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Update webpages to version 3.7.0
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@brian-j-smith
brian-j-smith committed Sep 11, 2023
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39 changes: 20 additions & 19 deletions example_ichomes.html
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<title>Example</title>

<script src="site_libs/header-attrs-2.20/header-attrs.js"></script>
<script src="site_libs/header-attrs-2.24/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
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h6 {font-size: 12px;}
code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
pre:not([class]) { background-color: white }</style>
<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
<script src="site_libs/jqueryui-1.13.2/jquery-ui.min.js"></script>
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
<script src="site_libs/navigation-1.1/tabsets.js"></script>
<link href="site_libs/highlightjs-9.12.0/textmate.css" rel="stylesheet" />
<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
<script src="site_libs/kePrint-0.0.1/kePrint.js"></script>
<link href="site_libs/lightable-0.0.1/lightable.css" rel="stylesheet" />
<link href="site_libs/font-awesome-5.1.0/css/all.css" rel="stylesheet" />
<link href="site_libs/font-awesome-5.1.0/css/v4-shims.css" rel="stylesheet" />
<link href="site_libs/font-awesome-6.4.2/css/all.min.css" rel="stylesheet" />
<link href="site_libs/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet" />

<style type="text/css">
code{white-space: pre-wrap;}
Expand Down Expand Up @@ -759,7 +759,7 @@ <h2>Training Set Analysis</h2>
<p><img src="example_ichomes_files/figure-html/ex_ichomes_tune-1.png" width="672" style="display: block; margin: auto;" /></p>
<pre class="r"><code>## Performance plotted over the grid points
(tuned_model &lt;- as.MLModel(model_fit))
#&gt; --- MLModel object ---------------------------------------------------------------------------
#&gt; --- MLModel object ----------------------------------------------------------------------------
#&gt;
#&gt; Model name: GBMModel
#&gt; Label: Trained Generalized Boosted Regression
Expand All @@ -778,25 +778,26 @@ <h2>Training Set Analysis</h2>
#&gt; $ shrinkage : num 0.1
#&gt; $ bag.fraction : num 0.5
#&gt;
#&gt; === $TrainingStep1 ===========================================================================
#&gt; === $TrainingStep1 ============================================================================
#&gt; === TrainingStep object ===
#&gt;
#&gt; Optimization method: Grid Search
#&gt; TunedModel log:
#&gt; # A tibble: 25 × 4
#&gt; name selected params$n.trees $interaction.depth metrics…¹ $R2 $MAE
#&gt; &lt;chr&gt; &lt;lgl&gt; &lt;int&gt; &lt;int&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt;
#&gt; 1 GBMModel.1 FALSE 50 1 56750. 0.592 36337.
#&gt; 2 GBMModel.2 FALSE 50 2 53242. 0.641 33061.
#&gt; 3 GBMModel.3 FALSE 50 3 51911. 0.659 31824.
#&gt; 4 GBMModel.4 FALSE 50 4 50832. 0.672 30828.
#&gt; 5 GBMModel.5 FALSE 50 5 50068. 0.685 29946.
#&gt; 6 GBMModel.6 FALSE 100 1 52998. 0.636 33458.
#&gt; 7 GBMModel.7 FALSE 100 2 50227. 0.677 31097.
#&gt; 8 GBMModel.8 FALSE 100 3 49925. 0.679 30182.
#&gt; 9 GBMModel.9 FALSE 100 4 49399. 0.691 29481.
#&gt; 10 GBMModel.10 FALSE 100 5 49226. 0.692 29170.
#&gt; # … with 15 more rows, and abbreviated variable name ¹​metrics$RMSE
#&gt; name selected params$n.trees $interaction.depth metrics$RMSE $R2
#&gt; &lt;chr&gt; &lt;lgl&gt; &lt;int&gt; &lt;int&gt; &lt;dbl&gt; &lt;dbl&gt;
#&gt; 1 GBMModel.1 FALSE 50 1 56750. 0.592
#&gt; 2 GBMModel.2 FALSE 50 2 53242. 0.641
#&gt; 3 GBMModel.3 FALSE 50 3 51911. 0.659
#&gt; 4 GBMModel.4 FALSE 50 4 50832. 0.672
#&gt; 5 GBMModel.5 FALSE 50 5 50068. 0.685
#&gt; 6 GBMModel.6 FALSE 100 1 52998. 0.636
#&gt; 7 GBMModel.7 FALSE 100 2 50227. 0.677
#&gt; 8 GBMModel.8 FALSE 100 3 49925. 0.679
#&gt; 9 GBMModel.9 FALSE 100 4 49399. 0.691
#&gt; 10 GBMModel.10 FALSE 100 5 49226. 0.692
#&gt; # ℹ 15 more rows
#&gt; # ℹ 1 more variable: metrics$MAE &lt;dbl&gt;
#&gt;
#&gt; Selected row: 24
#&gt; Metric: RMSE = 48572.58
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14 changes: 7 additions & 7 deletions example_info.html
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<title>Example</title>

