Repo url

https://github.com/quinnmoon11/QUINN-Rclass-project

Overview

A solution for the Palmer Penguins project done with R/Quarto/Github. The structure promotes a data science pipeline for reproducibility in research.

History

2023-02-16 First release with Data and Code folders with materials for data cleaning and initial exploration.
2023-03-20 Solutions added to the repository.

Acknowledgement

This repository was cloned and modified from https://github.com/mbutler808/Project-template

Software requirements

This repo contains a data analysis project and report writing using R, Quarto, Github and a reference manager for bibtex. A plain text editor is also necessary, and wordprocessing software to open any .docx files (e.g. MS Word, MacOS Pages, or LibreOffice).

For more R packages supporting reproducible research check out the taskview https://cran.r-project.org/web/views/ReproducibleResearch.html

Repository structure

The repository supports the notion that there should only be one copy of code and any outputs. Any time the intellectual content needs to be reused, it is referred to or linked from the one copy. This way we can prevent different copies of the same content from accidentally diverging, and it is easier to maintain the project.

This template also uses the convention that Folder names begin with a capital letter.

• All data goes into the Data folder and any subfolders.
• All code goes into the Code folder or subfolders.
• All results (figures, tables, computed values) go into Results folder or subfolders.
• All products (manuscripts, supplement, presentation slides, web apps, etc.) go into Products subfolders.
• See the various README.md files in those folders for some more information.

Repository content

Please see the README.md files in each folder for more details.

• This repo begins with the Palmer Penguins morphology and life history data in the Raw_data folder.
• The Processing_code folder contains several files that load the raw data, perform a bit of cleaning, and save the result in the Processed_data folder.

Planned additions:

• The Analysis_code folder will contains several files that load the processed data, do an exploratory analysis, and fit a simple model. These files produce figures and some numeric output (tables), which are saved to the results folder.
• The Products folder will contain an example bibtex and CSL style files for references. Those files are used by the example manuscript and slides.
• The Manuscript folder will contain a template for a report written as Quarto file. There is also a sub-folder containing an example template for a supplementary material file as is common in scientific articles these days.
• The slides folder contains a basic example of slides made with Quarto.

For the first project, we only have Data and Code folders. The rest will come soon.

Getting started

The project can be reproduced by executing the code in the following order:

1. First run the processing code, which will produce the processed data.

Planned additions:

2. Then run the analysis scripts, which will take the processed data and produce some results.
3. Then you can run the manuscript, poster and slides example files in any order. Those files pull in the generated results and display them. These files also pull in references from the bibtex file and format them according to the CSL style.