Merge pull request #250 from NBISweden/olga-tidymodels

Update tidymodels

session-tidymodels/_quarto.yml

@@ -10,11 +10,10 @@ book:
     - index.qmd
     - intro.qmd
     - case-study.qmd
-    - exercises.qmd
+    #- exercises.qmd
 
 bibliography: references.bib
 
-
 format:
   html:
     theme: spacebar

session-tidymodels/case-study.qmd

@@ -134,7 +134,6 @@ hist(data_diabetes$BMI, xlab = "", main = "BMI: all", 50)
 hist(data_other$BMI, xlab = "", main = "BMI: non-test", 50)
 hist(data_test$BMI, xlab = "", main = "BMI: test", 50)
 
-
 ```
 
 ## Feature engineering
@@ -236,7 +235,8 @@ model_tune %>%
   
 # best lambda value (min. RMSE)
 model_best <- model_tune %>%
-  select_best("rmse")
+  select_best(metric = "rmse")
+
 print(model_best)
 
 # finalize workflow with tuned model

session-tidymodels/docs/index.html

@@ -108,20 +108,14 @@
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./intro.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">Tidymodels</span></span></a>
+ <span class="menu-text"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">Introduction to Tidymodels</span></span></a>
   </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./case-study.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Demo: a predictive modelling case study</span></span></a>
   </div>
-</li>
-        <li class="sidebar-item">
-  <div class="sidebar-item-container"> 
-  <a href="./exercises.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text">Exercises</span></a>
-  </div>
 </li>
     </ul>
     </div>
@@ -168,6 +162,7 @@ <h1 class="unnumbered">Preface</h1>
 <p><strong>Aims</strong></p>
 <ul>
 <li>to introduce <code>tidymodels</code> framework for predictive modelling studies</li>
+<li>and show how to put all the common steps for building predictive model</li>
 </ul>
 <p><strong>Learning outcomes</strong></p>
 <ul>
@@ -418,7 +413,7 @@ <h1 class="unnumbered">Preface</h1>
   </div>
   <div class="nav-page nav-page-next">
       <a href="./intro.html" class="pagination-link">
-        <span class="nav-page-text"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">Tidymodels</span></span> <i class="bi bi-arrow-right-short"></i>
+        <span class="nav-page-text"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">Introduction to Tidymodels</span></span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
 </nav>

session-tidymodels/docs/intro.html

@@ -7,7 +7,7 @@
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
 
-<title>Tidymodels - 1&nbsp; Tidymodels</title>
+<title>Tidymodels - 1&nbsp; Introduction to Tidymodels</title>
 <style>
 code{white-space: pre-wrap;}
 span.smallcaps{font-variant: small-caps;}
@@ -93,7 +93,7 @@
       <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
-      <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./intro.html"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">Tidymodels</span></a></li></ol></nav>
+      <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./intro.html"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">Introduction to Tidymodels</span></a></li></ol></nav>
       <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
       </a>
       <button type="button" class="btn quarto-search-button" aria-label="" onclick="window.quartoOpenSearch();">
@@ -127,20 +127,14 @@
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./intro.html" class="sidebar-item-text sidebar-link active">
- <span class="menu-text"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">Tidymodels</span></span></a>
+ <span class="menu-text"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">Introduction to Tidymodels</span></span></a>
   </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./case-study.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Demo: a predictive modelling case study</span></span></a>
   </div>
-</li>
-        <li class="sidebar-item">
-  <div class="sidebar-item-container"> 
-  <a href="./exercises.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text">Exercises</span></a>
-  </div>
 </li>
     </ul>
     </div>
@@ -161,7 +155,7 @@ <h2 id="toc-title">Table of contents</h2>
 
 <header id="title-block-header" class="quarto-title-block default">
 <div class="quarto-title">
-<h1 class="title"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">Tidymodels</span></h1>
+<h1 class="title"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">Introduction to Tidymodels</span></h1>
 </div>
 
 
@@ -218,7 +212,7 @@ <h1 class="title"><span class="chapter-number">1</span>&nbsp; <span class="chapt
 </table>
 <section id="references" class="level2 unnumbered">
 <h2 class="unnumbered anchored" data-anchor-id="references">References</h2>
-<div id="refs" role="list">
+<div id="refs" role="list" style="display: none">
 
 </div>
 <!-- filtering non-informative features (variance threshold, univariate etc.) -->