Statistical Thinking for the 21st Century

https://github.com/statsthinking21/statsthinking21-core
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A comprehensive book that teaches statistical concepts and methods relevant to modern data analysis...
Tokens:78,472
Snippets:432
Trust Score:5.8
Update:11 months ago
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### GitBook Configuration and Startup Script

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/_book/hypothesis-testing.html

This JavaScript code initializes the GitBook plugin with configurations for sharing options (enabling Facebook and Twitter), font settings (white theme, sans family, size 2), an edit link to the GitHub repository for the R Markdown source, download options for PDF and EPUB, Fuse search engine, and a collapsible table of contents at subsection level. It requires the GitBook module and starts the book interface. No inputs or outputs beyond DOM manipulation; depends on GitBook being loaded. Limitations: hardcoded links and options may not adapt to different environments.

```javascript
gitbook.require(["gitbook"], function(gitbook) { gitbook.start({ "sharing": { "github": false, "facebook": true, "twitter": true, "linkedin": false, "weibo": false, "instapaper": false, "vk": false, "whatsapp": false, "all": ["facebook", "twitter", "linkedin", "weibo", "instapaper"] }, "fontsettings": { "theme": "white", "family": "sans", "size": 2 }, "edit": { "link": "https://github.com/statsthinking21/statsthinking21-core/edit/master/09-HypothesisTesting.Rmd", "text": "Edit" }, "history": { "link": null, "text": null }, "view": { "link": null, "text": null }, "download": ["StatsThinking21.pdf", "StatsThinking21.epub"], "search": { "engine": "fuse", "options": null }, "toc": { "collapse": "subsection" } }); });
```

--------------------------------

### Basic R for Statistical Analysis

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/_book/ci-effect-size-power.html

This snippet demonstrates fundamental R commands used for statistical analysis, including data import, manipulation, and basic plotting. It serves as a foundational example for users new to R in a statistical context.

```r
library(tidyverse)

# Load data
data <- read_csv("my_data.csv")

# Data manipulation
summary_data <- data %>%
  group_by(group) %>%
  summarise(mean_value = mean(value), sd_value = sd(value))

# Plotting
ggplot(summary_data, aes(x = group, y = mean_value)) +
  geom_bar(stat = "identity") +
  geom_error_bar(aes(ymin = mean_value - sd_value, ymax = mean_value + sd_value))
```

--------------------------------

### Python for Statistical Analysis with Pandas and Matplotlib

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/_book/ci-effect-size-power.html

This Python snippet showcases essential libraries like Pandas for data manipulation and Matplotlib for visualization. It provides a practical example of how to perform basic statistical analyses and create plots in Python.

```python
import pandas as pd
import matplotlib.pyplot as plt

# Load data
data = pd.read_csv("my_data.csv")

# Data manipulation
summary_data = data.groupby('group')['value'].agg(['mean', 'std'])

# Plotting
plt.bar(summary_data.index, summary_data['mean'])
plt.errorbar(summary_data.index, summary_data['mean'], yerr=summary_data['std'], fmt='none', ecolor='black')
plt.xlabel('Group')
plt.ylabel('Mean Value')
plt.title('Mean Value by Group with Standard Deviation')
plt.show()
```

--------------------------------

### R: Linear Regression Analysis

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/_book/the-general-linear-model.html

This snippet shows the output of a linear regression analysis performed in R. It demonstrates the estimated coefficients, standard errors, t-values, p-values, residual standard error, and R-squared values for the model. The example shows the assessment of significance.

```R
## 
## Call:
## lm(formula = grade ~ studyTime, data = df)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -10.656  -2.719   0.125   4.703   7.469 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept)    76.16       5.16   14.76  6.1e-06 ***
## studyTime       4.31       2.14    2.01    0.091 .  
## --- 
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 6.4 on 6 degrees of freedom
## Multiple R-squared:  0.403,  Adjusted R-squared:  0.304 
## F-statistic: 4.05 on 1 and 6 DF,  p-value: 0.0907
```

--------------------------------

### Initialize Gitbook

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/_book/bayesian-statistics.html

