Open Science Synthesis for the Delta Science Program: Week 1
0.1
Schedule
0.1.1
Code of Conduct
0.1.2
Logistics
0.1.3
About this book
1
Session 1: Setup and Introduction to RMarkdown
1.1
RStudio and Git/GitHub Setup
1.1.1
Learning Objectives
1.1.2
Logging into the RStudio server
1.1.3
Preparing to work in RStudio
1.1.4
Setting up the R environment on your local computer
1.2
Literate Analysis with RMarkdown
1.2.1
Learning Objectives
1.2.2
Introduction and motivation
1.2.3
Basic RMarkdown syntax
1.2.4
Code chunks
1.2.5
Literate analysis practice
1.2.6
RMarkdown and environments
1.2.7
Go Further
1.2.8
Resources
1.2.9
Troubleshooting
2
Session 2: Reproducible Papers with RMarkdown
2.1
Reproducible and Transparent Papers
2.1.1
Learning Objectives
Data Citation
2.1.2
Reproducible Papers with
rrtools
2.1.3
Reproducible Papers with
rticles
The 5th Generation of Reproducible Papers
3
Session 3: Version Control with git and GitHub
3.1
Learning Objectives
3.2
Introduction to git
3.2.1
A Motivating Example
Version control and Collaboration using Git and GitHub
Let’s look at a GitHub repository
The Git lifecycle
3.3
Create a remote repository on GitHub
Setup
Challenge
3.4
Working locally with Git via RStudio
Setup
Challenge
Aside
Collaboration and conflict free workflows
3.5
Setting up git on an existing project
Challenge
Challenge
3.6
Go Further
4
Session 4: Data Modeling Essentials
4.1
Data Modeling & Tidy Data
4.1.1
Learning Objectives
4.1.2
Introduction
4.1.3
Recognizing untidy data
4.1.4
Good enough data modeling
4.1.5
Using normalized data
4.1.6
Data modeling exercise
4.1.7
Resources
5
Session 5: Cleaning and Manipulating Data
5.1
Data Cleaning and Manipulation
5.1.1
Learning Objectives
5.1.2
Introduction
5.1.3
Data Cleaning Basics
5.1.4
Joins in dplyr
6
Session 6: Collaboration Practices
6.1
Thinking preferences
6.1.1
Learning Objectives
6.1.2
Thinking Preferences Activity
6.1.3
About the Whole Brain Thinking System
6.1.4
Bonus Activity: Your Complex Self
6.2
Collaboration, authorship and data policies
6.2.1
Developing a Code of Conduct
6.2.2
Authorship and Credit
6.2.3
Data Policies
6.2.4
Extra Reading
7
Session 7: Functions and Packages
7.1
Creating R Functions
7.1.1
Why functions?
7.1.2
Documenting R functions
7.1.3
Summary
7.1.4
Examples: Minimizing work with functions
7.2
Creating R Packages
7.2.1
Learning Objectives
7.2.2
Why packages?
7.2.3
Install and load packages
7.2.4
Create a basic package
7.2.5
Add your code
7.2.6
Add documentation
7.2.7
Test your package
7.2.8
Checking and installing your package
7.2.9
Sharing and releasing your package
7.2.10
More reading
8
Session 8: Hands On: Logic Models and Synthesis Development
8.1
Synthesis Development
8.1.1
Resources
8.2
Logic Models
8.2.1
Logic Models
8.2.2
Logic models for synthesis development
8.2.3
Resources
9
Session 9: Hands On: Exploration of Data Resources and Synthesis Development
9.1
Datasets of Interest
9.2
Finding more data
10
Session 10: Quantitative synthesis tools
10.1
Learning outcomes
10.2
Context
10.2.1
Summary of options
10.2.2
Evidence framing
10.3
Challenge
10.4
Products
10.5
Resources
10.6
Reflection questions
11
Session 11: Quantitative synthesis workflow reporting
11.1
Learning outcomes
11.2
Context
11.2.1
Checklist reporting
11.2.2
Purpose
11.2.3
Goals checklist
11.3
Challenge
11.4
Products
11.5
Resources
11.6
Reflection questions
12
Session 12: Synthesis Group Presentations and Feedback
13
Session 13: Meta-analysis in R
13.1
Learning outcomes
13.2
Context
13.3
The 5 primary steps for meta-analyses in R.
13.4
Challenge
13.5
Products
13.6
Resources
13.7
Reflection questions
14
Session 14: Interpretation of meta-analysis
14.1
Learning outcomes
14.2
Context
14.3
Challenge
14.4
Products
14.5
Resources
14.6
Reflection questions
15
Session 15: Hands On: Collaborative Data Review and Prep, Collaborative Synthesis Planning
16
Session 16: Additional Resources
16.1
Creating a data portal
16.1.1
What is a Portal?
16.1.2
Portal Uses
16.1.3
Portal Main Components
16.1.4
Creating Portals
16.1.5
Adding Data to Portals
16.1.6
Creating Unique Freeform Pages
16.1.7
Saving and Editing Portals
16.1.8
How to Publish Portals
16.1.9
Sharing Portals
Challenge
16.1.10
Tutorial Videos
16.1.11
Acknowledgements
Published with bookdown
Open Science Synthesis for the Delta Science Program: Week 1
15
Session 15: Hands On: Collaborative Data Review and Prep, Collaborative Synthesis Planning