diff options
Diffstat (limited to 'docs/reference')
| -rw-r--r-- | docs/reference/calplot.lm.html | 19 | ||||
| -rw-r--r-- | docs/reference/chemCal-package.html | 15 | ||||
| -rw-r--r-- | docs/reference/din32645.html | 58 | ||||
| -rw-r--r-- | docs/reference/index.html | 27 | ||||
| -rw-r--r-- | docs/reference/inverse.predict.html | 61 | ||||
| -rw-r--r-- | docs/reference/lod.html | 26 | ||||
| -rw-r--r-- | docs/reference/loq.html | 31 | ||||
| -rw-r--r-- | docs/reference/massart97ex1.html | 15 | ||||
| -rw-r--r-- | docs/reference/massart97ex3.html | 63 | ||||
| -rw-r--r-- | docs/reference/rl95_toluene.html | 153 | ||||
| -rw-r--r-- | docs/reference/utstats14.html | 154 |
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'><-</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'><-</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'><-</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'>#> $Prediction -#> [1] 0.1054792 -#> -#> $`Standard Error` -#> [1] 0.02215619 -#> -#> $Confidence -#> [1] 0.07434261 -#> -#> $`Confidence Limits` -#> [1] 0.03113656 0.17982178 -#> </div><div class='input'> +<span class='no'>prediction</span> <span class='kw'><-</span> <span class='fu'><a href='inverse.predict.html'>inverse.predict</a></span>(<span class='no'>m</span>, <span class='fl'>3500</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.01</span>) + <span class='co'># This should give 0.07434 according to test data from Dintest, which </span> <span class='co'># was collected from Procontrol 3.1 (isomehr GmbH) in this case</span> -<span class='fu'>round</span>(<span class='no'>prediction</span>$<span class='no'>Confidence</span>,<span class='fl'>5</span>)</div><div class='output co'>#> [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'>#> [1] 0.07434</div><div class='input'> <span class='co'>## Critical value:</span> -(<span class='no'>crit</span> <span class='kw'><-</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'>#> $x -#> [1] 0.0698127 -#> -#> $y -#> 1 -#> 3155.393 -#> </div><div class='input'> +<span class='no'>crit</span> <span class='kw'><-</span> <span class='fu'><a href='lod.html'>lod</a></span>(<span class='no'>m</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.01</span>, <span class='kw'>beta</span> <span class='kw'>=</span> <span class='fl'>0.5</span>) + <span class='co'># According to DIN 32645, we should get 0.07 for the critical value</span> <span class='co'># (decision limit, "Nachweisgrenze")</span> <span class='fu'>round</span>(<span class='no'>crit</span>$<span class='no'>x</span>, <span class='fl'>2</span>)</div><div class='output co'>#> [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'><-</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'><-</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'>#> [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'><-</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'>#> $x -#> [1] 0.2119575 -#> -#> $y -#> 1 -#> 4528.787 -#> </div><div class='input'><span class='fu'>round</span>(<span class='no'>loq</span>$<span class='no'>x</span>,<span class='fl'>4</span>)</div><div class='output co'>#> [1] 0.212</div><div class='input'> +<span class='no'>loq</span> <span class='kw'><-</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>$<span class='no'>x</span>, <span class='fl'>4</span>)</div><div class='output co'>#> [1] 0.212</div><div class='input'> <span class='co'># A similar value is obtained using the approximation </span> <span class='co'># LQ = 3.04 * LC (Currie 1999, p. 120)</span> -<span class='fl'>3.04</span> * <span class='fu'>lod</span>(<span class='no'>m</span>,<span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.01</span>, <span class='kw'>beta</span> <span class='kw'>=</span> <span class='fl'>0.5</span>)$<span class='no'>x</span></div><div class='output co'>#> [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'>#> [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'><-</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'>#> $Prediction #> [1] 6.09381 @@ -210,7 +222,44 @@ #> #> $`Confidence Limits` #> [1] 40.77134 47.10832 -#> </div></pre> +#> </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 > 0.2</span> +<span class='no'>weights</span> <span class='kw'><-</span> <span class='fu'>with</span>(<span class='no'>massart97ex3</span>, { + <span class='no'>yx</span> <span class='kw'><-</span> <span class='fu'>split</span>(<span class='no'>y</span>, <span class='no'>x</span>) + <span class='no'>ybar</span> <span class='kw'><-</span> <span class='fu'>sapply</span>(<span class='no'>yx</span>, <span class='no'>mean</span>) + <span class='no'>s</span> <span class='kw'><-</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'><-</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'><-</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'><-</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'>#> $Prediction +#> [1] 5.865367 +#> +#> $`Standard Error` +#> [1] 0.8926109 +#> +#> $Confidence +#> [1] 2.478285 +#> +#> $`Confidence Limits` +#> [1] 3.387082 8.343652 +#> </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'>#> $Prediction +#> [1] 