Initializes the Gitbook environment with specified configurations for sharing, font settings, editing, history, view, downloads, search, and table of contents.

```javascript
gitbook.require(["gitbook"], function(gitbook) {
  gitbook.start({
    "sharing": {
      "github": false,
      "facebook": true,
      "twitter": true,
      "linkedin": false,
      "weibo": false,
      "instapaper": false,
      "vk": false,
      "whatsapp": false,
      "all": ["facebook", "twitter", "linkedin", "weibo", "instapaper"]
    },
    "fontsettings": {
      "theme": "white",
      "family": "sans",
      "size": 2
    },
    "edit": {
      "link": "https://github.com/statsthinking21/statsthinking21-core/edit/master/11-BayesianStatistics.Rmd",
      "text": "Edit"
    },
    "history": {
      "link": null,
      "text": null
    },
    "view": {
      "link": null,
      "text": null
    },
    "download": ["StatsThinking21.pdf", "StatsThinking21.epub"],
    "search": {
      "engine": "fuse",
      "options": null
    },
    "toc": {
      "collapse": "subsection"
    }
  });
});
```

--------------------------------

### Initialize GitBook with Sharing and Font Settings

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/_book/resampling-and-simulation.html

Initializes the GitBook environment with specified sharing options (e.g., Facebook, Twitter) and font settings (theme, family, size). This code controls the visual presentation and interactivity of the GitBook documentation.

```javascript
gitbook.require(["gitbook"], function(gitbook) {
  gitbook.start({
    "sharing": {
      "github": false,
      "facebook": true,
      "twitter": true,
      "linkedin": false,
      "weibo": false,
      "instapaper": false,
      "vk": false,
      "whatsapp": false,
      "all": ["facebook", "twitter", "linkedin", "weibo", "instapaper"]
    },
    "fontsettings": {
      "theme": "white",
      "family": "sans",
      "size": 2
    },
    "edit": {
      "link": "https://github.com/statsthinking21/statsthinking21-core/edit/master/08-Resampling.Rmd",
      "text": "Edit"
    },
    "history": {
      "link": null,
      "text": null
    },
    "view": {
      "link": null,
      "text": null
    },
    "download": ["StatsThinking21.pdf", "StatsThinking21.epub"],
    "search": {
      "engine": "fuse",
      "options": null
    },
    "toc": {
      "collapse": "subsection"
    }
  });
});
```

--------------------------------

### Initialize GitBook - statsthinking21-core

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/_book/fitting-models.html

JavaScript code snippet used to initialize GitBook with specific configurations for sharing, font settings, editing links, history, view, downloads, search, and table of contents.

```javascript
gitbook.require(["gitbook"], function(gitbook) {
  gitbook.start({
    "sharing": {
      "github": false,
      "facebook": true,
      "twitter": true,
      "linkedin": false,
      "weibo": false,
      "instapaper": false,
      "vk": false,
      "whatsapp": false,
      "all": ["facebook", "twitter", "linkedin", "weibo", "instapaper"]
    },
    "fontsettings": {
      "theme": "white",
      "family": "sans",
      "size": 2
    },
    "edit": {
      "link": "https://github.com/statsthinking21/statsthinking21-core/edit/master/05-FittingModels.Rmd",
      "text": "Edit"
    },
    "history": {
      "link": null,
      "text": null
    },
    "view": {
      "link": null,
      "text": null
    },
    "download": ["StatsThinking21.pdf", "StatsThinking21.epub"],
    "search": {
      "engine": "fuse",
      "options": null
    },
    "toc": {
      "collapse": "subsection"
    }
  });
});
```

--------------------------------

### Initialize GitBook with sharing and font settings

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/_book/index.html

Configures GitBook platform settings including social sharing buttons, font preferences, edit links, downloadable formats, search engine, and table of contents behavior. Defines UI components and their properties for the statistics textbook interface. Requires GitBook framework to function.

```javascript
gitbook.require(\["gitbook"\], function(gitbook) { gitbook.start({ "sharing": { "github": false, "facebook": true, "twitter": true, "linkedin": false, "weibo": false, "instapaper": false, "vk": false, "whatsapp": false, "all": \["facebook", "twitter", "linkedin", "weibo", "instapaper"\] }, "fontsettings": { "theme": "white", "family": "sans", "size": 2 }, "edit": { "link": "https://github.com/statsthinking21/statsthinking21-core/edit/master/index.Rmd", "text": "Edit" }, "history": { "link": null, "text": null }, "view": { "link": null, "text": null }, "download": \["StatsThinking21.pdf", "StatsThinking21.epub"\], "search": { "engine": "fuse", "options": null }, "toc": { "collapse": "subsection" } }); });
```

