# Package

# blogdown: Creating Websites with R Markdown

## by Yihui Xie, Amber Thomas, Alison Presmanes Hill

A guide to creating websites with R Markdown and the R package blogdown. […] In the summer of 2012, I did my internship at AT&T Labs Research,1 where I attended a talk given by Carlos Scheidegger (https://cscheid.net), and Carlos said something along the lines of “if you don’t have a website nowadays, you don’t exist.” Later I paraphrased it as: “I web, therefore I am a spiderman.” Carlos’s words resonated very well with me, although they were a little exaggerated. A well-designed and maintained website can be extremely helpful for other people to know you, and you do not need to wait for … Read more →

# Mixed Models in R

## by Michael Clark

This is an introduction to mixed models in R. It covers a many of the most common techniques employed in such models, and relies heavily on the lme4 package. The basics of random intercepts and slopes models, crossed vs. nested models, etc. are covered. Discussion includes extensions into generalized mixed models and realms beyond. […] … Read more →

# The twinetverse

## by John Coene

A guide to visualise networks of Twitter interactions in R using the twinetverse. […] The goal of the twinetverse is to provide everything one might need to view Twitter interactions, from data collection to visualisation. The twinetverse package is available on Github and Bitbucket. The package is unlikely to make it onto CRAN, it may be considered once all of its children packages are on the archive network, but not until then. The source code for this book can be found on … Read more →

# Notes for ST463/ST683 Linear Models 1

## by Katarina Domijan, Catherine Hurley

These are the notes for ST463/ST683 Linear Models 1 course offered by the Mathematics and Statistics Department at Maynooth University. This module is offered at as a part of of MSc in Data Science and Data Analytics. It is an introductory course for students who have basic background in Statistics, Data analysis, R Programming and linear algebra (matrices). […] There are many good resources, e.g. Weisberg (2005), Fox (2005), Fox (2016), Ramsey and Schafer (2002), Draper and Smith (1966). We will use Minitab and R (R Core Team 2017). To create this document, I am using the bookdown package … Read more →

# Practical R Package Development (Japanese)

## by Hiroaki Yutani

Practical R Package Development […] Rのパッケージ開発については「R Packages」（Hadley Wickham、2015）に詳しいが、Rのパッケージ開発にはここ数年で様々な変化があった。 幸い、同書は第2版に向けて大幅に書き直される予定1なので、賢明なRパッケージ開発者はそれを待つのがいいだろう。本書は、あくまでもそれまでのつなぎのような存在として、むしろ筆者のメモ代わりとして、衝動的に書き殴られたものだ。Rパッケージ開発の基礎はすっとばし、新たなトピックを中心に取り扱う。信用がおける知識についてはあくまでも「R Packages」を参照されたい。 本書は、「R Packages」に載っていないことを中心に書く、という性質上、あまり初心者向けではないかもしれない … Read more →

# Statistical Rethinking with brms, ggplot2, and the tidyverse

## by A Solomon Kurz

This project is an attempt to re-express the code in McElreath’s textbook. His models are re-fit in brms, plots are redone with ggplot2, and the general data wrangling code predominantly follows the tidyverse style. […] I love McElreath’s Statistical Rethinking text. It’s the entry-level textbook for applied researchers I spent a couple years looking for. McElreath’s freely-available lectures on the book are really great, too. However, I’ve come to prefer using Bürkner’s brms package when doing Bayeisn regression in R. It’s just spectacular. I also prefer plotting with Wickham’s ggplot2, … Read more →

# Data Processing & Visualization

## by Michael Clark

The focus of this document is on common data processing and exploration techniques in R, especially as a prelude to visualization. The first part of the document will cover data structures, the dplyr and tidyverse packages, which enhance and facilitate the sorts of operations that typically arise when dealing with data, including faster I/O and grouped operations. For visualization, the focus will be on using ggplot2 and other packages that allow for interactivity. In addition, basic programming concepts and techniques are introduced. Exercises may be found in the document as well. In addition, the demonstrations of the data processing section are available in Python via Jupyter notebooks. Read more →

# Text Mining with R

## by Julia Silge and David Robinson

A guide to text analysis within the tidy data framework, using the tidytext package and other tidy tools […] This is the website for Text Mining with R! Visit the GitHub repository for this site, find the book at O’Reilly, or buy it on Amazon. This work by Julia Silge and David Robinson is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 United States … Read more →

