A brief introduction to using WebR and Quarto for client-side interactive lesson material
Last week an exciting new addition to the R ecosystem was announced: webR. webR lets you run R from inside your browser, without installing R1. This is a really exciting development for educational materials, because it makes it possible to provide interactive materials where students can modify, create, and run code right inside a web page with zero setup. While it has been possible to do this in the past it required that the website be setup to run code on a server, which both required expertise that a lot of folks teaching R don’t have and introduced a lot of complexities related to things like security and server costs. With webR that all goes away.
One of the key recent tools that makes developing lessons (and lots of other things) is Quarto, which lets you write documents in markdown with embedded code blocks and then automatically turn them into documents, like web pages. And almost as soon as the first release of webR was announced there was an extension to use it as part of Quarto. So I spent a few hours this weekend seeing how far I could get with putting together some demo interactive lessons.
Results
If you just want to see what you can do you can go checkout the interactive lessons demo site. There are example lessons for basic R, dplyr, and ggplot. Give webR a few seconds to load things, the click on some Run Code buttons, change the code in the box, and then click Run Code again. You can do whatever you want, it’s running on your local machine right in the browser.
Details
You can see the current state of the material producing the demo site in the GitHub repository.
Installation
You need to have Quarto installed to start. Then install the webR Quarto extension.
quarto install extension coatless/quarto-webrBasics
Inside a quarto document where you want to use webR you need to do two things. First, add this to you YAML front matter:
engine: knitr
filters:
- webrSecond, create code blocks for webR using:
```{webr}
# Your code
```Then just preview or render the quarto file and you should be able to run and modify those code cells right on the resulting webpage.
You can do everything you would in a normal R script, including downloading files from urls and then loading them into R (there’s an example of this in the dplyr demo).
Adding packages
Things get a little trickier if you need to install packages. The simplest option is to have the user install them using a webR code block. You can’t do this using install.packages, you need to use webR’s own package system. To install dplyr you run
webr::install('dplyr')This is fine, but it might be a little confusing since it’s not how you install packages normally, and you often want to jump straight to teaching without the boiler plate of package install.
Building on the webR docs and a great example by boB Rudis2, I used the following piece of Javascript, which can be copied and pasted directly into any quarto page:
<html>
<script type="module">
//=== WebR setup ===
import { WebR } from 'https://webr.r-wasm.org/latest/webr.mjs';
globalThis.webR = new WebR();
await globalThis.webR.init();
globalThis.webRCodeShelter = await new globalThis.webR.Shelter();
await globalThis.webR.installPackages(['dplyr', 'readr'])
</script>
</html>Just change the packages on the installPackages line to what you need. Not all R packages are available, but the main TidyVerse packages are.
Making things faster (& more secure)
Once you start installing packages things start to get a little slow. You can make things a lot faster3 (and more secure) by following the webR docs strong suggestion to “To ensure a web page is cross-origin isolated, serve the page with both the COOP and COEP HTTP headers set”. The docs provide an example for doing it locally. If you’re deploying using Netlify, a common way of putting Quarto sites on the web, you can do this by creating a file named _headers in your deploy directory that contains the following:
/*
Cross-Origin-Opener-Policy: same-origin
Cross-Origin-Embedder-Policy: require-corpOther bits and pieces
With the headers properly configured I found installing and loading dplyr and readr to both be fast enough that most folks won’t notice much. ggplot2, on the other hand, is a heavier dependency and it was slow enough that I felt the need to add a warning to the top of the page to avoid confusion. That said, once it’s loaded everything is super snappy, so it’s just a question of getting the student/user to understand that there will be a little bit of a lag at the very beginning.
I’ve also started playing with the use of callout boxes with webR code blocks for providing an in-browser way to work on exercises. Here’s what the example in the ggplot demo lesson looks like:
The student can type their own code directly into the code box, while easily scrolling up in the web page to remind themselves of what they’ve just learned. If they want to check if they have the right idea they can start by looking at the expected result (which expands when clicked to show the desired figure) or look at the solution code that the lesson designer created. Side note, even for graded material in my courses I always give the students access to the expected result so that they know what they are supposed to be producing. I’ve found it really helpful for avoiding confusion about the intent of questions.
Summary
After playing around with webR + Quarto for a day or so I think this (and related systems in other languages) are going to provide a lot of really cool opportunities for making it easy to deploy interactive lesson material both for formal classes and most importantly for open educational resources. I definitely recommend checking out this approach and I’m happy to answer questions in the comments if you decide to give it a try.