--------------------------------

### Initialize GitBook configuration and load MathJax in JavaScript

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/_book/comparing-means.html

Configures GitBook documentation platform with sharing options, font settings, and edit links. Dynamically loads MathJax library for mathematical rendering by injecting a script tag into the document head. Used for interactive statistical documentation websites. Requires GitBook environment and internet access for MathJax CDN.

```javascript
gitbook.require(["gitbook"], function(gitbook) { gitbook.start({ "sharing": { "github": false, "facebook": true, "twitter": true, "linkedin": false, "weibo": false, "instapaper": false, "vk": false, "whatsapp": false, "all": ["facebook", "twitter", "linkedin", "weibo", "instapaper"] }, "fontsettings": { "theme": "white", "family": "sans", "size": 2 }, "edit": { "link": "https://github.com/statsthinking21/statsthinking21-core/edit/master/15-ComparingMeans.Rmd", "text": "Edit" }, "history": { "link": null, "text": null }, "view": { "link": null, "text": null }, "download": ["StatsThinking21.pdf", "StatsThinking21.epub"], "search": { "engine": "fuse", "options": null }, "toc": { "collapse": "subsection" } }); });
(function () { var script = document.createElement("script"); script.type = "text/javascript"; var src = "true"; if (src === "" || src === "true") src = "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.9/latest.js?config=TeX-MML-AM_CHTML"; if (location.protocol !== "file:") if (/^https?:/.test(src)) src = src.replace(/^https?:/, ''); script.src = src; document.getElementsByTagName("head")[0].appendChild(script); })();
```

--------------------------------

### GitBook Initialization and Configuration

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/_book/references.html

This JavaScript code initializes and configures the GitBook environment for the STATS THINKING 21 project. It sets up sharing options, font settings, editing links, download options, search functionality, and table of contents behavior.

```javascript
gitbook.require(["gitbook"], function(gitbook) {
  gitbook.start({
    "sharing": {
      "github": false,
      "facebook": true,
      "twitter": true,
      "linkedin": false,
      "weibo": false,
      "instapaper": false,
      "vk": false,
      "whatsapp": false,
      "all": ["facebook", "twitter", "linkedin", "weibo", "instapaper"]
    },
    "fontsettings": {
      "theme": "white",
      "family": "sans",
      "size": 2
    },
    "edit": {
      "link": "https://github.com/statsthinking21/statsthinking21-core/edit/master/99-References.Rmd",
      "text": "Edit"
    },
    "history": {
      "link": null,
      "text": null
    },
    "view": {
      "link": null,
      "text": null
    },
    "download": ["StatsThinking21.pdf", "StatsThinking21.epub"],
    "search": {
      "engine": "fuse",
      "options": null
    },
    "toc": {
      "collapse": "subsection"
    }
  });
});
```

--------------------------------

### Google Analytics Initialization JavaScript

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/_book/index.html

Sets up Google Analytics tracking using gtag for the book website. Initializes dataLayer and configures the tracker with UA-129414074-1. No inputs required; outputs event tracking to Google Analytics.

```javascript
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'UA-129414074-1');
```

--------------------------------

### Initialize GitBook Settings in JavaScript

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/_book/the-general-linear-model.html

This code configures the GitBook environment with options for sharing, font settings, editing, navigation, and search functionality. It requires the GitBook library to be loaded via its require function. Inputs are configuration objects specifying enabled features and links, with no direct outputs but modifies the GitBook instance. Limitations include hardcoded values that may not adapt to dynamic content and reliance on the GitBook plugin ecosystem.

```javascript
gitbook.require(["gitbook"], function(gitbook) {
  gitbook.start({
    "sharing": {
      "github": false,
      "facebook": true,
      "twitter": true,
      "linkedin": false,
      "weibo": false,
      "instapaper": false,
      "vk": false,
      "whatsapp": false,
      "all": ["facebook", "twitter", "linkedin", "weibo", "instapaper"]
    },
    "fontsettings": {
      "theme": "white",
      "family": "sans",
      "size": 2
    },
    "edit": {
      "link": "https://github.com/statsthinking21/statsthinking21-core/edit/master/14-GeneralLinearModel.Rmd",
      "text": "Edit"
    },
    "history": {
      "link": null,
      "text": null
    },
    "view": {
      "link": null,
      "text": null
    },
    "download": ["StatsThinking21.pdf", "StatsThinking21.epub"],
    "search": {
      "engine": "fuse",
      "options": null
    },
    "toc": {
      "collapse": "subsection"
    }
  });
});
```

--------------------------------

### Initialize Gitbook with Sharing and Font Settings

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/_book/ci-effect-size-power.html