# Graphical & Latent Variable Modeling

## by Michael Clark m-clark.github.io

This document focuses on structural equation modeling. It is conceptually based, and tries to generalize beyond the standard SEM treatment. It includes special emphasis on the lavaan package. Topics include: graphical models, including path analysis, bayesian networks, and network analysis, mediation, moderation, latent variable models, including principal components analysis and ‘factor analysis’, measurement models, structural equation models, mixture models, growth curves, item response theory, Bayesian nonparametric techniques, latent dirichlet allocation, and more. Read more →

# R 语言入门，给一心只有学习的你

## by Chris Qi from Data Maniac

This is a minimal example of using the bookdown package to write a book. The output format for this example is bookdown::gitbook. […] 想直接上手的同学，可以跳过这一部分，从安装软件开始。如果软件已经安装了，可以跳到第二章。对于喜欢把书从头读到未的同学，欢迎从这里开始。 看到这个题目，你以为我会跟你絮絮叨叨讲一个软件的发展史？这种东西听一耳朵就可以了，写出来都浪费纸墨，噢，这是电子书，不用纸也不用墨，但是打字也费劲儿呀。所以在这里，我就做个大概介绍吧： R是一门用于统计计算和作图的语言，由S语言发展而来，以统计分析功能见长。 R 是新西兰的罗斯.伊哈卡 (Ross Ihaka)和罗伯特.金特尔曼（Robert … Read more →

# IsoriX: Isoscape Computation and Inference of Spatial Origins using R

## by The IsoriX core Team

This book is the official documentation for the R package IsoriX. […] This new documentation of the R package IsoriX which aims at replacing the former vignettes and will ultimately provide much more information than before. The chapters 1 to 5 are almost complete but you will have to wait for the other chapters to follow. … Read more →

# Data Visualization with R

## by Rob Kabacoff

A guide to creating modern data visualizations with R. Starting with data preparation, topics include how to create effective univariate, bivariate, and multivariate graphs. In addition specialized graphs including geographic maps, the display of change over time, flow diagrams, interactive graphs, and graphs that help with the interpret statistical models are included. Focus is on the 45 most popular graph types. The guide also includes detailed instructions on how to customizing graphs, and ends with a chapter on graphing best practices. Although strongly based on the ggplot2 package, other approaches are included as well. Read more →

# Generalized Additive Models

## by Michael Clark

An introduction to generalized additive models (GAMs) is provided, with an emphasis on generalization from familiar linear models. It makes extensive use of the mgcv package in R. Discussion includes common approaches, standard extensions, and relations to other techniques. More technical modeling details are described and demonstrated as well. […] … Read more →

# Basic Social Justice Orientations scale testing

## by Cristóbal Moya

This is a minimal example of using the bookdown package to write a book. The output format for this example is bookdown::gitbook. […] The original publication has three tables where ALLBUS-2014 is used: The following analysis are focused on the first two tables (Table 15 and Table 8), because they contain the main resutls regarding this data source and the table from supplementary materials should not matter as long as factor loadings in Table 8 are correct. The descriptive statistics of the eight items displayed in Table 15 of the original article are reproduced from the article’s website … Read more →

# recoding Introduction to Mediation, Moderation, and Conditional Process Analysis

## by A Solomon Kurz

This project is an effort to connect his Hayes’s conditional process analysis work with the Bayesian paradigm. Herein I refit his models with my favorite R package for Bayesian regression, Bürkner’s brms. I use syntax based on sensibilities from the tidyverse and plot with Wickham’s ggplot2. […] Andrew Hayes’s Introduction to Mediation, Moderation, and Conditional Process Analysis text, the second edition of which just came out, has become a staple in social science graduate education. Both editions of his text have been from a frequentist OLS perspective. This project is an effort to … Read more →

# An Incomplete Solutions Guide to the NIST/SEMATECH e-Handbook of Statistical Methods

## by Ray Hoobler

Analysis of case studies and exercies with a focus on using the tidyverse and ggplot2. This handbook was created using the bookdown package in RStudio. The output format for this example is bookdown::gitbook. […] Exploratory Data Analysis (EDA) is a philosophy on how to work with data, and for many applications, the workflow is better suited for most working scientist and engineers. As a scientist, we are trained to formulate a hypothesis and design a series of experiments that will allow us to test the hypothesis effectively. Unfortunately, most data doesn’t from carefully controlled … Read more →

