chapter about SIMCA added to the tutorial

svkucheryavski · Oct 30, 2016 · 1e2af91 · 1e2af91
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: mdatools
 Title: Multivariate Data Analysis for Chemometrics
-Version: 0.8.0
-Date: 2016-10-07
+Version: 0.8.1
+Date: 2016-10-30
 Author: Sergey Kucheryavskiy
 Maintainer: Sergey Kucheryavskiy <[email protected]>
 Description: Package implements projection based methods for preprocessing,

diff --git a/NEWS b/NEWS
@@ -1,3 +1,9 @@
+v.0.8.1
+=======
+* fixed a bug in PCA when explained variance was calculated incorrectly for data with excluded rows
+* fixed several issues with SIMCA (cross-validation) and SIMCAM (Cooman's plot)
+* added a chapter about SIMCA to the tutorial
+
 v.0.8.0
 =======
 * tutorial has been moved from GitBook to Bookdown and fully rewritten

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+v.0.8.1
+=======
+* fixed a bug in PCA when explained variance was calculated incorrectly for data with excluded rows
+* fixed several issues with SIMCA (cross-validation) and SIMCAM (Cooman's plot)
+* added a chapter about SIMCA to the tutorial
+
 v.0.8.0
 =======
 * tutorial has been moved from GitBook to Bookdown and fully rewritten

diff --git a/R/simcam.R b/R/simcam.R
@@ -166,7 +166,6 @@ predict.simcam = function(object, x, c.ref = NULL, cv = F, ...) {
       pred.res[[i]] = predict(object$models[[i]], x, c.ref)
       c.pred[, , i] = pred.res[[i]]$c.pred[, object$models[[i]]$ncomp.selected, ]
    }
-
    dimnames(c.pred) = list(rownames(x), paste('Comp'), object$classnames)
    c.pred = mda.setattr(c.pred, attrs, 'row')
    attr(c.pred, 'name') = 'SIMCAM predictions'

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diff --git a/docs/attributes-and-factors.html b/docs/attributes-and-factors.html
@@ -25,7 +25,7 @@
 
 <meta name="author" content="Sergey Kucheryavskiy">
 
-<meta name="date" content="2016-10-16">
+<meta name="date" content="2016-10-30">
 
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@@ -107,7 +107,7 @@
 <ul class="summary">
 <li class="chapter" data-level="" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i>Introduction</a></li>
 <li class="chapter" data-level="" data-path="what-is-new.html"><a href="what-is-new.html"><i class="fa fa-check"></i>What is new</a><ul>
-<li class="chapter" data-level="" data-path="what-is-new.html"><a href="what-is-new.html#what-to-expect-from-future-releases"><i class="fa fa-check"></i>What to expect from future releases</a></li>
+<li class="chapter" data-level="" data-path="what-is-new.html"><a href="what-is-new.html#what-expect-from-future-releases"><i class="fa fa-check"></i>What expect from future releases</a></li>
 <li class="chapter" data-level="" data-path="what-is-new.html"><a href="what-is-new.html#last-changes-and-improvements-to-book-and-package"><i class="fa fa-check"></i>Last changes and improvements to book and package</a></li>
 </ul></li>
 <li class="chapter" data-level="" data-path="overview.html"><a href="overview.html"><i class="fa fa-check"></i>Overview</a><ul>
@@ -159,6 +159,12 @@
 </ul></li>
 <li class="chapter" data-level="" data-path="variable-selection.html"><a href="variable-selection.html"><i class="fa fa-check"></i>Variable selection</a></li>
 </ul></li>
+<li class="chapter" data-level="" data-path="simca-classification.html"><a href="simca-classification.html"><i class="fa fa-check"></i>SIMCA classification</a><ul>
+<li class="chapter" data-level="" data-path="calibration-and-validation.html"><a href="calibration-and-validation.html"><i class="fa fa-check"></i>Calibration and validation</a><ul>
+<li class="chapter" data-level="" data-path="calibration-and-validation.html"><a href="calibration-and-validation.html#predictions-and-validation-with-a-test-set"><i class="fa fa-check"></i>Predictions and validation with a test set</a></li>
+</ul></li>
+<li class="chapter" data-level="" data-path="multiclass-classification.html"><a href="multiclass-classification.html"><i class="fa fa-check"></i>Multiclass classification</a></li>
+</ul></li>
 </ul>
 