This JavaScript snippet initializes the Gitbook library, configuring sharing options for social media platforms (Facebook, Twitter, LinkedIn, etc.), and setting font display properties like theme, family, and size. It's a common pattern for embedding interactive books or documentation.

```javascript
gitbook.require(["gitbook"], function(gitbook) {
  gitbook.start({
    "sharing": {
      "github": false,
      "facebook": true,
      "twitter": true,
      "linkedin": false,
      "weibo": false,
      "instapaper": false,
      "vk": false,
      "whatsapp": false,
      "all": ["facebook", "twitter", "linkedin", "weibo", "instapaper"]
    },
    "fontsettings": {
      "theme": "white",
      "family": "sans",
      "size": 2
    },
    "edit": {
      "link": "https://github.com/statsthinking21/statsthinking21-core/edit/master/10-ConfIntEffectSize.Rmd",
      "text": "Edit"
    },
    "history": {
      "link": null,
      "text": null
    },
    "view": {
      "link": null,
      "text": null
    },
    "download": ["StatsThinking21.pdf", "StatsThinking21.epub"],
    "search": {
      "engine": "fuse",
      "options": null
    },
    "toc": {
      "collapse": "subsection"
    }
  });
});
```

--------------------------------

### Configure GitBook Settings

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/_book/data-visualization.html

Initializes GitBook with custom settings for social sharing, font preferences, edit links, downloadable formats, search functionality, and table of contents behavior. This code configures the interactive features of the statistics textbook website.

```javascript
gitbook.require(["gitbook"], function(gitbook) { gitbook.start({ "sharing": { "github": false, "facebook": true, "twitter": true, "linkedin": false, "weibo": false, "instapaper": false, "vk": false, "whatsapp": false, "all": ["facebook", "twitter", "linkedin", "weibo", "instapaper"] }, "fontsettings": { "theme": "white", "family": "sans", "size": 2 }, "edit": { "link": "https://github.com/statsthinking21/statsthinking21-core/edit/master/04-VisualizingData.Rmd", "text": "Edit" }, "history": { "link": null, "text": null }, "view": { "link": null, "text": null }, "download": ["StatsThinking21.pdf", "StatsThinking21.epub"], "search": { "engine": "fuse", "options": null }, "toc": { "collapse": "subsection" } }); });
```

--------------------------------

### Dynamically load MathJax script for equations

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/_book/index.html

Injects MathJax library from CDN to render mathematical equations in the browser. Creates script element, configures source URL with TeX-MML-AM_CHTML config, and handles HTTP/HTTPS protocol normalization. Appends to document head and requires internet connectivity.

```javascript
(function () { var script = document.createElement("script"); script.type = "text/javascript"; var src = "true"; if (src === "" || src === "true") src = "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.9/latest.js?config=TeX-MML-AM\_CHTML"; if (location.protocol !== "file:") if (/^https?:/.test(src)) src = src.replace(/^https?:/, ''); script.src = src; document.getElementsByTagName("head")\[0\].appendChild(script); })();
```

--------------------------------

### Load MathJax - statsthinking21-core

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/_book/fitting-models.html

JavaScript code snippet to dynamically load the MathJax library, which is used for rendering mathematical formulas and equations on the webpage. It checks the protocol to ensure correct loading.

```javascript
(function () {
  var script = document.createElement("script");
  script.type = "text/javascript";
  var src = "true";
  if (src === "" || src === "true") src = "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.9/latest.js?config=TeX-MML-AM_CHTML";
  if (location.protocol !== "file:") if (/^https?:/.test(src)) src = src.replace(/^https?:/, '');
  script.src = src;
  document.getElementsByTagName("head")[0].appendChild(script);
})();
```

--------------------------------

### Initialize Source Embed and Code Folding (JavaScript)

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/data/countries/country_data_wrangling.nb.html

Initializes source embedding for a specific Rmd file and enables code folding based on a configuration parameter. This script is responsible for interactive features within the document. It runs on document ready.

```javascript
$(document).ready(function () { window.initializeSourceEmbed("country_data_wrangling.Rmd"); window.initializeCodeFolding("show" === "show"); });

```

--------------------------------

### MathJax Loading Script

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/_book/references.html

This JavaScript snippet dynamically loads the MathJax library, which is used for rendering mathematical formulas. It checks the protocol and ensures the correct MathJax URL is used, appending the script to the document's head.

```javascript
var script = document.createElement("script");
script.type = "text/javascript";
var src = "true";
if (src === "" || src === "true") src = "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.9/latest.js?config=TeX-MML-AM_CHTML";
if (location.protocol !== "file:")
  if (/^https?:/.test(src))
    src = src.replace(/^https?:/, '');
script.src = src;
document.getElementsByTagName("head")[0].appendChild(script);
```

--------------------------------

### Initialize Tabset Dropdown (JavaScript)

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/data/countries/country_data_wrangling.nb.html