# Field Epidemiology with R

## by Tomás J. Aragón

A book example for a Chapman & Hall book. […] The document format “R Markdown” was first introduced in the knitr package (Xie, 2015, 2018) in early 2012. The idea was to embed code chunks (of R or other languages) in Markdown documents. In fact, knitr supported several authoring languages from the beginning in addition to Markdown, including LaTeX, HTML, AsciiDoc, reStructuredText, and Textile. Looking back over the five years, it seems to be fair to say that Markdown has become the most popular document format, which is what we expected. The simplicity of Markdown clearly stands out among … Read more →

# Thucydides the Neorealist?

## by J.W.Biggs

This is a minimal example of using the bookdown package to write a book. The output format for this example is bookdown::gitbook. […] Thucydides has long been viewed as an early exemplar of realist thinking in International Relations Theory. More recently, neorealist authors have claimed that Thucydides’ History offers insights into the importance of the anarchy in shaping interstate relations, and should be recognised as a neorealist. This neorealist appropriation has met substantial criticism and many revisionist scholars have urged a re-examining of Thucydides. This dissertation serves … Read more →

# Introduction to Digital Currency

## by J.W.Biggs

A summary of research conducted hitherto. […] This is research I have conducted for personal use. Using the bookdown package has enabled me to piece together my research in a quick and neat manner. I have tried to convey complex terms as simply as possible utilizing visual examples where I can. Constructive criticism is welcomed - I will regularly be updating this … Read more →

# Machine Learning

## by Michael Clark

This document provides an introduction to machine learning for applied researchers. While conceptual in nature, demonstrations are provided for several common machine learning approaches of a supervised nature. In addition, all the R examples, which utilize the caret package, are also provided in Python via scikit-learn. […] Michael Clark https://m-clark.github.io … Read more →

# 统计学习方法 – 基于R的算法实现

## by lcrfromfzu@qq.com

This is a minimal book created by using the bookdown package. The output format for this little book is bookdown::gitbook. […] 本文档的发布依赖于bookdown包, 对作者表示感谢! 文档所写R代码的依据算法来源于统计学习方法(李航著), 对作者表示感谢! 文档章节内容具体包括: … Read more →

# The Queens College Guide to Life

## by The Queens College Collective Consciousness

This is a minimal example of using the bookdown package to write a book. The output format for this example is bookdown::gitbook. […] This is a collaboratively written guide for courses at Queens College that focus on the biology of tiny things, which … Read more →

# The Queens College Stats Guide

## by The Queens College Collective Consciousness

This is a minimal example of using the bookdown package to write a book. The output format for this example is bookdown::gitbook. […] This is a guide to learning statistics at Queens College. Currently we support the following courses directly with … Read more →

# The Queens College Guide to Ecosystems

## by The Queens College Collective Consciousness

This is a minimal example of using the bookdown package to write a book. The output format for this example is bookdown::gitbook. […] This is a collaboratively written guide for courses at queens college that focus on the biology of big things, like communities and cats, which … Read more →

# The Queens College Alchemy Guide

## by The Queens College Collective Consciousness

This is a minimal example of using the bookdown package to write a book. The output format for this example is bookdown::gitbook. […] This is a collaboratively written guide for chemistry courses at Queens College, … Read more →

# Numerical Analysis: Notes

## by Brynjólfur Gauti Jónsson

This is a minimal example of using the bookdown package to write a book. The output format for this example is bookdown::gitbook. […] This is a collection of my notes and algorithms from a course on Numerical Analysis at the University of Iceland. The book used in the course was Numerical Analysis by Timothy … Read more →

# Math 390.4: Data Science with R

## by The Queens College Collective Consciousness

This is a minimal example of using the bookdown package to write a book. The output format for this example is bookdown::gitbook. […] This is a book published using the R Markdown language. R Markdown supports Latex, so you can make pretty equations like Professor Kapelner likes: (a^2 + b^2 = c^2). To type inline latex, just surround your code with dollar signs. That was published like this: $a^2 + b^2 = c^2$ You can edit the markdown for this book from RStudio just like you would edit a regular R Markdown (.Rmd) file. Here’s a picture of what it looks like as I edit this book and the R … Read more →

