boxplot_expression

Boxplots to show range of model predictors to identify exceptional predictors
with excessively low or high values.

Implements nested k*l-fold cross-validation for lasso and elastic-net regularised linear models via the 'glmnet' package and other machine learning models via the 'caret' package <doi:10.1093/bioadv/vbad048>. Cross-validation of 'glmnet' alpha mixing parameter and embedded fast filter functions for feature selection are provided. Described as double cross-validation by Stone (1977) <doi:10.1111/j.2517-6161.1977.tb01603.x>. Also implemented is a method using outer CV to measure unbiased model performance metrics when fitting Bayesian linear and logistic regression shrinkage models using the horseshoe prior over parameters to encourage a sparse model as described by Piironen & Vehtari (2017) <doi:10.1214/17-EJS1337SI>.

Myles Lewis

nestedcv

Nested Cross-Validation with 'glmnet' and 'caret'

Athina Spiliopoulou

Cankut Cubuk

David Rios Santini

Katriona Goldmann

Ryan C. Thompson

boxplot_expression function

<dl><dt>x</dt>
<dd>a "nestedcv" object</dd>
<dt>scheme</dt>
<dd>colour scheme</dd>
<dt>palette</dt>
<dd>palette name (one of <code><a href="/link/hcl.pals()?package=nestedcv&version=0.9.0" data-mini-rdoc="nestedcv::hcl.pals()">hcl.pals()</a></code>) which is passed to
<a href="/link/hcl.colors?package=nestedcv&version=0.9.0" data-mini-rdoc="nestedcv::hcl.colors">hcl.colors</a></dd>
<dt>...</dt>
<dd>other arguments passed to <a href="/link/boxplot?package=nestedcv&version=0.9.0" data-mini-rdoc="nestedcv::boxplot">boxplot</a>.</dd></dl>

Arguments

Author

Boxplot expression levels of model predictors — boxplot_expression

<dl>

<dt>x</dt>
<dd>a "nestedcv" object</dd>


<dt>scheme</dt>
<dd>colour scheme</dd>


<dt>palette</dt>
<dd>palette name (one of <code><a href='https://rdrr.io/r/grDevices/palettes.html'>hcl.pals()</a></code>) which is passed to
<a href='https://rdrr.io/r/grDevices/palettes.html'>hcl.colors</a></dd>


<dt>...</dt>
<dd>other arguments passed to <a href='https://rdrr.io/r/graphics/boxplot.html'>boxplot</a>.</dd>

</dl>

boxplot_expression: Boxplot expression levels of model predictors

Description

Usage

Value

Arguments

Author

See Also