Initializes the tabset dropdown functionality, allowing users to toggle the visibility of tabset navigation. This script adds a click event listener to toggle a class on the parent element. It runs on document ready.

```javascript
$(document).ready(function () { $('.tabset-dropdown > .nav-tabs > li').click(function () { $(this).parent().toggleClass('nav-tabs-open'); }); });

```

--------------------------------

### Load MathJax for Math Rendering (JavaScript)

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/data/countries/country_data_wrangling.nb.html

Dynamically loads the MathJax library to render mathematical equations in the document. It creates a script tag and appends it to the head of the document. This ensures that mathematical content is displayed correctly.

```javascript
(function () { var script = document.createElement("script"); script.type = "text/javascript"; script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"; document.getElementsByTagName("head")[0].appendChild(script); })();

```

--------------------------------

### Load tidyverse library in R

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/data/countries/country_data_wrangling.nb.html

Loads the tidyverse package, which is a collection of R packages designed for data science. This is a common first step for data manipulation and visualization tasks in R.

```r
library(tidyverse)
```

--------------------------------

### Load MathJax for Mathematical Rendering

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/_book/ci-effect-size-power.html

This JavaScript code dynamically loads the MathJax library to render mathematical equations within the HTML page. It checks the protocol to ensure correct loading and appends the script tag to the document's head, enabling the display of LaTeX and MathML content.

```javascript
(function () {
  var script = document.createElement("script");
  script.type = "text/javascript";
  var src = "true";
  if (src === "" || src === "true") src = "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.9/latest.js?config=TeX-MML-AM_CHTML";
  if (location.protocol !== "file:")
    if (/^https?:/.test(src))
      src = src.replace(/^https?:/, '');
  script.src = src;
  document.getElementsByTagName("head")[0].appendChild(script);
})();
```

--------------------------------

### CSS Syntax Highlighting for Code Blocks

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/_book/index.html

Defines styles for preformatted code blocks, including line numbering, overflow handling, and syntax coloring for various languages using Pandoc. Applies to elements like sourceCode spans; supports print and screen media. Limitations include browser-specific rendering for selections.

```css
pre > code.sourceCode { white-space: pre; position: relative; }
pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
pre > code.sourceCode > span:empty { height: 1.2em; }
.sourceCode { overflow: visible; }
code.sourceCode > span { color: inherit; text-decoration: inherit; }
pre.sourceCode { margin: 0; }
@media screen { div.sourceCode { overflow: auto; } }
@media print { pre > code.sourceCode { white-space: pre-wrap; } pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; } }
pre.numberSource code { counter-reset: source-line 0; }
pre.numberSource code > span { position: relative; left: -4em; counter-increment: source-line; }
pre.numberSource code > span > a:first-child::before { content: counter(source-line); position: relative; left: -1em; text-align: right; vertical-align: baseline; border: none; display: inline-block; -webkit-touch-callout: none; -webkit-user-select: none; -khtml-user-select: none; -moz-user-select: none; -ms-user-select: none; user-select: none; padding: 0 4px; width: 4em; color: #aaaaaa; }
pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa; padding-left: 4px; }
div.sourceCode { }
@media screen { pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; } }
code span.al { color: #ff0000; font-weight: bold; } /* Alert */
code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
code span.at { color: #7d9029; } /* Attribute */
code span.bn { color: #40a070; } /* BaseN */
code span.bu { color: #008000; } /* BuiltIn */
code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
code span.ch { color: #4070a0; } /* Char */
code span.cn { color: #880000; } /* Constant */
code span.co { color: #60a0b0; font-style: italic; } /* Comment */
code span.cv { color: #60a0b0; font-weight: bold; font-style: italic; } /* CommentVar */
code span.do { color: #ba2121; font-style: italic; } /* Documentation */
code span.dt { color: #902000; } /* DataType */
code span.dv { color: #40a070; } /* DecVal */
code span.er { color: #ff0000; font-weight: bold; } /* Error */
code span.ex { } /* Extension */
code span.fl { color: #40a070; } /* Float */
code span.fu { color: #06287e; } /* Function */
code span.im { color: #008000; font-weight: bold; } /* Import */
code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
code span.kw { color: #007020; font-weight: bold; } /* Keyword */
code span.op { color: #666666; } /* Operator */
code span.ot { color: #007020; } /* Other */
code span.pp { color: #bc7a00; } /* Preprocessor */
code span.sc { color: #4070a0; } /* SpecialChar */
code span.ss { color: #bb6688; } /* SpecialString */
code span.st { color: #4070a0; } /* String */
code span.va { color: #19177c; } /* Variable */
code span.vs { color: #4070a0; } /* VerbatimString */
code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
/* Used with Pandoc 2.11+ new --citeproc when CSL is used */
div.csl-bib-body { }
div.csl-entry { clear: both; }
.hanging div.csl-entry { margin-left:2em; text-indent:-2em; }
div.csl-left-margin { min-width:2em; float:left; }
div.csl-right-inline { margin-left:2em; padding-left:1em; }
div.csl-indent { margin-left: 2em; }
```