A huge thanks to all of the folks making these incredible tools including George Stag and Lionel Henry for webR and James Balamuta for the Quarto extension. Also a huge thanks to boB Rudis for all his work sharing these tools and how to use them.
Read more
Footnotes
1This is part of a larger set of work to bring more meaningful computing to the browser including implementations for Python.
2I couldn’t have done most of this without boB’s excellent posts on Mastodon. Checkout his webR blog post for a full write up.
Is it OK to cite preprints? Yes, yes it is.
Should you cite preprints in your papers and should journals allow this? This is a topic that gets debated periodically. The most recent round of Twitter debate started last week when Martin Hunt pointed out that the journal Nucleic Acids Research wouldn’t allow him to cite them. A couple of days later I suggested that journals that don’t allow citing preprints are putting their authors’ at risk by forcing them not to cite relevant work. Roughly forty games of Sleeping Queens later (my kid is really into Sleeping Queens) I reopened Twitter and found a roiling debate over whether citing preprints was appropriate at all.
The basic argument against citing preprints is that they aren’t peer reviewed. E.g.,
and that this could lead to the citation of bad work and the potential decay of science. E.g.,
There are three reasons I disagree with this argument:
- We already cite lots of non-peer reviewed things in ecology
- Lots of fields already do this and they are doing just fine.
- Responsibility for the citation lies with the citer
We already cite non-peer reviewed things in ecology
As Auriel Fournier, Stephen Heard, Michael Hoffman, TerryMcGlynn and ATMoody pointed out we already cite lots of things that aren’t peer reviewed including government agency reports, white papers, and other “grey literature”.
We also cite lots of other really important non-peer reviewed things like data and software. We been doing this for decades. Ecology hasn’t become polluted with pseudo science. It will all be OK.
Lots of other fields already do this
One of the things I find amusing/exhausting about biologists debating preprints is ignorance of their history and use in other fields. It’s a bit like debating the name of an actor for two hours when you could easily look it up on Google.
In this particular case (as Eric Pedersen pointed out) we know that citation of preprints isn’t going to cause problems for the field because it hasn’t caused issues in other fields and has almost invariably become standard practice in fields that use preprints. Unless you think Physics and Math are having real issues it’s difficult to argue that this is a meaningful problem. Just ask a physicist
You are responsible for your citations
Why hasn’t citing unreviewed work caused the wheels to fall off of science? Because citing appropriate work in the proper context is part of our job. There are good preprints and bad preprints, good reports and bad reports, good data and bad data, good software and bad software, and good papers and bad papers. As Belinda Phipson, Casey Green, Dave Harris and Sebastian Raschka point out it is up to us as the people citing research to make professional judgments about what is good science and should be cited. Casey’s take captures my thoughts on this exactly:
TLDR
So yes, you should cite preprints and other unreviewed things that are important for your work. That’s called proper attribution. It has worked in ecology and other fields for decades. It will continue to work because we are scientists and evaluating the science we cite is part of our jobs. You can even cite this blog post if you want to.
Thanks to everyone both linked here and not for the spirited discussion. Sorry I wasn’t there, but Sleeping Queens is a pretty awesome game.
UPDATE: For those of you new to this discussion, it’s been going on for a long time even in biology. Here is Graham Coop’s excellent post from nearly 4 years ago.
UPDATE: Discussion of why it’s important to put preprint citations are in the reference list
Data Analyst position in ecology research group
The Weecology lab group run by Ethan White and Morgan Ernest at the University of Florida is seeking a Data Analyst to work collaboratively with faculty, graduate students, and postdocs to understand and model ecological systems. We’re looking for someone who enjoys tidying, managing, manipulating, visualizing, and analyzing data to help support scientific discovery.
The position will include:
- Organizing, analyzing, and visualizing large amounts of ecological data, including spatial and remotely sensed data. Modifying existing analytical approaches and data protocols as needed.
- Planning and executing the analysis of data related to newly forming questions from the group. Assisting in the statistical analysis of ecological data, as determined by the needs of the research group.
- Providing assistance and guidance to members of the research group on existing research projects. Working collaboratively with undergraduates, graduate students and postdocs in the group and from related projects.
- Learning new analytical tools and software as needed.
This is a staff position in the group and will be focused on data management and analysis. All members of this collaborative group are considered equal partners in the scientific process and this position will be actively involved in collaborations. Weecology believes in the importance of open science, so most work done as part of this position will involve writing open source code, use of open source software, and production and use of open data.