# The Queens College Guide to the Foundations of Life

## by The Queens College Collective Consciousness

This is a minimal example of using the bookdown package to write a book. The output format for this example is bookdown::gitbook. […] This is a sample book written in Markdown which uses Yihui Xie’s Bookdown Package for R. Every section (except for these first 2 sentences and section 3, the biochemistry guide) is from their sample book. You can use anything that Pandoc’s Markdown supports, e.g., a math equation (a^2 + b^2 = c^2). The bookdown package can be installed from CRAN or Github: Remember each Rmd file contains one and only one chapter, and a chapter is defined by the first-level … Read more →

# Economic Forum

## by Mau-Ting Lin

This is a minimal example of using the bookdown package to write a book. The output format for this example is bookdown::gitbook. … Read more →

# Selected Solutions to R4DS Exercises

## by Chunji Wang

This book provides selected solutions to the exercises in the wonderful book R for Data Science by Wickham Hadley. […] This is the website for “Selected Solutions to R4DS Exercises”. This is a joint advanture between Chunji Wang, Ron, Luna, Zhiyin, Chengcheng…. We started the “R4DS Study Club” on Sep 22nd, 2017; If you want to join us, please contact us! The chapter labels in this book is the same as the original R4DS book; go to the corresponding chapter for solutions. You might need to read the beginning of the chapter to load some packages or create some variables that are … Read more →

# R bookdownplus Textbook

## by Peng Zhao

A tutorial to R bookdownplus, an extension of R bookdown package. This books shows helps you write academic journal articles, guitar books, chemical equations, mails, calendars, and diaries, on the basis of R bookdown. […] A book titled R bookdownplus Textbook is surely talking about ‘bookdownplus’ (Zhao 2017b), but let’s start with ‘bookdown’ (Xie 2016). ‘bookdown’ is a software package for writing books or documents based on R language (R Core Team 2016) and Markdown syntax. It is something like Microsoft Word, but more elegant, more powerful, and … Read more →

# Mastering Software Development in R

## by Roger D. Peng, Sean Kross, and Brooke Anderson

The book covers R software development for building data science tools. As the field of data science evolves, it has become clear that software development skills are essential for producing useful data science results and products. You will obtain rigorous training in the R language, including the skills for handling complex data, building R packages and developing custom data visualizations. You will learn modern software development practices to build tools that are highly reusable, modular, and suitable for use in a team-based environment or a community of developers. Read more →

# Data Science and Visualizations with R

## by Jonathan Wong

Data Science and Visualizations with R […] This is a course on the use of tidyverse packages tidyverse provides a complete suite of modern data-handling tools. It is an essential toolbox for any data scientist using R. The tidyverse package is designed to be easy to install. This course will dive into using tidyverse. It will assume you have already installed r and rstudio and how some familiarity on how to use the rstudio. This book will use the nycflights13 dataset This package contains information about all flights that departed from NYC in 2013: 336,776 flights with 16 variables. To … Read more →

# R語言套件之道

## by Cheng-Chung Li

寫這本書有幾個原因，除了將自己對於R語言所學做一個整理之外，還希望能讓更多人將自己製作的R functions包裝成符合CRAN規定的R packages, 放到網路上讓大家共享。其實國內R語言的高手很多，但是卻很少人知道如何將寫好的functions包成套件，而國內的參考資料也不多。因此頂多只能在公司內部分享，這實在是很可惜的事情。 我也希望藉由這樣的資料，讓臺灣的高手們被世界看到，一起為R語言貢獻一份心力。 […] This is a sample book written in Markdown. You can use anything that Pandoc’s Markdown supports, e.g., a math equation (a^2 + b^2 = c^2). For now, you have to install the development versions of bookdown from Github: Remember each Rmd file contains one … Read more →

# The Art of Data Science

## by Roger D. Peng and Elizabeth Matsui

The book covers R software development for building data science tools. As the field of data science evolves, it has become clear that software development skills are essential for producing useful data science results and products. You will obtain rigorous training in the R language, including the skills for handling complex data, building R packages and developing custom data visualizations. You will learn modern software development practices to build tools that are highly reusable, modular, and suitable for use in a team-based environment or a community of developers. Read more →