--------------------------------

### Apply Bootstrap Table Styles (JavaScript)

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/data/countries/country_data_wrangling.nb.html

Adds Bootstrap table classes to Pandoc-generated tables for improved styling. It targets specific table elements and applies 'table' and 'table-condensed' classes. This script runs on document ready.

```javascript
function bootstrapStylePandocTables() { $('tr.odd').parent('tbody').parent('table').addClass('table table-condensed'); }
$(document).ready(function () { bootstrapStylePandocTables(); });

```

--------------------------------

### Load and Process Population Data (R)

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/data/countries/country_data_wrangling.nb.html

Loads population data over years from a World Bank CSV file, skipping initial rows, selecting specific columns, renaming them, and filtering out rows with missing GDP data. Dependencies include 'read_csv' and 'select' functions.

```r
# from worldbank, this contains population over time
# years are in columns
population <- read_csv('worldbank/API_SP.POP.TOTAL_DS2_en_csv_v2_3469297.csv', show_col_types = FALSE, skip=4) %>%
  select(-`...66`) %>%
  rename(CountryName = `Country Name`,
         CountryCode = `Country Code`,
         Population2020 = `2020`) %>%
  select(CountryName, CountryCode, Population2020)

```

--------------------------------

### MathJax Dynamic Script Loader

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/_book/hypothesis-testing.html

This self-invoking anonymous function dynamically creates and appends a script element to the document head to load MathJax version 2.7.9 from CDN with TeX-MML-AM_CHTML configuration for rendering mathematical expressions. It sets the source to the CDN URL if not specified otherwise and strips the protocol for flexible loading (http/https). Depends on browser DOM access; outputs MathJax library for LaTeX rendering. Limitations: assumes CDN availability and may fail in offline or restricted environments; uses regex for protocol handling.

```javascript
(function () { var script = document.createElement("script"); script.type = "text/javascript"; var src = "true"; if (src === "" || src === "true") src = "https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.9/latest.js?config=TeX-MML-AM_CHTML"; if (location.protocol !== "file:") if (/^https?:/.test(src)) src = src.replace(/^https?:/, ''); script.src = src; document.getElementsByTagName("head")[0].appendChild(script); })();
```

--------------------------------

### Compute chi-squared test statistic using R

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/_book/practical-example.html

Runs Pearson's chi-squared test on a contingency table (contTable) to evaluate differences across groups. Requires the base R stats package. Input is a table of counts; output includes the chi-squared value, degrees of freedom, and p‑value. Suitable for categorical data with expected counts ≥5.

```R
## 
##  Pearson's Chi-squared test
## 
## data:  contTable
## X-squared = 4, df = 3, p-value = 0.3
```

--------------------------------

### Proof: Sum of Errors from the Mean is Zero (LaTeX)

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/_book/fitting-models.html

Provides a mathematical proof in LaTeX that the sum of deviations (errors) of data points from their mean is always zero. This is a fundamental property used in statistical analysis.

```latex
\\[ error = \sum_{i=1}^{n}(x_i - \bar{X}) = 0 \\]
\\[ \sum_{i=1}^{n}x_i - \sum_{i=1}^{n}\bar{X}=0 \\]
\\[ \sum_{i=1}^{n}x_i = \sum_{i=1}^{n}\bar{X} \\]
\\[ \sum_{i=1}^{n}x_i = n\bar{X} \\]
\\[ \sum_{i=1}^{n}x_i = \sum_{i=1}^{n}x_i \\]
```

--------------------------------

### Enhance Kable Tables with Captions (JavaScript)

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/data/countries/country_data_wrangling.nb.html

Adds 'kable-table' class to elements with 'knitsql-table' class and moves table captions above the table for better visibility. This script targets specific table structures and modifies their presentation. It runs on document ready.

```javascript
$(document).ready(function () { $('.knitsql-table').addClass('kable-table'); var container = $('.kable-table'); container.each(function() { // move the caption out of the table var table = $(this).children('table'); var caption = table.children('caption').detach(); caption.insertBefore($(this)).css('display', 'inherit'); }); });

```

--------------------------------

### Compute Beta Estimates Using Linear Algebra in R

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/_book/the-general-linear-model.html