Weecology is a partnership between the White Lab, which studies ecology using quantitative and computational approaches and the Ernest Lab, which tends to be more field and community ecology oriented. The Weecology group supports and encourages members interested in a variety of career paths. Former weecologists are currently employed in the tech industry, with the National Ecological Observatory Network, as faculty at teaching-focused colleges, and as postdocs and faculty at research universities. We are also committed to supporting and training a diverse scientific workforce. Current and former group members encompass a variety of racial and ethnic backgrounds from the U.S. and other countries, members of the LGBTQ community, military veterans, people with chronic illnesses, and first-generation college students. More information about the Weecology group and respective labs is available on our website. You can also check us out on Twitter (@skmorgane, @ethanwhite, @weecology, GitHub, and our blog Jabberwocky Ecology.
The ideal candidate will have:
- Experience working with data in R or Python, some exposure to version control (preferably Git and GitHub), and potentially some background with database management systems (e.g., PostgreSQL, SQLite, MySQL) and spatial data.
- Research experience in ecology
- Interest in open approaches to science
- Experience collecting or working with ecological data
That said, don’t let the absence of any of these stop you from applying. If this sounds like a job you’d like to have please go ahead and put in an application.
We currently have funding for this position for 2.5 years. Minimum salary is $40,000/year (which goes a pretty long way in Gainesville), but there is significant flexibility in this number for highly qualified candidates. We are open to the possibility of someone working remotely. The position will remain open until filled, with initial review of applications beginning on May 5th. If you’re interested in applying you can do so through the official UF position page. If you have any questions or just want to let us know that you’re applying you can email Weecology’s project manager Glenda Yenni at glenda@weecology.org.
Postdoctoral research position in the Temporal Dynamics of Communities
The Weecology lab group run by Morgan Ernest and Ethan White at the University of Florida is seeking a post-doctoral researcher to study changes in ecological communities through time. This position will primarily involve broad-scale comparative analyses across communities using large time-series datasets and/or in-depth analyses of our own long-term dataset (the Portal Project). Experience with any of the following is useful, but not required: long-term data, macroecology, paleoecology, quantitative/theoretical ecology, and programming/data analysis in R or Python. The successful applicant will be expected to collaborate on lab projects on community dynamics and develop their own research projects in this area according to their interests.
Weecology is a partnership between the Ernest Lab, which tends to be more field and community ecology oriented and the White Lab, which tends to be more quantitative and computationally oriented. The Weecology group supports and encourages students interested in a variety of career paths. Former weecologists are currently employed in the tech industry, with the National Ecological Observatory Network, as faculty at teaching-focused colleges, and as postdocs and faculty at research universities. We are also committed to supporting and training a diverse scientific workforce. Current and former group members encompass a variety of racial and ethnic backgrounds from the U.S. and other countries, members of the LGBTQ community, military veterans, people with chronic illnesses, and first-generation college students. More information about the Weecology group and respective labs is available on our website. You can also check us out on Twitter (@skmorgane, @ethanwhite, @weecology), GitHub, and our blog Jabberwocky Ecology.
This 2-year postdoc has a flexible start date, but can start as early as June 1st 2017. Interested students should contact Dr. Morgan Ernest (skmorgane@ufl.edu) with their CV including a list of three references, a cover letter detailing their research interests/experiences, and one or more research samples (a PDF or link to a scientific product such as a published paper, preprint, software, data analysis code, etc). The position will remain open until filled, with initial review of applications beginning on April 24th.
Data Retriever 2.0: We handle the data so you can focus on the analysis
We are very exited to announce a major new release of the Data Retriever, our software for making it quick and easy to get clean, ready to analyze, versions of publicly available data.
The Data Retriever, automates the downloading, cleaning, and installing of ecological and environmental data into your choice of databases and flat file formats. Instead of hours tracking down the data on the web, downloading it, trying to import it, running into issues (e.g, non-standard nulls, problematic column names, encoding issues), fixing one problem, and then encountering the next, all you need to do is run a single command from the command line:
$ retriever install csv iris $ retriever install sqlite breed-bird-survey -f bbs.sqlite
or from R:
>>> rdataretriever::install('postgres', 'wine-quality')
>>> portal_data <- rdataretriever::fetch('portal')
The Data Retriever uses information in Frictionless Data datapackage.json files to automatically handle all of the complexities of “simple” data for you. For more complicated complicated datasets, with dozens of components or major data structure issues, the Retriever uses Python scripts as plugins to handle the major data cleaning work and then automatically handles the rest.