# Tidyverse Cookbook

## by Malte Grosser

Simple cookbook for functions and idioms within the scope of the tidyverse. […] The basic idea of this book is to provide a documentation of the tidyverse written in a solution driven cookbook style. As an extra I would like to provide similar solutions based on base R functionality. Some reasons to write this book: One strength of the tidyverse is that it hides a lot of quirks that base R provides and inherits to many packages that rely on it. This allows to stick to a specific workflow from the point you enter the tidyverse until you leave it. This is why I highly recommend to head your … Read more →

# Data lunch 2feb: The use of Bookdown to write documents and reports

## by Gabriel Muñoz

Data lunch 2feb: The use of Bookdown to write documents and reports […] Make sure you have installed the latest version of R and the Preview Release of RStudio. The following packages should be installed. If you have them already make sure they are updated. The most up to date versions are the “in development” versions from gitHub. Do you have Pandoc installed? RStudio should come along with Pandoc. and latex ? ( if you want to have PDF outputs as well) note that PDF does not allow interactive plots If you do not have latex installed Mac OS X –> MacTeX (http://www.tug.org/mactex/) Linux … Read more →

# A Minimal Book Example

## by Yihui Xie (Daniel Kim translated it into Korean)

This is a minimal example of using the bookdown package to write a book. The output format for this example is bookdown::gitbook. […] This is a sample book written in Markdown. You can use anything that Pandoc’s Markdown supports, e.g., a math equation (a^2 + b^2 = c^2). For now, you have to install the development versions of bookdown from Github: Remember each Rmd file contains one and only one chapter, and a chapter is defined by the first-level heading #. To compile this example to PDF, you need to install XeLaTeX. 이 예제를 PDF로 컴파일하려면, XeLaTeX을 … Read more →

# R Powered Web Applications with Shiny

## by Zev Ross (with Andrew Clark)

R Powered Web Applications with Shiny […] This is a book version, transcribed by Andrew Clark using RStudio’s bookdown package, of an extensive blog post by Zev Ross. The book version has the advantage of being available in several formats, more easily updated and downloadable. However, for an interactive version refer to the above mentioned blog … Read more →

# GerminaQuant

## by Flavio Lozano Isla, Omar Benites Alfaro, Marcelo Francisco Pompelli

A guide for analisis of germination variables and usage of GerminaQuant. […] GerminaQuant allows make the calculation of the germination variables incredibly easy in an interactive applications build in R (R Core Team 2016), based in GerminaR and Shiny (Chang et al. 2016) package. GerminaQuant app is reactive!. Outputs change instantly as users modify inputs, without requiring a reload the app. The principal features of the application allow calculate the princiapal germination Variables, statistical analysis and easy way to plot the results. … Read more →

# A Minimal Book Example

## by Yihui Xie

This is a minimal example of using the bookdown package to write a book. The output format for this example is bookdown::gitbook. […] This is a sample book written in Markdown. You can use anything that Pandoc’s Markdown supports, e.g., a math equation (a^2 + b^2 = c^2). For now, you have to install the development versions of bookdown from Github: Remember each Rmd file contains one and only one chapter, and a chapter is defined by the first-level heading … Read more →

# Spreadsheet Munging Strategies

## by Duncan Garmonsway

Spreadsheet Munging Strategies […] This is a work-in-progress book about getting data out of spreadsheets, no matter how peculiar. The book is designed primarily for R users who have to extract data from spreadsheets and who are already familiar with the tidyverse. It has a cookbook structure, and can be used as a reference, but readers who begin in the middle might have to work backwards from time to time. R packages that feature heavily are Tidyxl and unpivotr are much more complicated than readxl, and that’s the point. Tidyxl and unpivotr give you more power and complexity when you need … Read more →

# plotly for R

## by Carson Sievert

An overview of the R package plotly […] This website explains and partially documents the R package plotly, a high-level interface to the open source JavaScript graphing library plotly.js (which powers plot.ly). The R package already has numerous examples and documentation on https://plot.ly/r and https://plot.ly/ggplot2, but this website provides more of a cohesive narrative to help explain fundamental concepts and recent developments. By reading from start to finish, readers new to R and plotly should be able to get up and running fairly quickly. That being said, advanced R and plotly … Read more →