This code block shows how to compute beta estimates for a linear model using R's linear algebra capabilities. It involves creating the Y (dependent variable) and X (design matrix) matrices, then using the general inverse function (ginv) and matrix multiplication to calculate beta_hat.

```R
# compute beta estimates using linear algebra

#create Y variable 8 x 1 matrix
Y <- as.matrix(df$grade) 
 #create X variable 8 x 2 matrix
X <- matrix(0, nrow = 8, ncol = 2)
#assign studyTime values to first column in X matrix
X[, 1] <- as.matrix(df$studyTime) 
#assign constant of 1 to second column in X matrix
X[, 2] <- 1 

# compute inverse of X using ginv()
# %*% is the R matrix multiplication operator

beta_hat <- ginv(X) %*% Y #multiple the inverse of X by Y
print(beta_hat)
```

--------------------------------

### Generate Q-Q Plots in R

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/_book/the-general-linear-model.html

This R code creates a dataset with 100 normal and uniform random samples, then produces Q-Q plots for each distribution using ggplot2 to visualize normality. It requires the tidyverse and cowplot packages. The plots are titled and combined into a grid for comparison, demonstrating divergence from normality in non-normal data.

```R
qq_df <- tibble(norm=rnorm(100),
                unif=runif(100))

p1 <- ggplot(qq_df,aes(sample=norm)) + 
  geom_qq() + 
  geom_qq_line() + 
  ggtitle('Normal data')

p2 <- ggplot(qq_df,aes(sample=unif)) + 
  geom_qq() + 
  geom_qq_line()+ 
  ggtitle('Non-normal data')

plot_grid(p1,p2)
```

--------------------------------

### Create Data Frame and Convert to Matrix in R

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/_book/the-general-linear-model.html

This snippet demonstrates how to create a tibble with study time and prior class data, then generates a 'grade' column based on these variables and adds random noise. Finally, it selects specific columns and converts the data frame subset into a matrix.

```R
df <-
  tibble(
    studyTime = c(2, 3, 5, 6, 6, 8, 10, 12) / 3,
    priorClass = c(0, 1, 1, 0, 1, 0, 1, 0)
  ) %>%
  mutate(
    grade = 
      studyTime * betas[1] + 
      priorClass * betas[2] + 
      round(rnorm(8, mean = 70, sd = 5))
  )

df_matrix <- 
  df %>%
  dplyr::select(studyTime, grade) %>%
  as.matrix()
```

--------------------------------

### Load and Process GDP Data (R)

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/data/countries/country_data_wrangling.nb.html

Loads GDP data from a World Bank CSV file, skipping initial rows, selecting and renaming relevant columns (Country Name, Country Code, GDP2020), and removing rows with missing GDP values. Dependencies include 'read_csv', 'select', and 'rename' functions.

```r
gdp <- read_csv('worldbank_gdp/API_NY.GDP.MKTP.CD_DS2_en_csv_v2_3469429.csv', show_col_types = FALSE, skip=4) %>%
  select(-`...66`) %>%
  rename(CountryName = `Country Name`,
         CountryCode = `Country Code`,
         GDP2020 = `2020`)  %>%
  select(CountryCode, GDP2020) %>%
  drop_na(GDP2020)

```

--------------------------------

### Linear Model Fit for Group Comparison (R)

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/_book/comparing-means.html

This R output shows the results of fitting a linear model to compare means between two groups using a dummy variable for group membership. It provides coefficient estimates (intercept and group difference), standard errors, t-values, and p-values for each term in the model. This demonstrates the equivalence between t-tests and linear regression for comparing means.

```R
## 
## Call:
## lm(formula = TVHrsNum ~ RegularMarij, data = NHANES_sample)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -2.2843 -1.0067 -0.0067  0.9933  2.9933 
## 
## Coefficients:
##                 Estimate Std. Error t value Pr(>|t|)    
## (Intercept)        2.007      0.116   17.27  < 2e-16 ***
## RegularMarijYes    0.778      0.230    3.38  0.00087 ***
## --- 
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 1.4 on 198 degrees of freedom
## Multiple R-squared:  0.0546, Adjusted R-squared:  0.0498 
## F-statistic: 11.4 on 1 and 198 DF,  p-value: 0.000872

```

--------------------------------

### Calculate Bayes factor for contingency table using R

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/_book/practical-example.html

