melindahiggins2000 / bookreptemplates

Book - Reproducible Templates for Analysis and Dissemination (rt4ad)

Reproducible Templates for Analysis and Dissemination

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This book details tools and skills to improve your analyses by linking data, code and results dissemination (e.g., report, presentation, website, dashboard) into a seamless workflow. This book will help you create reusable workflow templates to improve your own efficiency. This information will also assist you with recreating a workflow that a previous coworker completed, revisiting a project you abandoned some time ago, or simply reproducing a document with a consistent format and process. Incomplete information about how the work was done, where the files are, and which is the most recent version can give rise to many complications. This book focuses on the proper end product creation process, allowing you and your colleagues to easily reproduce the components of your analyses. Throughout the exercises in this book, you will work with the R programming language, the RStudio IDE (interactive development interface) and the R Markdown package to help you build a portfolio of effective templates for reproducible analysis workflows.

Academic Level: Beginner to Intermediate

Table of Contents - WORK IN PROGRESS

1. What is reproducibility and why should I care?
   • a little history
   • data, workflow, products
   • real-world examples
2. Setup your tools and get started
   • GIT
   • GITHUB
   • R
   • RStudio
   • R markdown
   • workflow template
   • my first document
3. Main R markdown components
   • YAML
   • markdown
   • code chunks
   • tables
   • figures
   • other files and media
4. Document formats
   • HTML
   • DOC, OTF
   • PDF
5. Slide Presentations
   • ioslides, slidy
   • reveal.js
   • beamer
   • powerpoint
6. Online content
   • websites
   • dashboards
7. Books and other output formats
8. One analysis - multiple products
9. Automating your workflow
10. Creating your own template package
11. Appendices: TBA

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This book is based on the Coursera Course "Reproducible Templates for Analysis and Dissemination", https://www.coursera.org/learn/reproducible-templates-analysis

Coursera Course Description: "This course will assist you with recreating work that a previous coworker completed, revisiting a project you abandoned some time ago, or simply reproducing a document with a consistent format and workflow. Incomplete information about how the work was done, where the files are, and which is the most recent version can give rise to many complications. This course focuses on the proper documentation creation process, allowing you and your colleagues to easily reproduce the components of your workflow. Throughout this course, you'll receive helpful demonstrations of RStudio and the R Markdown language and engage in active learning opportunities to help you build a professional online portfolio."

The Course consists of 5 Modules:

1. Introduction to Reproducible Research and Dynamic Documentation

   • This module provides an introduction to the concepts surrounding reproducibility and the Open Science movement, RStudio and GitHub, and foundational cases and authors in the field.
   • 11 videos, 6 readings, 1 practice quiz

2. R Markdown: Syntax, Document, and Presentation Formats

   • This module explores the R Markdown syntax to format and customize the layout of presentations or reports and will also look at inserting and creating objects such as tables, images, or video within documents.
   • 8 videos, 11 readings, 1 practice quiz

3. R Markdown Templates: Processing and Customizing

   • This module goes further with R Markdown to help turn documents, reports, and presentations into templates for easier automation, reproducibility, and customization.
   • 9 videos, 6 readings, 1 practice quiz

4. Leveraging Custom Templates from Leading Scientific Journals

   • This module delves into custom templates available for websites, books, and scientific publishers, such as Elsevier and the IEEE, with the chance to create your first R Package.
   • 6 videos, 3 readings, 1 practice quiz

5. Working in Teams and Disseminating Templates and Reports

   • This module focuses on helpful tips for sharing and using the templates you create, as well as methods for organizing content. We'll also look at a few web-publishing services.
   • 6 videos, 2 readings, 1 practice quiz

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This book was written using the R Markdown and bookdown packages. Please see "Get Started" at https://bookdown.org/ for more information.

Last Updated on 07/04/2020

Link to book in docs https://melindahiggins2000.github.io/BookRepTemplates/