<script src="site_libs/header-attrs-2.20/header-attrs.js"></script>
<script src="site_libs/header-attrs-2.24/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
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h6 {font-size: 12px;}
code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
pre:not([class]) { background-color: white }</style>
<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
<script src="site_libs/jqueryui-1.13.2/jquery-ui.min.js"></script>
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
<script src="site_libs/navigation-1.1/tabsets.js"></script>
<link href="site_libs/highlightjs-9.12.0/textmate.css" rel="stylesheet" />
<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
<link href="site_libs/font-awesome-5.1.0/css/all.css" rel="stylesheet" />
<link href="site_libs/font-awesome-5.1.0/css/v4-shims.css" rel="stylesheet" />
<link href="site_libs/font-awesome-6.4.2/css/all.min.css" rel="stylesheet" />
<link href="site_libs/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet" />

<style type="text/css">
code{white-space: pre-wrap;}
Expand Down Expand Up @@ -383,7 +383,7 @@ <h1 class="title toc-ignore">Example</h1>
<h1>Model Information</h1>
<p>A named list of package-supplied models can be obtained interactively
with the <a
href="https://www.rdocumentation.org/packages/MachineShop/versions/3.6.0/topics/modelinfo"><code>modelinfo()</code></a>
href="https://www.rdocumentation.org/packages/MachineShop/versions/3.7.0/topics/modelinfo"><code>modelinfo()</code></a>
function, and includes a descriptive <code>"label"</code> for each,
source <code>"packages"</code> on which the models depend, supported
response variable <code>"types"</code>, and <code>"arguments"</code>
Expand Down Expand Up @@ -518,12 +518,12 @@ <h2>Response Variable-Specific</h2>
<div id="metric-information" class="section level1">
<h1>Metric Information</h1>
<p>A named list of supplied metrics can be obtained with the <a
href="https://www.rdocumentation.org/packages/MachineShop/versions/3.6.0/topics/metricinfo"><code>metricinfo()</code></a>
href="https://www.rdocumentation.org/packages/MachineShop/versions/3.7.0/topics/metricinfo"><code>metricinfo()</code></a>
function, and includes a descriptive <code>"label"</code> for each,
whether to <code>"maximize"</code> the metrics for better performance,
their function <code>"arguments"</code>, and supported observed and
predicted response variable <code>"types"</code>. Function <a
href="https://www.rdocumentation.org/packages/MachineShop/versions/3.6.0/topics/metricinfo"><code>metricinfo()</code></a>
href="https://www.rdocumentation.org/packages/MachineShop/versions/3.7.0/topics/metricinfo"><code>metricinfo()</code></a>
may be called without arguments, with one or more metric functions, an
observed response variable, an observed and predicted response variable
pair, response variable types, or resampled output; and will return
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26 changes: 13 additions & 13 deletions example_iris.html
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<title>Example</title>

<script src="site_libs/header-attrs-2.20/header-attrs.js"></script>
<script src="site_libs/header-attrs-2.24/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
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h6 {font-size: 12px;}
code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
pre:not([class]) { background-color: white }</style>
<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
<script src="site_libs/jqueryui-1.13.2/jquery-ui.min.js"></script>
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
<script src="site_libs/navigation-1.1/tabsets.js"></script>
<link href="site_libs/highlightjs-9.12.0/textmate.css" rel="stylesheet" />
<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
<script src="site_libs/kePrint-0.0.1/kePrint.js"></script>
<link href="site_libs/lightable-0.0.1/lightable.css" rel="stylesheet" />
<link href="site_libs/font-awesome-5.1.0/css/all.css" rel="stylesheet" />
<link href="site_libs/font-awesome-5.1.0/css/v4-shims.css" rel="stylesheet" />
<link href="site_libs/font-awesome-6.4.2/css/all.min.css" rel="stylesheet" />
<link href="site_libs/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet" />

<style type="text/css">
code{white-space: pre-wrap;}
Expand Down Expand Up @@ -554,7 +554,7 @@ <h2>Training and Test Set Analysis</h2>

