https://github.com/aaronpeikert/workflow-showcase

https://github.com/aaronpeikert/workflow-showcase

Last synced: 6 days ago
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• Host: GitHub
• URL: https://github.com/aaronpeikert/workflow-showcase
• Owner: aaronpeikert
• License: cc-by-4.0
• Created: 2019-08-29T09:58:55.000Z (over 5 years ago)
• Default Branch: master
• Last Pushed: 2022-03-31T14:07:49.000Z (about 3 years ago)
• Last Synced: 2025-03-23T22:35:11.327Z (23 days ago)
• Language: Makefile
• Size: 162 KB
• Stars: 6
• Watchers: 2
• Forks: 0
• Open Issues: 3
• Metadata Files:
  • Readme: README.Rmd
  • License: LICENSE
  • Code of conduct: CODE_OF_CONDUCT.md

Awesome Lists containing this project

• jimsghstars - aaronpeikert/workflow-showcase - (Makefile)

README

        
---

output:

  md_document:

    variant: gfm

---

```{r setup, include=FALSE}

knitr::opts_chunk$set(echo = TRUE)

library(here)

```

This is the accompanying GitHub repository to a work in progress paper by Aaron Peikert[![ORCID iD](https://orcid.org/sites/default/files/images/orcid_16x16.png)](https://orcid.org/0000-0001-7813-818X) and Andreas M. Brandmaier [![ORCID iD](https://orcid.org/sites/default/files/images/orcid_16x16.png)](http://orcid.org/0000-0001-8765-6982).

[![licensebuttons by](https://licensebuttons.net/l/by/3.0/88x31.png)](https://creativecommons.org/licenses/by/4.0) [![Ask Me Anything !](https://img.shields.io/badge/Ask%20me-anything-1abc9c.svg)](https://github.com/aaronpeikert/workflow-showcase/issues/new) ![Open Source Love](https://badges.frapsoft.com/os/v2/open-source.svg?v=103)

# Abstract

```{r abstract, child = 'abstract.Rmd'}

```

# Compile

The following paragraphs describe how you can obtain a copy of the source files of our manuscript describing reproducible workflows, and create the PDF. Either, you can go the 'standard' way of downloading a local copy of the repository and knit the manuscript file in R, or you can use the reproducible workflow as suggested and use Make to create a container and build the final PDF file in exactly the same virtual computational environment that we used to render the PDF.

## Standard Way

Requires: `Git`, `RStudio`, `pandoc`, `pandoc-citeproc` & `rmarkdown`.

Open RStudio -> File -> New Project -> Version Control -> Git

Insert:

```

https://github.com/aaronpeikert/workflow-showcase.git

```

Open `manuscript.Rmd` click on `Knit`.

## Using a Reproducible Workflow

Does not require R or RStudio, but `make` & `docker`.

Execute in Terminal:

```{bash, eval=FALSE}

git clone https://github.com/aaronpeikert/workflow-showcase.git

cd workflow-showcase

make build

make all DOCKER=TRUE

```

**Note: Windows user need to manually edit the `Makefile` and set current_path to the current directory and use `make all DOCKER=TRUE WINDOWS=TRUE`. We hope that future releases of Docker for Windows will not require that workaround.**

## Rebuild Everything

In case you experience some unexpected behavior with this workflow, you should check that you have the most recent version (`git pull`), rebuild the docker image (`make build`) and force the rebuild of all targets (`make -B DOCKER`).

```{bash, eval=FALSE}

git pull && make rebuild && make -B DOCKER=TRUE

```

# Session Info

```{r}

sessioninfo::session_info()

```