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How you can do better science in less time:

Open science lessons from the Ocean Health Index & Openscapes

Julia Stewart Lowndes, PhD

Marine Ecologist & Open Data Science Champion

Openscapes Director, Senior Fellow, Mozilla Fellow

National Center for Ecological Analysis & Synthesis University of California Santa Barbara, USA

@juliesquid

slides: openscapes.org/media

University of South Florida – College of Marine Science

All artwork by @allison_horst

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Open science was a means to meet our analytical needs.

Open habits reframed our culture & how we do science

An example with the Ocean Health Index

Required new skillsets & mindsets
Possible because of trust, teamwork, & leadership
Enduring benefits beyond data analysis

Reimagine public engagement & scicomm
Code & data sharing, open access publishing
Broadened collaborations and learning

ohi-science.org

Lowndes et al . 2017

Key design elements for Openscapes

We found out the hard way that our default approaches for

data analysis were not reproducible by even ourselves.

There is a lot to say about the Ocean Health Index but what’s relevant here is that my team found out the hard way that our defaut approaches to data analysis was not reproducible by even ourselves. Getting through this involved quite a reckoning, but when we got through it, we knew we had a story to tell.

[animate] We found our path to better science in less time with open data science tools and the R programming language community. This publication still resonates with researchers today because we also shared about how hard the transformation was.

[animate] It was hard because we had to learn not only new skillsets like switching to R and GitHub, but new and mindsets like letting go of our personally crafted systems and sharing imperfect work with each other. This meant changing the way we had always worked for our whole careers, which was very intimidating.

But it was possible because we trusted each other as a team and we had strong vertical leadership from our PI and horizontal leadership within our team.

We’ve had enduring benefits to this approach well beyond efficiency in data analysis:

we’ve been able to reimagine public engagement because R has made communication part of our analytical workflow. This has increase our impact incredibly – the Ocean Health Index to be used by the United Nations and over 20 groups around the world.

It’s also increased our participation in open science, since sharing code and data is part of our whole workflow rather than extra work upon publication like it had been before.

[animate] 2 big lessons coming out of this was first that open science was a means to meet our analytical needs. Open science was not a goal in itself, but a secret power that was unlocked through engaging with the open community. And the second is that the open habits we developed are enduring because they are built on trust and teamwork.

Transition: These 2 things have been key design elements for Openscapes, which I founded last year with a fellowship from Mozilla.

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Openscapes helps research groups reimagine data analysis, develop modern skills that are of immediate value to them,

and cultivate collaborative and inclusive research communities.

Engage • Empower • Amplify

openscapes.org

@openscapes

Supercharge your research (Lowndes et al. 2019, Nature)

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3 things that will change your (research) life:

Tidy data

R Markdown

Kinder science

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Tidy Data

Tidy Data for reproducibility, efficiency, and collaboration (Lowndes & Horst 2020)

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Learn more about tidy data:

Wickham (2014). Tidy Data. Journal of Statistical Software. http://jstatsoft.org/v59/i10

“Informal and code-heavy version”: https://tidyr.tidyverse.org/articles/tidy-data

Broman & Woo (2018). Data Organization in Spreadsheets. https://peerj.com/preprints/3183/

Grolemund & Wickham (2016). R for Data Science: Ch 12 https://r4ds.had.co.nz/

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R Markdown

Stats illustrations (Allison Horst)

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R Markdown

R Markdown powerfully combines executable R code with simple text formatting and for efficient, automatable, reproducible research

Analyses and figures are in the same place as your reporting document:

saves time as you iterate!

Enables good practices for reproducibility & versioning

Simple text formatting

Learn: markdown.rstudio.com

Code – R, Python, SQL, bash, others

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R Markdown

R Markdown’s familiar outputs for science: Word documents and PDFs

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Learn: markdown.rstudio.com

Our RMarkdown file renders to:

Word!

Imagine never copy-pasting a graph into your report again!!!!

R Markdown can also manage citations, cross- referencing figures and section headers.

PDF!

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R Markdown

R Markdown creates HTML files that can be shared openly on the web

We can store and distribute html files on GitHub, which also offers display options for publishing.

Let’s look at some real-world examples from the Ocean Health Index...

Learn: rmarkdown.rstudio.com

Our RMarkdown file renders to:

HTML!

Suddenly you can share a URL rather than attaching a file!

And that same URL will update rather than re-attaching a new version of the file!

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R Markdown

Transformed communication with OHI partners: methods, websites, tutorials

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Learn: markdown.rstudio.com

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R Markdown

rstudio.github.io/reticulate

Not only R – supports Python, SQL, and much more!

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Learn more about R Markdown:

RStudio (2021). RMarkdown https://rmarkdown.rstudio.com

Hill (2020). How I teach RMarkdown https://alison.rbind.io/post/2020-05-28-how-i-teach-r-markdown

Tierney (2020). R Markdown for scientists https://rmd4sci.njtierney.com

Lowndes & Horst (2020). R for Excel Users https://rstudio-conf-2020.github.io/r-for-excel

Lowndes (2016). RMarkdown website tutorial http://jules32.github.io/rmarkdown-website-tutorial

Ovando (2020) danovando.github.io/publications-with-rmarkdown/presentations/pubs-with-rmarkdown

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Kinder science

Open science is not just about improving the way we share data and methods, it’s about improving the way we think, work, and interact with each other.

It’s about technology enabling social infrastructure towards kinder science.

Open software means kinder science (Lowndes 2019, Scientific American)

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How can open science help us shift culture to make science more diverse, equitable, inclusive, and just?

How can our decisions and actions be more open, empathetic, and anti-racist?

What can we do each day to do better and support others?

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Learn more, listen, reflect, and act:

Schell et al (2020). Recreating Wakanda by promoting Black excellence in ecology and evolution https://www.nature.com/articles/s41559-020-1266-7

Carpenter (2020). Get it wrong for me: What I need from allies www.linkedin.com/pulse/get-wrong-me-what-i-need-from-allies-megan-carpenter

Harriot (2020)- A Practical Guide to Mentoring Across Intersections https://conversations.vanguardstem.com/a-practical-guide-to-mentoring-across-intersections-c596496ee334

Ariel (2017). For Our White Friends Desiring to Be Allies https://sojo.net/articles/our-white-friends-desiring-be-allies

Tunstall (2020). Dr. Dori Tunstall on Respectful Design: Models for Diversity, Inclusion, & Decolonization www.youtube.com/watch?v=oaesVb7O38s

Witze (2018). Sexual harassment is rife in the sciences, finds landmark US study www.nature.com/articles/d41586-018-05404-6

Johnson & Wilkerson (2020). All We Can Save. www.allwecansave.earth

Kimmerer (2013). Braiding Sweetgrass. https://milkweed.org/book/braiding-sweetgrass

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Thank you!

University of South Florida – College of Marine Science

Julia Stewart Lowndes, PhD

Marine Ecologist & Open Data Science Champion

Openscapes Director, Senior Fellow, Mozilla Fellow

National Center for Ecological Analysis & Synthesis University of California Santa Barbara, USA

@juliesquid

slides: openscapes.org/media

All artwork by @allison_horst

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My internal monologue:

Cool visualization!
I want to represent my data this way
He includes his code!
Package from @sckottie at rOpenSci
rnoaa is a package making NOAA data more accessible!

Twitter for community learning