To find out more about the Data Retriever checkout the websites, the full documentation, and the GitHub repositories for both the Data Retriever and the R Data Retriever package.
Expanded focus and name change
For those of you familiar with the EcoData Retriever, this is the same software with a new name. Challenges with the data end of the analysis pipeline occur across disciplines and our tools work just as well for non-ecological data, so we’ve started adding non-ecological data and changed our name to reflect that. We’d love to hear from anyone interested in leading a push to add data from another discipline or just interested in adding a single favorite dataset.
As part of this we’ve changed the name of the R package from ecoretriever to rdataretriever.
Major changes
The 2.0 release includes a number of major changes including:
- Python 3 support (a single code base runs on both Python 2 and 3)
- Adoption of the frictionless data datapackage.json standard (replacing our old YAML like metadata system), including a command line interface for creating and editing datapackage.json files
- Add json and xml as available output formats
- Major expansion of the documentation and hosting of the documentation at Read the Docs
- Remove the graphical user interface (to allow us to focus that development time on wrappers for other languages)
- Lots of work under the hood and major improvements in testing
- Broaden scope to include non-ecological data
We are also in the process of releasing version 1.0 of the R package. This version adds the new features in the Data Retriever and also includes major stability improvements, in particular in RStudio and on Windows.
We also have a brand new website.
Upgrading to the new version (UPDATED)
To ensure the smoothest upgrade to the new version we recommend:
- Run
retriever reset scriptsfrom the command line - Uninstall the old version of the EcoData Retriever
- Install the new version
- Run
retriever updatefrom the command line
Acknowledgments
Henry Senyondo is the lead developer for the Data Retriever and has done an amazing job over the past year developing new features and shoring up the fundamentals for the software. He lead the work on 2.0 start to finish.
Akash Goel was a Google Summer of Code student with the project last summer and was responsible for the majority of the work adding Python 3 support and switching the project over to the datapackage.json standard.
Dan McGlinn, the creator of the R package, has continued his excellent leadership of the development of this package. Shawn Taylor, a new contributor, was instrumental in solving the stability issues on Windows/RStudio.
In addition to these core folks our growing group of contributors to both projects have been invaluable for adding new functionality, fixing bugs, and testing new changes. We are super excited to have contributions from 30 different people and will keep working hard to make sure that everyone feels welcome and supported in contributing to the project.
The level of work done to get these releases out the door was only possible due to generous support of the Gordon and Betty Moore Foundation’s Data Driven Discovery Initiative. This support allowed my group to employ Henry as a full time software engineer to work on these and other projects. This kind of active support for the development and maintenance of research oriented software makes sustainable software development at universities possible.
The potential for collaborative open lesson development for college coursework
Last week Zack Brym and I formally announced a semester long Data Carpentry course that we’ve have been building over the last year. One of the things I’m most excited about in this effort is our attempt to support collaborative lesson development for university/college coursework.
I’ve experience first hand the potential for this sort of collaborative lesson development though the development of workshop lessons in Software Carpentry and Data Carpentry. Many of the workshop lessons developed by these two organizations now have 100+ contributors. As far as I’m aware, Software Carpentry was the first demonstration that large-scale open collaboration on lessons could work (but I’d love to hear of earlier examples if folks are aware of them) and it has resulted in what is widely regarded as really high quality lesson material. Having seen this work so effectively for workshops, I’m interested in seeing how well it can work for full length courses.
Most college and university courses that I’m aware of start in one of three ways: 1) someone sites down and develops a course completely from scratch; 2) the course directly follows a text book; or 3) a new professor inherits a course from the person who taught it previously and adapts it.
Developing a course from scratch, even one following a text book fairly closely, is a huge time commitment. In contrast, with collaboratively developed courses new faculty, or faculty teaching new courses, wouldn’t need to start from scratch. They would be able to pick up an existing course to adapt and improve. I can’t even begin to describe how much easier this would have made my first few years as a faculty member. More generally, if we are teaching similar courses across dozens or hundreds of universities, it is much more efficient to share the effort of building and improving those courses than to have each person who teaches them do so independently.
In addition to the time and energy, there are often a lot of things that don’t work well the first time you teach a course and it typically takes a few rounds of teaching it to figure what works best. One of the challenges of developing lessons in isolation is that you only teach a class every 1 or 2 years. This makes it hard and slow to figure out what needs work. In contrast, a collaboratively developed course might be taught dozens or hundreds of times each year, allowing the course to be improved much more rapidly through large scale sampling and discussion of what works and what doesn’t. In addition to having more information, the fact that faculty are spending less time developing courses from scratch should leave them with more time for improving the materials. In combination this results in the potential for higher quality courses across institutions.
