Replication Package Template

Session 2: AEA Replication in Quarto

Cynthia Huang

Tuesday, July 18, 2023

Standards, guidelines, and policies

DCAS

The Data and Code Availability Standard is a standard for sharing research code and data, endorsed by leading journals in social sciences.

Unofficial Guidance

AEA Policies and Guidance

Journals which endorse DCAS aim to have polices which are compliant with the standards.¹ AEA resources include:

Replication packages

Step 0: Read the Guidelines?

Step 1 of the AEA Replication Package involves Preparing your files for verification. Again, this is a fairly long and detailed read.

TLDR: Press play and replicate!

A replication package should:

reproduce all analysis, figures, tables in the associated paper
fully document, cite and license all data used in analysis
fully document and license code used in analysis
include all data and code subject to confidentiality and licensing restrictions
specify computational requirements
set-up any packages/tools/modules required to run the analysis
run free of manual intervention (as far as possible)

Recommended Components

Code
Data
Documentation
- README, LICENSE
(Output)
- figures, tables, etc.

.
└── replication-pkg
    ├── LICENSE.txt
    ├── README.qmd
    ├── README.pdf
    ├── code
    │   ├── 00_setup
    │   ├── 01_dataprep
    │   ├── 02_analysis
    │   └── 03_appendix
    ├── data
    │   ├── analysis
    │   ├── interim
    │   └── raw
    └── (output)

README Template

The Social Science Data Editors also maintain a template README that includes the following components:

Overview
Data Availability and Provenance Statements
Dataset List
Code/Program Descriptions
Computational Requirements
Instructions to Replicators
References and Acknowledgements

So what can Quarto offer?

reusability and flexibility
combine multiple work streams
reuse existing text format outputs
citation and references
get a website (almost) for free!

Quarto Replication Template

Our Turn: Get the Template

Go to 🔗 github.com/cynthiahqy/quarto-replication-template
Click “Use this Template”
Make a new repository in your GitHub account
Get the Template on your computer:
- Download a copy,
- open with GitHub Desktop,
- or clone via Command Line
Make an Rproject in the template
Render the website

Template: README.qmd

AEA does not prescribe a set format for the README file
Different formats are useful for different venues
- .pdf –> into the .zip archive
- .md –> GitHub repo
- .html –> showcase website
All are possible with .qmd!

Template: BYO Code and Data

Bring your existing projects or workflows as they are.
Add, remove or modify folders as you like!
Maybe even develop your STATA scripts from inside the replication-pkg folder

Template Structure: Replication

The replication package is contained INSIDE the Quarto website project.
replication-pkg/ contains all code, data and replication documentation.
Compress to to replication-pkg.zip for submission

./
├── _quarto.yml
├── index.qmd
├── paper/
└── replication-pkg/
    ├── LICENSE.txt
    ├── README.qmd
    ├── code/
    │   ├── 00_setup/
    │   ├── 01_dataprep/
    │   ├── 02_analysis/
    │   └── 03_appendix/
    ├── data/
    │   ├── analysis/
    │   ├── interim/
    │   └── raw/
    ├── output/
    └── references.bib

Template Structure: Website

Place your finished publication in paper/
Update _quarto.yml and index.qmd
Render and you have a website for your paper!
Publish and share with the world

./
├── _quarto.yml
├── index.qmd
├── paper/
└── replication-pkg/
    ├── LICENSE.txt
    ├── README.qmd
    ├── code/
    │   ├── 00_setup/
    │   ├── 01_dataprep/
    │   ├── 02_analysis/
    │   └── 03_appendix/
    ├── data/
    │   ├── analysis/
    │   ├── interim/
    │   └── raw/
    ├── output/
    └── references.bib

Template: Website Defaults

_quarto.yml

project:
  type: website
  output-dir: docs 

website:
  title: "Data and Code for: Matching Mechanisms for Monkey Placement"
  description: "Supplementary materials and replication package"
  
  sidebar:
    pinned: true
    align: center
    style: docked
    search: false
    collapse-level: 2
 
    contents:
      - text: Code
        href: code.qmd
      - text: Data
      - text: Paper

format:
  html:
    theme: cosmos
    toc: true

Your Turn: replication-pkg/

Add at least one file to these template folders:
- code/
- data/
- paper/
Modify at least one section in the README.qmd using a Quarto feature you’ve learnt today.
Render README.qmd

15:00