    </div>
+
+        
+    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+
+    <p>A tibble containing three replicate observations of the response for five
+  calibration concentrations.</p>
+    
+    <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
+
+    <p>David Stone and Jon Ellis (2011) Statistics in Analytical Chemistry. Tutorial website
+  maintained by the Departments of Chemistry, University of Toronto.
+  <a href='http://www.chem.utoronto.ca/coursenotes/analsci/stats/index.html'>http://www.chem.utoronto.ca/coursenotes/analsci/stats/index.html</a></p>
+    
+
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+    <h2>Contents</h2>
+    <ul class="nav nav-pills nav-stacked">
+      
+      <li><a href="#format">Format</a></li>
+
+      <li><a href="#source">Source</a></li>
+          </ul>
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