## Variable importance
(vi &lt;- varimp(iris_fit))
#&gt; --- VariableImportance object ----------------------------------------------------------------
#&gt; --- VariableImportance object -----------------------------------------------------------------
#&gt; Permute.mean.brier
#&gt; Petal.Length 100.0000000
#&gt; Petal.Width 42.4880573
Expand Down Expand Up @@ -589,7 +589,7 @@ <h2>Training and Test Set Analysis</h2>
<h2>Resampling</h2>
<pre class="r"><code>## Resample estimation of model performance
(res &lt;- resample(fo, data = iris, model = GBMModel, control = CVControl))
#&gt; --- Resample object --------------------------------------------------------------------------
#&gt; --- Resample object ---------------------------------------------------------------------------
#&gt;
#&gt; Model: GBMModel
#&gt; Sampling variables:
Expand All @@ -606,7 +606,7 @@ <h2>Resampling</h2>
#&gt; 8 8 setosa
#&gt; 9 9 setosa
#&gt; 10 10 setosa
#&gt; # … with 140 more rows
#&gt; # ℹ 140 more rows
#&gt;
#&gt; === CVControl object ===
#&gt;
Expand Down Expand Up @@ -660,7 +660,7 @@ <h2>Model Tuning</h2>

## Variable importance
varimp(iris_fit)
#&gt; --- VariableImportance object ----------------------------------------------------------------
#&gt; --- VariableImportance object -----------------------------------------------------------------
#&gt; Permute.mean.brier
#&gt; Petal.Length 100.00000000
#&gt; Petal.Width 24.47878599
Expand Down Expand Up @@ -754,7 +754,7 @@ <h2>Model Comparisons</h2>
#&gt; RF - NNet 0.021000000 0 0.04690053 -0.06666667 0.16666667 0

t.test(perfdiff)
#&gt; --- PerformanceDiffTest object ---------------------------------------------------------------
#&gt; --- PerformanceDiffTest object ----------------------------------------------------------------
#&gt;
#&gt; Upper diagonal: mean differences (Model1 - Model2)
#&gt; Lower diagonal: p-values
Expand Down Expand Up @@ -828,9 +828,9 @@ <h2>Calibration Curves</h2>
<div id="confusion-matrices" class="section level2">
<h2>Confusion Matrices</h2>
<pre class="r"><code>(conf &lt;- confusion(res1, cutoff = NULL))
#&gt; --- ConfusionList object ---------------------------------------------------------------------
#&gt; --- ConfusionList object ----------------------------------------------------------------------
#&gt;
#&gt; === $GBMModel ================================================================================
#&gt; === $GBMModel =================================================================================
#&gt; === ConfusionMatrix object ===
#&gt; Observed
#&gt; Predicted setosa versicolor virginica
Expand All @@ -839,7 +839,7 @@ <h2>Confusion Matrices</h2>
#&gt; virginica 0.01637160 19.53094980 225.60351367

summary(conf)
#&gt; --- $GBMModel --------------------------------------------------------------------------------
#&gt; --- $GBMModel ---------------------------------------------------------------------------------
#&gt; Number of responses: 750
#&gt; Accuracy (SE): 0.9401729 (0.008660086)
#&gt; Majority class: 0.3333333
Expand Down Expand Up @@ -871,7 +871,7 @@ <h2>Preprocessing Recipe</h2>

iris_fit &lt;- fit(rec, model = GBMModel)
varimp(iris_fit)
#&gt; --- VariableImportance object ----------------------------------------------------------------
#&gt; --- VariableImportance object -----------------------------------------------------------------
#&gt; Permute.mean.brier
#&gt; Petal.Length 100.000000
#&gt; Petal.Width 26.116233
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16 changes: 8 additions & 8 deletions example_pima.html
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<title>Example</title>

<script src="site_libs/header-attrs-2.20/header-attrs.js"></script>
<script src="site_libs/header-attrs-2.24/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
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h6 {font-size: 12px;}
code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
pre:not([class]) { background-color: white }</style>
<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
<script src="site_libs/jqueryui-1.13.2/jquery-ui.min.js"></script>
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
<script src="site_libs/navigation-1.1/tabsets.js"></script>
<link href="site_libs/highlightjs-9.12.0/textmate.css" rel="stylesheet" />
<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
<script src="site_libs/kePrint-0.0.1/kePrint.js"></script>
<link href="site_libs/lightable-0.0.1/lightable.css" rel="stylesheet" />
<link href="site_libs/font-awesome-5.1.0/css/all.css" rel="stylesheet" />
<link href="site_libs/font-awesome-5.1.0/css/v4-shims.css" rel="stylesheet" />
<link href="site_libs/font-awesome-6.4.2/css/all.min.css" rel="stylesheet" />
<link href="site_libs/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet" />