By involving large numbers of lesson developers, collaborative development also has the potential to help make courses more accurate, more up-to-date, and more approachable by novices. More lesson developers means a greater chance of having an expert on any particular topic involved, thus making the material more accurate and reducing the amount of bad practice/knowledge that gets taught. New faculty with more recent training on the development team can help keep both the material and the pedagogical practices up-to-date (this is hard when the same person teaches the same course for 20 years). More lesson developers also increases the likelihood that someone who isn’t an expert in any given piece of material is also involved, which should help make sure that the lesson avoids issues with expert blindness, thus making the material more accessible to students.
Collaborative college/university lesson development will not be without challenges. The skills required for collaborative lesson development in the style of Software and Data Carpentry require proficiency with computational approaches not familiar to many academics. The necessary skills include things like version control, developing materials in markdown, and working with static site generators like Jekyll. This means this approach is currently most accessible for those with some computational training and may initially work best for computing focused courses. In addition, organizing open collaborations takes time and energy, as does collectively deciding on how to design and update classes. Universities and colleges are not typically good at valuing time invested in non-traditional efforts and that would need to change to help support those managing development of courses with large numbers of faculty involved. More substantial may be the fact that faculty are not used to collaborating with other people on course development and are therefore not used to compromising and negotiating what should go into a course. This can be compensated for to some degree by making courses easy to modify and customize, as we’ve tried to do with the Data Carpentry Semester course, but ultimately there will still need to be a shift from prioritizing the personal desires of the faculty member to the best interests of the course more broadly. This approach will likely work best where there are a number of places that all want to teach the same general material.
Is it time? When I built my first version of Programming for Biologists back in 2010 I was really excited about the potential for collaborative open course development. I built the course using Drupal, emailed a bunch of my friends who were teaching similar courses and said “Hey, we should work together on this stuff”, and stuck some welcoming language on the homepage. Nothing happened. A few years later I was on sabbatical at the University of North Carolina and got the opportunity to talk a fair bit with Elliot Hauser who was part of a team trying to encourage this through a start-up called Coursefork. I was somewhat skeptical that this approach would work broadly at the time, but I thought it was really awesome that they were trying. They ended up pivoting to focus on helping computing education through a somewhat different route and became trinket. A couple of years I converted my course to Jekyll on GitHub and told a lot of people about it. There was much excited. Still nothing happened. So why might this work now? I think there are three things that increase the possibility of this becoming a bigger deal going forward. First, open source software development is becoming more frequent in academia. It still isn’t rewarded anywhere close to sufficiently, but the ethos of using and contributing to collaboratively developed tools is growing. Second, the technical tools that make this kind of collaboration easier are becoming more widely used and easier to learn through training efforts like Software Carpentry. Third, more and more people are actively developing university courses using these tools and making them available under open source licenses. Two of my favorites are Jenny Bryan’s Stat 545 and Karl Broman’s Tools for Reproducible Research. Our development of the Data Carpentry semester course has already benefited from using openly available materials like these and feedback from members of the computational teaching community. I guess we’ll see what happens next.
This post benefited from a number of comments and suggestions by Zack Brym, who has also played a central and absolutely essential role in the development of the Data Carpentry semester long course. The post also benefited from several conversations with Tracy Teal, the Executive Director of Data Carpentry about the potential value of these approaches for college courses
Fork our course: A semester-long Data Carpentry course for biologists
This is post is co-authored by Zack Brym and Ethan White
Over the last year and a half we have been actively developing a semester-long Data Carpentry course designed to be easily customized and integrated into existing graduate and undergraduate curricula.
Data Carpentry for Biologists contains course materials for teaching scientists how to work more effectively with data. The course provides introductions to data management and relational databases, data manipulation and analysis, and data visualization. It covers the same general types of material as a two-day Data Carpentry workshop, but expands the materials and opportunities for practice into a full-length university course. The teaching material uses R and SQLite, with some corresponding materials for Python as well. To help students understand the direct applications to their interests, the examples and exercises focus on biological questions and working with real data. The course emphasizes using best practices to produce reusable and reproducible data analysis.
