Get your Research Project/Article Organized, Shareable and Reproducible using and friends Emerson M. Del Ponte Open Plant Pathology Universidade Federal de Viçosa 4-h Workshop

Why Reproducible Research (RR)? Data + Protocols + Code Knowledge Reproducible Documenting and Sharing Efficiency short term effect Accessibility short and long term effect Transparency Information pen Reproducibility Research Practices Replicability

- Sponsors/journals require data (standard in molecular) - Work more efficiently and facilitate collaborations - Improved reproducibility (data and/or methods) - Technology (less cumbersome) is becoming available - Enhanced visibility and transparency - Multiple citable outcomes: data, code, manuscript, etc. Why to change/learn new things?

When RR? Idea Register (proposal) Run experiments Get data Analyze Communicate

Idea Register Preregistration Of studies University/Institution Laboratory computer When RR?

Idea Register Preregistration of Studies University/Institution Laboratory computer https://osf.io/6tsnj When RR?

Run experiments When RR?

Run experiments When RR?

Get data Submit datasets accompanying data descriptors to: Discipline-specific repositories Generalist repositories When RR?

Analyze Research Compendium When RR?

Communicate Abstract When RR? Preprint OA paper Paywalled paper Quick Files Talk Poster

How RR? Science Collect Analyse Publish Write Summarise Reproduce Re-analyse (meta-analysis) Share data Open Repository Share code open/free tools Collaborative tools Citation manager Pre-prints Open Access

Sparks et al. (unpublished) 101 99 Count How are we plant pathologists doing?

Sparks et al. (unpublished) No Upon request Paywalled Free access Are data made available?

Sparks et al. (unpublished) No Free access Are codes made available?

Sparks et al. (unpublished) No Name only Version # Full citation Is Software properly cited?

Sparks et al. (unpublished) What are the software being used?

- Lack of interest/knowledge (supplemental rarely posted) - Low incentive/pressure - that may change! - Perception that it takes time and effort - Document data and code - Versioning code and maintaining - FOBS - Fear of being scooped? - Not valued/taught in our graduate programs Why is it being so slow to adopt RR?

Tools Workflows Environments Collaborative & sharing platforms Ok, I want do it differently, but how? Research Project Organized Documented Shared Accessible Reproducible

Data wrangling - Excel Data visualization - Excel Data analysis - SAS, STATA Scientific plots - SigmaPlot Text editor - MSWord BIB Save money in Software! Use R and Friends

Start small! Then build on it... Article Article (+ preprint) Supplemental (zip) - Protocols - Data Article + preprint Repository (citable) - Protocols - Data - Code Article + preprint Research compendium - Raw Data - Clean Data - Analysis (reproducible) Reproducibility 0 1 2 3 level

A new research/submission workflow? Project Data Analysis Manuscript Preprint Journal Submission system Early view Final publication Poster/Talk Research Compendium

http://inundata.org/talks/rstd19/ https://research-compendium.science/ How RR? Source: https://research-compendium.science/

http://inundata.org/talks/rstd19/ How RR ?

https://www.tandfonline.com/doi/full/10.1080/00031305.2017.1375986 https://peerj.com/preprints/3192/ How RR?

R package structure as inspiration Small Medium Large

BIB Minimal RC Short RC webpage Full RC Website + manuscript Structures/templates for RC (not a package) CSL

Let's work? 5 Workout Sessions (45 min each) 1) Introduction 2) RStudio project + GitHub 3) The research compendium 4) Manuscript in RMarkdown 5) Packages for automating tasks & RStudio Cloud

Everything starts as a PROJECT!

