Open and reproducible science with R

Scott Chamberlain

UC Berkeley / rOpenSci

open science/research

Emergent findings

open data can make a new finding possible

Cultural barriers

Lack of incentives (carrots)

Lack of pressure (sticks)

Getting scooped ()

Takes too much time! ()

Open science as a lego set

Open science as a lego set

open science may be hard to do

but - you can work on different components

and - individual components are useful on their own

Open Data

make your data open

funders/journals often requiring this anyway

future self will thank you

Open Data: Venues

• Include data with publications
• Data specific repositories
• Code sharing sites: e.g., GitHub
• so-called Institutional Repositories (IRs)

Open Access

make your papers open

funders often requiring this anyway

talk to your librarians!

Open Access: Preprints

Preprints increasingly allowed by publishers

++ preprint outlets

SSRN^*, SocArXiv, PsyArXiv

talk to your librarians!

*: think twice maybe

Open Access: Green OA

Allowed to put up your "authors copy" on your website/etc.

the internet will surface it

Versioning

Versioning

Versioning

Including basically all research components:

• Code
• Data
• Metadata
• Text: manuscripts

Why use Versioning?

• failure proofs your work
• allows you to experiment freely!
• Metadata
• Text: manuscripts

Versioning: Git
Resources

• Happy Git with R 
• Take a Software Carpentry course
• canonical link git source code and manual

Do all work programatically

Do all work programatically

Key to reproduciblity:

Most important person that wants to reproduce your work is you!

Do all work programatically

you and yourself

- one week from now

- two months from now

- & so on

Do all work programatically

allows others to:

- contribute to your work

- check your work

- build on top of your work

scientific programming languages

are:
the canvas on which to do science

important scientific programming languages

R language

• used widely in biology, psychology, medicine, etc.

• rapidly growing user base, companies surrounding it

• includes all tools for open science workflow

• salaries for R skills up there (1, 2)

Tools

• writing: knitr, rmarkdown

• IDEs: RStudio (includes versioning help, projects support)

• projects: packrat

• sharing: github, gitlab, bitbucket

• version control: git

Workflows

• A script (i.e., a .R file)

• Script + Text = Markdown/Latex (e.g., journal article)

• Any files + Dropbox

• Any files + versioning (git)

• Any files + versioning (git) + Pandoc

What to aim for

• Do as much as possible in code

• Version control all products

• Combine text and code together

• Share/open up your work

workflow demo

Open science ecosytsem

rOpenSci does:

rOpenSci staff

• 4 full time

• now including a community manager!

• leadership team

• advisory board

the research workflow

the research workflow

the research workflow

the research workflow

the research workflow

use case 1

use case 2

use case 3: OKMaps

Wrap Up

• Open science is essential

• Open science tools are useful on their own

• rOpenSci: one of the tool makers




• Challenges going forward

• Largely cultural - will slowly change

Wrap Up

• rOpenSci is a community project

• Let us know what you need

• Help us make better tools

scotttalks.info/uofo

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rOpenSci Tools

Data Publication | Data Access |

Literature

| Altmetrics | Scalable & Reproducible Computing | Databases | Data Vizualization | Image Processing | Data Tools | Taxonomy | HTTP tools | Geospatial | Data Analysis

rOpenSci Tools

Data Publication | Data Access |

Literature

| Altmetrics | Scalable & Reproducible Computing | Databases | Data Vizualization | Image Processing | Data Tools | Taxonomy | HTTP tools | Geospatial | Data Analysis

rOpenSci Literature Tools

Public Library of Science

using rplos we can access metadata and fulltext for any PLOS article

install rplos like

install.packages("rplos")

Exercise

Create a .Rmd file

Use rplos to get fulltext for 1000 articles
-calculate number of authors per article
-make a simple plot of authors per article

Render the .Rmd to .html

Send the .Rmd version to your partner via email

Render the .Rmd file you received

Does your .html look the same?

rOpenSci Tools

Data Publication | Data Access | Literature | Altmetrics | Scalable & Reproducible Computing | Databases | Data Vizualization | Image Processing | Data Tools | Taxonomy | HTTP tools |

Geospatial

| Data Analysis

rOpenSci Geospatial Tools

using openadds (link) get addresses for Lane County

using leaflet visualize locations on map

Exercise

Create a .Rmd file

Use openadds to get a data.frame of addresses, then leaflet to visualize the map

Render the .Rmd to .html