Active-learning Teaching Materials
Learning computing requires active practice by working through programming problems. Just diving in to computing is challenging for most scientists, so the course instruction is designed to combine short live-coding introductions to concepts followed immediately by the students working on a related exercise. Additional exercises are assigned later for practice. This follows the “I do”, “We do”, “You do” approach to teaching, which leverages the benefits of active-learning and flipped classrooms without leaving students who are less comfortable with the material feeling lost. The bulk of class time is spent working on assigned exercises with the instructor moving around the room helping guide students through things they don’t understand and engaging with students who are thinking about advanced applications of what they’ve learned.
This approach is the result of lots of reading about effective teaching methods and Ethan’s experience teaching this and related courses over the last six years at Utah State University and the University of Florida. It seems to work well for both students that get the material easily and those that find it more challenging. We’ve also tried to make these materials as useful as possible for self-guided students.
Open course development
Software Carpentry and Data Carpentry have shown how powerful collaborative lesson development can be and we’re interested in bringing that to the university classroom. We have designed the course materials to be modular and easy to modify, and the course website easy to clone and set up. All of the teaching materials and associated website files are openly available at the Data Carpentry for Biologists repository on GitHub under CC-BY and MIT licenses. The course materials are all written in Markdown and everything runs on Jekyll through GitHub Pages. Making your own version of the course should take less than an hour. We’ve developed documentation for how to create your own version of the course and how to contribute to development. Exercises and assignments are modular and changing exercises and assignments simply involves reordering items in a list. Adding a new exercise involves creating a new Markdown file and then adding its title to the list of exercises for an assignment.
Get Involved
If you teach, or want to teach, a course like this, we’d love to get you involved. Here are some useful links for getting started.
– I want to teach the course.
– I have some feedback.
– I want to contribute to the project.
We want to be sure getting involved is as easy as possible. We’ve worked hard to provide documentation and help resources for students and instructors. Students can find all they need to know at our student start guide. Instructors have access to course content and site design documentation.
If your having trouble finding something or getting something to work, or simply have some feedback about the course please open a new issue at GitHub or send us an email.
Acknowledgements
Development of this course was generously support by the Gordon and Betty Moore Foundation’s Data-Driven Discovery Initiative through Grant GBMF4563 to Ethan White and the National Science Foundation as part of a CAREER award to Ethan White.
New release of the EcoData Retriever
We are very exited to announce the newest release of the EcoData Retriever, our software for automating the downloading, cleaning, and installing of ecological and environmental data. Instead of hours or days trying to get complicated datasets like the Breeding Bird Survey ready for analysis, the Retriever lets you simply click a button or run a single command from R or the command line, and your computer does the rest.
It’s been over a year since the last retriever release and there are lots of new features and improvements to be excited about.
- We’ve added 21 new datasets, including major ecological and environmental datasets like eBird, Vertnet, and the Global Wood Density Database, and the PRISM climate data.
- To support all of these datasets we’ve added support for additional data types including greater than memory archive files, and we’ve also improved the ability to control where downloaded files are stored and how they are clustered together.
- We’ve significantly improved documentation and now have a new automatically built documentation site at Read The Docs.
- We’ve also made a lot of under the hood improvements.
This is also the first release that has been overseen by Weecology’s new software engineer, Henry Senyondo. We’re excited to have Henry on the team, and now that he’s around development of both the EcoData Retriever and other lab software projects will be happening more quickly.
A big thanks to the Gordon and Betty Moore Foundation’s Data-Driven Discovery Initiative for funding this development through Grant GBMF4563 and to the National Science Foundation for funding as part of a CAREER award to Ethan White.
UPDATE: Led by Dan McGlinn we also released a new version of the ecoretriever R interface for the Retriever last fall. This makes using the Retriever from R as simple as:
data <- ecoretriever::fetch("BBS")
GEB adds unlimited data references section to papers
In a big step forward for allowing proper credit to be provided to all of the awesome folks collecting and publishing data, the journal Global Ecology & Biogeography has just announced that they will start supporting an unlimited set of references to datasets used in a paper.
A growing concern in the macroecological community has been that many papers whose data are used in meta-analyses or data-compilation papers have not been getting citation credit because most journals require these papers to only be listed in the supplemental material (which is not indexed by most indexing services). GEB is proud to support the inclusion of a second list of references within the main paper for all data papers used… To our knowledge, GEB is the first journal in the ecological field to do this. And we’ll be working with Wiley to further improve options in this area.
These references will be included immediately following the traditional references section in both the html and pdf versions of the paper. You can see an example in Olds et al. (2016).
What this means is that when you combine data from dozens or hundreds of studies to conduct a synthetic analysis, you can cite all of the sources in a way that will provide citation credit to those collecting the data1. It also means that scientists using large data compilations can cite the original data sources as well as the compilation itself2.