44.06025 +#> +#> $`Standard Error` +#> [1] 2.829162 +#> +#> $Confidence +#> [1] 7.855012 +#> +#> $`Confidence Limits` +#> [1] 36.20523 51.91526 +#> </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'><-</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'><-</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'>#> $x #> [1] 0.08655484 #> #> $y -#> 1 -#> 3317.154 +#> [1] 3317.154 #> </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 @@ #> [1] 0.0698127 #> #> $y -#> 1 -#> 3155.393 +#> [1] 3155.393 #> </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'><-</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'><-</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'>#> $x #> [1] 13.97764 #> #> $y -#> 1 -#> 30.6235 +#> [1] 30.6235 #> </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'>#> $x #> [1] 9.971963 #> #> $y -#> 1 -#> 22.68539 +#> [1] 22.68539 #> </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'>#> <span class='message'>The following objects are masked from massart97ex3 (pos = 3):</span> -#> <span class='message'></span> -#> <span class='message'> x, y</span></div><div class='input'><span class='no'>yx</span> <span class='kw'><-</span> <span class='fu'>split</span>(<span class='no'>y</span>, <span class='no'>x</span>) -<span class='no'>ybar</span> <span class='kw'><-</span> <span class='fu'>sapply</span>(<span class='no'>yx</span>, <span class='no'>mean</span>) -<span class='no'>s</span> <span class='kw'><-</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'><-</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'><-</span> <span class='no'>w</span>[<span class='fu'>factor</span>(<span class='no'>x</span>)] -<span class='no'>m</span> <span class='kw'><-</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'>#> <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 > 0.2</span> +<span class='no'>weights</span> <span class='kw'><-</span> <span class='fu'>with</span>(<span class='no'>massart97ex3</span>, { + <span class='no'>yx</span> <span class='kw'><-</span> <span class='fu'>split</span>(<span class='no'>y</span>, <span class='no'>x</span>) + <span class='no'>ybar</span> <span class='kw'><-</span> <span class='fu'>sapply</span>(<span class='no'>yx</span>, <span class='no'>mean</span>) + <span class='no'>s</span> <span class='kw'><-</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'><-</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'><-</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'><-</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'>#> $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'>#> $Prediction #> [1] 5.865367 #> #> $`Standard Error` @@ -137,7 +149,7 @@ #> #> $`Confidence Limits` #> [1] 3.387082 8.343652 -#> </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'>#> $Prediction +#> </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'>#> $Prediction #> [1] 44.06025 #> #> $`Standard Error` @@ -151,33 +163,30 @@ #> </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'><-</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'>#> $x +<span class='no'>m0</span> <span class='kw'><-</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'>#> $x #> [1] 5.407085 #> #> $y -#> 1 -#> 13.63911 +#> [1] 13.63911 #> </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'>#> $x -#> [1] 13.97764 +<span class='fu'><a href='loq.html'>loq</a></span>(<span class='no'>m0</span>)</div><div class='output co'>#> $x +#> [1] 9.627349 #> #> $y -#> 1 -#> 30.6235 +#> [1] 22.00246 #> </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'>#> $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'>#> $x #> [1] 7.346195 #> #> $y -#> 1 -#> 17.90777 +#> [1] 17.90777 #> </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" 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class="nav navbar-nav"> + <li> + <a href="../index.html"> + <span class="fa fa-home fa-lg"></span> + + </a> +</li> +<li> + <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> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </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> + +<div class="pkgdown"> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + + + </body> +</html> + 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"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>Example data for calibration with replicates 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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]--> + + + </head> + + <body> + <div class="container template-reference-topic"> + <header> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </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">0.2.1</span> + </span> + </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> + + </a> +</li> +<li> + <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> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + +<div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <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> + + + </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> + +<div class="pkgdown"> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + + + </body> +</html> + |