RStudio and his friend Git 1. Download and install Git (GitHub Desktop) 2. Download and install RStudio 3. Go to GitHub and create a new repository Let's practice

RStudio and his friend Git 1. Create a new RStudio Project from Git 2. Add your repository URL Your turn

No content

1. Clone a repository (open in Desktop) 2. https:/ /github.com/emdelponte/paper-FHB-yield-loss 3. Change files 4. Create a pull request to the owner

Let's explore a research compendium Short RC webpage 1. Fork the repository (short webpage compendium) a. https:/ /github.com/emdelponte/RC-example-webpage 2. Explore the files 3. Reproduce the analysis 4. Knit to generate the webpage 5. Commit and push to your GH

GitHub and Open Science Framework 1. Link GitHub and Open Science Framework 2. Create an OSF Project

1. Link GitHub and Open Science Framework 2. Name your project 3. Enable GitHub Add-on GitHub and Open Science Framework

1. Link GitHub and Open Science Framework 2. Name your project 3. Select GitHub Add-on 4. Configure Add-on GitHub and Open Science Framework

1. Finish description GitHub and Open Science Framework

Let's practice: Data management 1. Create/Open an RMarkdown file a. Modify the output parameters 2. Load data a. .csv file b. .xlsx file c. .gsheet file 3. Add some basic commenting 4. Do some basic wrangling 5. Export data to .csv

How RR for data management Get data Data file types Binary Text files web-based

Data management: must read!

Organizing, naming, shaping! Data management Broman and Woo (2018)

Analyze

Analyze

Fork or download a Repository 1. Fork the RC as webpage template a. https://github.com/emdelponte/RC-example-webpage 2. Download the files from GitHub 3. Start with a new RStudio Project + Git 4. Reproduce the analysis 5. Change some content/parameters 6. Push it to your GH account

Add local folder and create a GitHub Repository

Add local folder and create a GitHub Repository

Let's practice 1. Fork the RC as website template a. https:/ /github.com/emdelponte/RC-example-website 2. Change and/or generate the website (knit) 3. Push changes to your GitHub 4. Create a GH webpage for it 5. Send it to OSF project

RMarkdown templates 1. RMarkdown html from the basic RStudio templates 2. Rmdformats: https:/ /github.com/juba/rmdformats 3. Distill for RMarkdown: https:/ /github.com/rstudio/distill 4. RMarkdown websites: https:/ /rmarkdown.rstudio.com/lesson-13.html

YML header Manuscript in RMarkdown? --- title: "The title goes here" author: "Author name goes here" output: html_document: default word_document: reference_docx: template.docx linestretch: 2 link-citations: yes linkcolor: blue csl: chicago-author-date.csl bibliography: crossref.bib --- BIB CSL https://www.zotero.org/styles

Automating RC website creation Workflowr package Organized ● Provides a project template with organized subdirectories ● Mixes code and results with R Markdown ● Uses Git to version both source code and results Reproducible ● Displays the code version used to create each result ● Runs each analysis in an isolated R session ○ Records the session information of each analysis ○ Sets the same seed for random number generation for each analysis Shareable ○ Creates a website to present your research results ○ Documents how to host your website for free via GitHub Pages or GitLab Pages ○ Creates links to past versions of results https://jdblischak.github.io/workflowr

Workflowr pkg https:/ /jdblischak.github.io/workflowr/articles/wflow-01-getting-started.html

rrtools, an R package to create RC as package! https://github.com/benmarwick/rrtools

rrtools, pkg to facilitate creation of RC as a pkg!

rrtools, pkg to facilitate creation of RC as a pkg! https:/ /rstudio.cloud/project/424109

Let's make it reproducible for future?

remotes::install_github("karthik/holepunch") library(holepunch) write_compendium_description(package = "RC template ", description = "A template for a research compendium") write_dockerfile(maintainer = "Your name") generate_badge() # This generates a badge for your readme. # At this time push the code to GitHub # And click on the badge or use the function below to get the build # ready ahead of time. build_binder() Let's make it reproducible for future?

https:/ /github.com/emdelponte/RC-template RC was a website template Live examples: https://emdelponte.github.io/paper-FHB-Brazil-meta-analysis/ https://emdelponte.github.io/paper-fungicides-whitemold/ https://mladencucak.github.io/AnalysisPLBIreland/index.html

www.openplantpathology.org