Organize, document and share research data and codes using Emerson Del Ponte Prof. of Plant Pathology Editor in Chief TPP Co-founder OPP Prepared for: Re:produce workshop Session 5: Open data, materials and code 11 Dec 2019

www.openplantpathology.org

Research cycle Idea Register (proposal) Run experiments Get data Analyze Communicate

Research → Scientific Paper Idea Register (proposal) Run experiments Get data Analyze Communicate

Is the extra effort worth it ? Organizing, Documenting and Sharing (Openly) Research Data and Codes

Information Reproducible pen Research Practices Data Protocols Codes Share Why? How?

Accessibility Efficiency Transparency Reproducibility Reusability Reliability Data Protocols Codes Organizing Documenting Sharing

Get data General-purposes repositories Close/Open your data?

Run experiments Close/Open your protocol?

Analyse Research Compendium Close/open code?

Communicate Abstract Close/open your findings? Preprint Quick Files Talk Poster OA paper Paywalled paper

Do you WANT to change and be open? Challenging! Knowledge Technology

Software Workflows Environments Collaborative & sharing platforms Learn: technology for productivity

Start small… then GROW Article only Article (+ preprint) Supplemental (zip) - Protocols - Data Article + preprint Repository (citable) - Protocols - Data - Code Article + preprint Research compendium - Raw Data - Clean Data - Analysis (reproducible) eproducible research level 1 2 3 0

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

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

How to build a RC in R? Project template package Manually Semi-automated Automated Creation

Creation of RC project templates Manually (DIY) Semi-automated Automated "The workflowr R package helps researchers organize their analyses in a way that promotes effective project management, reproducibility, collaboration, and sharing of results" https://github.com/jdblischak/workflowr

Project templates + website

https://www.tandfonline.com/doi/full/10.1080/00031305.2017.1375986 https://peerj.com/preprints/3192/ RC as an R package

Manually (RStudio) creating a as R package

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

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

Automating RC website creation Organized ● Provides a project template with organized subdirectories ● Mixes code and results with R Markdown 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 R package https:/ /jdblischak.github.io/workflowr/articles/wflow-01-getting-started.html

Reproducible for future? "holepunch will read the contents of your R project on GitHub... write a Dockerfile, add a badge to your README, and build a Docker image. .. dropped into a free, live, RStudio server.." https://karthik.github.io/holepunch/

https:/ /github.com/emdelponte/RC-template Example RC template + holepunch 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

Example RC template + holepunch

Example RC template + holepunch

How to master to create and share RC?

emdelponte https://osf.io/jb6yd/ Emerson_Del_Ponte edelponte emdelponte