<style type="text/css">
code{white-space: pre-wrap;}
Expand Down Expand Up @@ -605,17 +605,17 @@ <h2>ROC Curve</h2>
<div id="confusion-matrices" class="section level2">
<h2>Confusion Matrices</h2>
<pre class="r"><code>(conf &lt;- confusion(res))
#&gt; --- ConfusionList object ---------------------------------------------------------------------
#&gt; --- ConfusionList object ----------------------------------------------------------------------
#&gt;
#&gt; === $SelectedModel ===========================================================================
#&gt; === $SelectedModel ============================================================================
#&gt; === BinaryConfusionMatrix object ===
#&gt; Observed
#&gt; Predicted neg pos
#&gt; neg 228 50
#&gt; pos 34 80

summary(conf)
#&gt; --- $SelectedModel ---------------------------------------------------------------------------
#&gt; --- $SelectedModel ----------------------------------------------------------------------------
#&gt; Number of responses: 392
#&gt; Accuracy (SE): 0.7857143 (0.02072459)
#&gt; Majority class: 0.6683673
Expand All @@ -635,7 +635,7 @@ <h2>Confusion Matrices</h2>
<p><img src="example_pima_files/figure-html/ex_pima_conf-1.png" width="672" style="display: block; margin: auto;" /></p>
<pre class="r"><code>## Variable probability cutoff
summary(confusion(res, cutoff = 0.25))
#&gt; --- $SelectedModel ---------------------------------------------------------------------------
#&gt; --- $SelectedModel ----------------------------------------------------------------------------
#&gt; Number of responses: 392
#&gt; Accuracy (SE): 0.75 (0.02187044)
#&gt; Majority class: 0.6683673
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14 changes: 7 additions & 7 deletions example_settings.html
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<title>Example</title>

<script src="site_libs/header-attrs-2.20/header-attrs.js"></script>
<script src="site_libs/header-attrs-2.24/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
Expand All @@ -29,14 +29,14 @@
h6 {font-size: 12px;}
code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
pre:not([class]) { background-color: white }</style>
<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
<script src="site_libs/jqueryui-1.13.2/jquery-ui.min.js"></script>
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
<script src="site_libs/navigation-1.1/tabsets.js"></script>
<link href="site_libs/highlightjs-9.12.0/textmate.css" rel="stylesheet" />
<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
<link href="site_libs/font-awesome-5.1.0/css/all.css" rel="stylesheet" />
<link href="site_libs/font-awesome-5.1.0/css/v4-shims.css" rel="stylesheet" />
<link href="site_libs/font-awesome-6.4.2/css/all.min.css" rel="stylesheet" />
<link href="site_libs/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet" />

<style type="text/css">
code{white-space: pre-wrap;}
Expand Down Expand Up @@ -383,7 +383,7 @@ <h1 class="title toc-ignore">Example</h1>
<h1>Global Settings</h1>
<p>Core default behaviors of functions in the package can be viewed or
changed globally through the <a
href="https://www.rdocumentation.org/packages/MachineShop/versions/3.6.0/topics/settings"><code>settings()</code></a>
href="https://www.rdocumentation.org/packages/MachineShop/versions/3.7.0/topics/settings"><code>settings()</code></a>
function. The function accepts one or more character names of settings
to view, <code>name = value</code> pairs giving the values of settings
to change, a vector of these, or <code>"reset"</code> to restore all
Expand Down Expand Up @@ -413,7 +413,7 @@ <h1>Global Settings</h1>
#&gt; [1] &quot;empirical&quot;
#&gt;
#&gt; $grid
#&gt; --- TuningGrid object ------------------------------------------------------------------------
#&gt; --- TuningGrid object -------------------------------------------------------------------------
#&gt;
#&gt; Grid size: 3
#&gt; Random samples: FALSE
Expand Down Expand Up @@ -531,7 +531,7 @@ <h1>Global Settings</h1>
#&gt; [1] &quot;BootControl&quot;
#&gt;
#&gt; $grid
#&gt; --- TuningGrid object ------------------------------------------------------------------------
#&gt; --- TuningGrid object -------------------------------------------------------------------------
#&gt;
#&gt; Grid size: 10
#&gt; Random samples: FALSE
Expand Down
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