       </nav>

diff --git a/docs/calibration-and-validation.html b/docs/calibration-and-validation.html
diff --git a/docs/datasets-and-plots.html b/docs/datasets-and-plots.html
@@ -25,7 +25,7 @@
 
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 <li class="chapter" data-level="" data-path="what-is-new.html"><a href="what-is-new.html"><i class="fa fa-check"></i>What is new</a><ul>
-<li class="chapter" data-level="" data-path="what-is-new.html"><a href="what-is-new.html#what-to-expect-from-future-releases"><i class="fa fa-check"></i>What to expect from future releases</a></li>
+<li class="chapter" data-level="" data-path="what-is-new.html"><a href="what-is-new.html#what-expect-from-future-releases"><i class="fa fa-check"></i>What expect from future releases</a></li>
 <li class="chapter" data-level="" data-path="what-is-new.html"><a href="what-is-new.html#last-changes-and-improvements-to-book-and-package"><i class="fa fa-check"></i>Last changes and improvements to book and package</a></li>
 </ul></li>
 <li class="chapter" data-level="" data-path="overview.html"><a href="overview.html"><i class="fa fa-check"></i>Overview</a><ul>
@@ -159,6 +159,12 @@
 </ul></li>
 <li class="chapter" data-level="" data-path="variable-selection.html"><a href="variable-selection.html"><i class="fa fa-check"></i>Variable selection</a></li>
 </ul></li>
+<li class="chapter" data-level="" data-path="simca-classification.html"><a href="simca-classification.html"><i class="fa fa-check"></i>SIMCA classification</a><ul>
+<li class="chapter" data-level="" data-path="calibration-and-validation.html"><a href="calibration-and-validation.html"><i class="fa fa-check"></i>Calibration and validation</a><ul>
+<li class="chapter" data-level="" data-path="calibration-and-validation.html"><a href="calibration-and-validation.html#predictions-and-validation-with-a-test-set"><i class="fa fa-check"></i>Predictions and validation with a test set</a></li>
+</ul></li>
+<li class="chapter" data-level="" data-path="multiclass-classification.html"><a href="multiclass-classification.html"><i class="fa fa-check"></i>Multiclass classification</a></li>
+</ul></li>
 </ul>
 
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diff --git a/docs/how-to-install.html b/docs/how-to-install.html
@@ -25,7 +25,7 @@
 
 <meta name="author" content="Sergey Kucheryavskiy">
 
-<meta name="date" content="2016-10-16">
+<meta name="date" content="2016-10-30">
 
 <script type="text/x-mathjax-config">
 MathJax.Hub.Config({
@@ -107,7 +107,7 @@
 <ul class="summary">
 <li class="chapter" data-level="" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i>Introduction</a></li>
 <li class="chapter" data-level="" data-path="what-is-new.html"><a href="what-is-new.html"><i class="fa fa-check"></i>What is new</a><ul>
-<li class="chapter" data-level="" data-path="what-is-new.html"><a href="what-is-new.html#what-to-expect-from-future-releases"><i class="fa fa-check"></i>What to expect from future releases</a></li>
+<li class="chapter" data-level="" data-path="what-is-new.html"><a href="what-is-new.html#what-expect-from-future-releases"><i class="fa fa-check"></i>What expect from future releases</a></li>
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 </ul></li>
 <li class="chapter" data-level="" data-path="overview.html"><a href="overview.html"><i class="fa fa-check"></i>Overview</a><ul>
@@ -159,6 +159,12 @@
 </ul></li>
 <li class="chapter" data-level="" data-path="variable-selection.html"><a href="variable-selection.html"><i class="fa fa-check"></i>Variable selection</a></li>
 </ul></li>
+<li class="chapter" data-level="" data-path="simca-classification.html"><a href="simca-classification.html"><i class="fa fa-check"></i>SIMCA classification</a><ul>
+<li class="chapter" data-level="" data-path="calibration-and-validation.html"><a href="calibration-and-validation.html"><i class="fa fa-check"></i>Calibration and validation</a><ul>
+<li class="chapter" data-level="" data-path="calibration-and-validation.html"><a href="calibration-and-validation.html#predictions-and-validation-with-a-test-set"><i class="fa fa-check"></i>Predictions and validation with a test set</a></li>
+</ul></li>
+<li class="chapter" data-level="" data-path="multiclass-classification.html"><a href="multiclass-classification.html"><i class="fa fa-check"></i>Multiclass classification</a></li>
+</ul></li>
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diff --git a/docs/index.html b/docs/index.html
@@ -25,7 +25,7 @@
 