Computes a Bayes factor for the same contingency table to measure evidence for the null hypothesis versus the alternative. Utilizes a Bayes factor function (e.g., from the BayesFactor package). Input is the same count table; output shows the factor and interpretation. Helpful when NHST p‑values are inconclusive.

```R
## Bayes factor analysis
## --------------
## [1] Non-indep. (a=1) : 0.058 ±0%
## 
## Against denominator:
##   Null, independence, a = 1 
## ---
## Bayes factor type: BFcontingencyTable, independent multinomial
```

--------------------------------

### Write Combined Country Data to CSV (R)

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/data/countries/country_data_wrangling.nb.html

Writes the final merged and cleaned dataset, containing country information, population, geographical data, and GDP, to a CSV file named 'country_data.csv'. Dependencies include the 'write_csv' function.

```r
write_csv(popdata_with_geodata_and_gdp, 'country_data.csv')

```

--------------------------------

### R: Fit ANOVA model with dummy coding

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/_book/comparing-means.html

This R code fits a linear model to analyze variance between groups using dummy coding. It takes 'sysBP' as the dependent variable and 'd1', 'd2' as dummy variables representing different drug conditions, with placebo as the baseline. The output includes coefficients, standard errors, t-values, p-values, and overall model fit statistics like R-squared and the F-statistic.

```R
lm(formula = sysBP ~ d1 + d2, data = df)
```

--------------------------------

### Bayesian Correlation Analysis with BayesFactor in R

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/_book/modeling-continuous-relationships.html

This R code snippet demonstrates Bayesian correlation analysis using the BayesFactor package. It provides a Bayes factor for the alternative hypothesis against a null hypothesis of zero correlation and summarizes the posterior distribution of the correlation coefficient (rho).

```r
## Bayes factor analysis
## --------------
## [1] Alt., r=0.333 : 21 ±0%
## 
## Against denominator:
##   Null, rho = 0 
## ---
## Bayes factor type: BFcorrelation, Jeffreys-beta*

## Summary of Posterior Distribution
## 
## Parameter | Median |       95% CI |     pd |          ROPE | % in ROPE |    BF |         Prior
## ----------------------------------------------------------------------------------------------
## rho       |   0.38 | [0.13, 0.58] | 99.88% | [-0.05, 0.05] |        0% | 20.85 | Beta (3 +- 3)
```

--------------------------------

### Merge Population Data with GeoData (R)

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/data/countries/country_data_wrangling.nb.html

Merges the cleaned population data with geographical data based on 'CountryName'. This step combines demographic and location information. Dependencies include the 'merge' function.

```r
popdata_with_geodata <- merge(popdata, countries, by="CountryName")

```

--------------------------------

### Load and Process Country Metadata (R)

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/data/countries/country_data_wrangling.nb.html

Loads country metadata from a CSV file, excluding specific columns like 'SpecialNotes' and 'TableName', and renames 'Country Code' to 'CountryCode'. Dependencies include 'read_csv' and 'select' functions.

```r
country_metadata <- read_csv('worldbank/Metadata_Country_API_SP.POP.TOTAL_DS2_en_csv_v2_3469297.csv', show_col_types = FALSE) %>%
  select(-`...66`) %>%
  rename(CountryCode = `Country Code`) %>%
  select(-SpecialNotes, -TableName)

```

--------------------------------

### Load and Process Geographical Data (R)

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/data/countries/country_data_wrangling.nb.html

Loads geographical data (latitude/longitude) from a CSV file and renames the 'name' column to 'CountryName'. Dependencies include the 'read_delim' function.

```r
# from google, this contains latitude/longitude
countries <- read_delim('countries/countries.csv') %>%
  rename(CountryName = name)

```

--------------------------------

### Merge GeoData with GDP Data (R)

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/data/countries/country_data_wrangling.nb.html

Merges the population data (which includes geographical information) with the processed GDP data. This combines demographic, geographic, and economic indicators. Dependencies include the 'merge' function.

```r
popdata_with_geodata_and_gdp <- merge(popdata_with_geodata, gdp)

```

--------------------------------

### Compute mixed model for paired t-test using lmer in R

Source: https://github.com/statsthinking21/statsthinking21-core/blob/master/_book/comparing-means.html

Fits a linear mixed model to perform a paired t-test using lmer() from the lme4 package. Models systolic blood pressure (BPsys) as a function of timepoint with random intercepts for each subject ID. The summary() function provides parameter estimates, random effects variances, and Satterthwaite's method for degrees of freedom. Requires the lme4 package and a tidy data frame with subject ID and timepoint variables.

```r
# compute mixed model for paired test

lmrResult <- lmer(BPsys ~ timepoint + (1 | ID), 
                  data = NHANES_sample_tidy)
summary(lmrResult)
```
Tokens:
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