This is important for encouraging the publication of data, since one of the common reasons that scientists don’t publish data is a lack of credit, and citation only in non-indexed supplementary materials sections is a common concern.
Facilitating proper citation of all data sources is something the community has been requesting and it’s great to see GEB taking the lead in this area. Since Wiley, the publisher of GEB, is the largest publisher of ecology journals, it should be straightforward to implement this new approach widely. If other journals follow GEB’s lead, we will enter a new era where citation of data can be as complete as possible, allowing proper credit to everyone who collects and publishes data.
1GEB will need to make sure that this section gets properly picked up by the indexers, and tweak the presentation as necessary if it isn’t.
2Provided that the compilation provides a method for compiling a citation list of all associated sources.
White Lab PhD openings at the University of Florida
I’m looking for one or more graduate students to join my group next fall. In addition to the official add (below) I’d like to add a few extra thoughts. As Morgan Ernest noted in her recent ad, we have a relatively unique setup at Weecology in that we interact actively with members of the Ernest Lab. We share space, have joint lab meetings, and generally maintain a very close intellectual relationship. We do this with the goal of breaking down the barriers between the quantitative side of ecology and the field/lab side of ecology. Our goal is to train scientists who span these barriers in a way that allows them to tackle interesting and important questions.
I also believe it’s important to train students for multiple potential career paths. Members of my lab have gone on to faculty positions, postdocs, and jobs in both science non-profits and the software industry.
Scientists in my group regularly both write papers (e.g., these recent papers from dissertation chapters: Locey & White 2013, Xiao et al. 2014) and develop or contribute to software (e.g., EcoData Retriever, ecoretriever, rpartitions & pypartitions) even if they’ve never coded before they joined my lab.
My group generally works on problems at the population, community, and ecosystem levels of ecology. You can find out more about what we’ve been up to by checking out our website. If you’re interested in learning more about where the lab is headed I recommend reading my recently funded Moore Investigator in Data-Driven Discovery proposal.
PH.D STUDENT OPENINGS IN QUANTITATIVE, COMPUTATIONAL, AND MACRO- ECOLOGY
The White Lab at the University of Florida has openings for one or more PhD students in quantitative, computational, and/or macro- ecology to start fall 2015. The student(s) will be supported as graduate research assistants from a combination of NSF, Moore Foundation, and University of Florida sources depending on their research interests.
The White Lab uses computational, mathematical, and advanced statistical/machine learning methods to understand and make predictions/forecasts for ecological systems using large amounts of data. Background in quantitative and computational techniques is not necessary, only an interest in learning and applying them. Students are encouraged to develop their own research projects related to their interests.
The White Lab is currently at Utah State University, but is moving to the Department of Wildlife Ecology and Conservation at the University of Florida starting summer 2015.
Interested students should contact Dr. Ethan White (ethan@weecology.org) by Nov 15th, 2014 with their CV, GRE scores, and a brief statement of research interests.
UPDATE: Added a note that we work at population, community, and ecosystem levels.
EcoData Retriever now supports R and environmental data, and has more datasets
We are very excited to announce the newest release of our EcoData Retriever software and the first release of a supporting R package, ecoretriever. If you’re not familiar with the EcoData Retriever you can read more here.
The biggest improvement to the Retriever in this set of releases is the ability to run it directly from R. Dan McGlinn did a great job leading the development of this package and we got ton of fantastic help from the folks at rOpenSci (most notably Scott Chamberlain, Gavin Simpson, and Karthik Ram). Now, once you install the main EcoData Retriever, you can run it from inside R by doing things like:
install.packages('ecoretriever')
library(ecoretriever)
# List the datasets available via the Retriever
ecoretriever::datasets()
# Install the Gentry dataset into csv files in your working directory
ecoretriever::install('Gentry', 'csv')
# Download the raw Gentry dataset files, without any processing,
# to the subdirectory named data
ecoretriever::download('Gentry', './data/')
# Install and load a dataset as a list
Gentry = ecoretriever::fetch('Gentry')
names(Gentry)
head(Gentry$counts)
The other big advance in this release is the ability to have the Retriever directly download files instead of processing them. This allows us to support data that doesn’t come in standard tabular forms. So, we can now include things like environmental data in GIS formats and phylogenetic data such as supertrees. We’ve used this new capability to allow the automatic downloading of the Bioclim data, one of the most widely used climate datasets in ecology, and the supertree for mammals from Fritz et al. 2009.