 <meta name="author" content="Sergey Kucheryavskiy">
 
-<meta name="date" content="2016-10-16">
+<meta name="date" content="2016-10-30">
 
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@@ -107,7 +107,7 @@
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 <li class="chapter" data-level="" data-path="what-is-new.html"><a href="what-is-new.html"><i class="fa fa-check"></i>What is new</a><ul>
-<li class="chapter" data-level="" data-path="what-is-new.html"><a href="what-is-new.html#what-to-expect-from-future-releases"><i class="fa fa-check"></i>What to expect from future releases</a></li>
+<li class="chapter" data-level="" data-path="what-is-new.html"><a href="what-is-new.html#what-expect-from-future-releases"><i class="fa fa-check"></i>What expect from future releases</a></li>
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 </ul></li>
 <li class="chapter" data-level="" data-path="overview.html"><a href="overview.html"><i class="fa fa-check"></i>Overview</a><ul>
@@ -159,6 +159,12 @@
 </ul></li>
 <li class="chapter" data-level="" data-path="variable-selection.html"><a href="variable-selection.html"><i class="fa fa-check"></i>Variable selection</a></li>
 </ul></li>
+<li class="chapter" data-level="" data-path="simca-classification.html"><a href="simca-classification.html"><i class="fa fa-check"></i>SIMCA classification</a><ul>
+<li class="chapter" data-level="" data-path="calibration-and-validation.html"><a href="calibration-and-validation.html"><i class="fa fa-check"></i>Calibration and validation</a><ul>
+<li class="chapter" data-level="" data-path="calibration-and-validation.html"><a href="calibration-and-validation.html#predictions-and-validation-with-a-test-set"><i class="fa fa-check"></i>Predictions and validation with a test set</a></li>
+</ul></li>
+<li class="chapter" data-level="" data-path="multiclass-classification.html"><a href="multiclass-classification.html"><i class="fa fa-check"></i>Multiclass classification</a></li>
+</ul></li>
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@@ -179,7 +185,7 @@ <h1>
 <div id="header">
 <h1 class="title">Getting started with mdatools for R</h1>
 <h4 class="author"><em>Sergey Kucheryavskiy</em></h4>
-<h4 class="date"><em>October 16, 2016</em></h4>
+<h4 class="date"><em>October 30, 2016</em></h4>
 </div>
 <div id="introduction" class="section level1 unnumbered">
 <h1>Introduction</h1>

diff --git a/docs/models-and-results-1.html b/docs/models-and-results-1.html
@@ -25,7 +25,7 @@
 
 <meta name="author" content="Sergey Kucheryavskiy">
 
-<meta name="date" content="2016-10-16">
+<meta name="date" content="2016-10-30">
 
 <script type="text/x-mathjax-config">
 MathJax.Hub.Config({
@@ -107,7 +107,7 @@
 <ul class="summary">
 <li class="chapter" data-level="" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i>Introduction</a></li>
 <li class="chapter" data-level="" data-path="what-is-new.html"><a href="what-is-new.html"><i class="fa fa-check"></i>What is new</a><ul>
-<li class="chapter" data-level="" data-path="what-is-new.html"><a href="what-is-new.html#what-to-expect-from-future-releases"><i class="fa fa-check"></i>What to expect from future releases</a></li>
+<li class="chapter" data-level="" data-path="what-is-new.html"><a href="what-is-new.html#what-expect-from-future-releases"><i class="fa fa-check"></i>What expect from future releases</a></li>
 <li class="chapter" data-level="" data-path="what-is-new.html"><a href="what-is-new.html#last-changes-and-improvements-to-book-and-package"><i class="fa fa-check"></i>Last changes and improvements to book and package</a></li>
 </ul></li>
 <li class="chapter" data-level="" data-path="overview.html"><a href="overview.html"><i class="fa fa-check"></i>Overview</a><ul>
@@ -159,6 +159,12 @@
 </ul></li>
 <li class="chapter" data-level="" data-path="variable-selection.html"><a href="variable-selection.html"><i class="fa fa-check"></i>Variable selection</a></li>
 </ul></li>
+<li class="chapter" data-level="" data-path="simca-classification.html"><a href="simca-classification.html"><i class="fa fa-check"></i>SIMCA classification</a><ul>
+<li class="chapter" data-level="" data-path="calibration-and-validation.html"><a href="calibration-and-validation.html"><i class="fa fa-check"></i>Calibration and validation</a><ul>
+<li class="chapter" data-level="" data-path="calibration-and-validation.html"><a href="calibration-and-validation.html#predictions-and-validation-with-a-test-set"><i class="fa fa-check"></i>Predictions and validation with a test set</a></li>
+</ul></li>
+<li class="chapter" data-level="" data-path="multiclass-classification.html"><a href="multiclass-classification.html"><i class="fa fa-check"></i>Multiclass classification</a></li>
+</ul></li>
 </ul>
 
       </nav>
@@ -313,7 +319,7 @@ <h3>Model validation</h3>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">m2 =<span class="st"> </span><span class="kw">pls</span>(X.c, y.c, <span class="dv">7</span>, <span class="dt">scale =</span> T, <span class="dt">cv =</span> <span class="dv">1</span>, <span class="dt">ncomp.selcrit =</span> <span class="st">&#39;wold&#39;</span>)
 <span class="kw">show</span>(m2$ncomp.selected)</code></pre></div>
 <pre><code>## [1] 4</code></pre>
-<p>And here is the RMSE plots (they are identical of course):</p>
+<p>And here are the RMSE plots (they are identical of course):</p>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">par</span>(<span class="dt">mfrow =</span> <span class="kw">c</span>(<span class="dv">1</span>, <span class="dv">2</span>))
 <span class="kw">plotRMSE</span>(m1)
 <span class="kw">plotRMSE</span>(m2)</code></pre></div>
@@ -329,7 +335,7 @@ <h3>Model validation</h3>
 ##     X cumexpvar Y cumexpvar  RMSE Slope   Bias  RPD
 ## Cal       97.64       98.19 0.521  0.98  0e+00 7.59
 ## CV        92.90       96.22 0.753  0.98 -2e-04 5.26</code></pre>
-<p>If you want more details run <code>summury()</code> for one of the result objects.</p>
+<p>If you want more details run <code>summary()</code> for one of the result objects.</p>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m1$calres)</code></pre></div>
 <pre><code>## 
 ## PLS regression results (class plsres) summary

diff --git a/docs/models-and-results.html b/docs/models-and-results.html
@@ -25,7 +25,7 @@
 
 <meta name="author" content="Sergey Kucheryavskiy">
 
-<meta name="date" content="2016-10-16">
+<meta name="date" content="2016-10-30">
 
 <script type="text/x-mathjax-config">
 MathJax.Hub.Config({
@@ -107,7 +107,7 @@
 <ul class="summary">
 <li class="chapter" data-level="" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i>Introduction</a></li>
 <li class="chapter" data-level="" data-path="what-is-new.html"><a href="what-is-new.html"><i class="fa fa-check"></i>What is new</a><ul>
-<li class="chapter" data-level="" data-path="what-is-new.html"><a href="what-is-new.html#what-to-expect-from-future-releases"><i class="fa fa-check"></i>What to expect from future releases</a></li>
+<li class="chapter" data-level="" data-path="what-is-new.html"><a href="what-is-new.html#what-expect-from-future-releases"><i class="fa fa-check"></i>What expect from future releases</a></li>
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 </ul></li>
 <li class="chapter" data-level="" data-path="overview.html"><a href="overview.html"><i class="fa fa-check"></i>Overview</a><ul>
@@ -159,6 +159,12 @@
 </ul></li>
 <li class="chapter" data-level="" data-path="variable-selection.html"><a href="variable-selection.html"><i class="fa fa-check"></i>Variable selection</a></li>
 </ul></li>
+<li class="chapter" data-level="" data-path="simca-classification.html"><a href="simca-classification.html"><i class="fa fa-check"></i>SIMCA classification</a><ul>
+<li class="chapter" data-level="" data-path="calibration-and-validation.html"><a href="calibration-and-validation.html"><i class="fa fa-check"></i>Calibration and validation</a><ul>
+<li class="chapter" data-level="" data-path="calibration-and-validation.html"><a href="calibration-and-validation.html#predictions-and-validation-with-a-test-set"><i class="fa fa-check"></i>Predictions and validation with a test set</a></li>
+</ul></li>
+<li class="chapter" data-level="" data-path="multiclass-classification.html"><a href="multiclass-classification.html"><i class="fa fa-check"></i>Multiclass classification</a></li>
+</ul></li>
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