Finally, we’ve also add the very cool mammalian diet dataset from Dryad
Sharing in Science: my full reply to Eli Kintisch
A couple of weeks ago Eli Kintisch (@elikint) interviewed me for what turned out to be a great article on “Sharing in Science” for Science Careers. He also interviewed Titus Brown (@ctitusbrown) who has since posted the full text of his reply, so I thought I’d do the same thing.
How has sharing code, data, R methods helped you with your scientific research?
Definitely. Sharing code and data helps the scientific community make more rapid progress by avoiding duplicated effort and by facilitating more reproducible research. Working together in this way helps us tackle the big scientific questions and that’s why I got into science in the first place. More directly, sharing benefits my group’s research in a number of ways:
- Sharing code and data results in the community being more aware of the research you are doing and more appreciative of the contributions you are making to the field as a whole. This results in new collaborations, invitations to give seminars and write papers, and access to excellent students and postdocs who might not have heard about my lab otherwise.
- Developing code and data so that it can be shared saves us a lot of time. We reuse each others code and data within the lab for different projects, and when a reviewer requests a small change in an analysis we can make a small change in our code and then regenerate the results and figures for the project by running a single program. This also makes our research more reproducible and allows me to quickly answer questions about analyses years after they’ve been conducted when the student or postdoc leading the project is no longer in the lab. We invest a little more time up front, but it saves us a lot of time in the long run. Getting folks to work this way is difficult unless they know they are going to be sharing things publicly.
- One of the biggest benefits of sharing code and data is in competing for grants. Funding agencies want to know how the money they spend will benefit science as a whole, and being able to make a compelling case that you share your code and data, and that it is used by others in the community, is important for satisfying this goal of the funders. Most major funding agencies have now codified this requirement in the form of data management plans that describe how the data and code will be managed and when and how it will be shared. Having a well established track record in sharing makes a compelling argument that you will benefit science beyond your own publications, and I have definitely benefited from that in the grant review process.
What barriers exist in your mind to more people doing so?
There is a lot of fear about openly sharing data and code. People believe that making their work public will result in being scooped or that their efforts will be criticized because they are too messy. There is a strong perception that sharing code and data takes a lot of extra time and effort. So the biggest barriers are sociological at the moment.
To address these barriers we need to be a better job of providing credit to scientists for sharing good data and code. We also need to do a better job of educating folks about the benefits of doing so. For example, in my experience, the time and effort dedicated to developing and documenting code and data as if you plan to share it actually ends up saving the individual research time in the long run. This happens because when you return to a project a few months or years after the original data collection or code development, it is much easier if the code and data are in a form that makes it easy to work with.
How has twitter helped your research efforts?
Twitter has been great for finding out about exciting new research, spreading the word about our research, getting feedback from a broad array of folks in the science and tech community, and developing new collaborations. A recent paper that I co-authored in PLOS Biology actually started as a conversation on twitter.
How has R Open Science helped you with your work, or why is it important or not?
rOpenSci is making it easier for scientists to acquire and analyze the large amounts of scientific data that are available on the web. They have been wrapping many of the major science related APIs in R, which makes these rich data sources available to large numbers of scientists who don’t even know what an API is. It also makes it easier for scientists with more developed computational skills to get research done. Instead of spending time figuring out the APIs for potentially dozens of different data sources, they can simply access rOpenSci’s suite of packages to quickly and easily download the data they need and get back to doing science. My research group has used some of their packages to access data in this way and we are in the process of developing a package with them that makes one of our Python tools for acquiring ecological data (the EcoData Retriever) easy to use in R.
Any practical tips you’d share on making sharing easier?
One of the things I think is most important when sharing both code and data is to use standard licences. Scientists have a habit of thinking they are lawyers and writing their own licenses and data use agreements that govern how the data and code and can used. This leads to a lot of ambiguity and difficulty in using data and code from multiple sources. Using standard open source and open data licences vastly simplifies the the process of making your work available and will allow science to benefit the most from your efforts.
And do you think sharing data/methods will help you get tenure? Evidence it has helped others?
I have tenure and I certainly emphasized my open science efforts in my packet. One of the big emphases in tenure packets is demonstrating the impact of your research, and showing that other people are using your data and code is a strong way to do this. Whether or not this directly impacted the decision to give me tenure I don’t know. Sharing data and code is definitely beneficial to competing for grants (as I described above) and increasingly to publishing papers as many journals now require the inclusion of data and code for replication. It also benefits your reputation (as I described above). Since tenure at most research universities is largely a combination of papers, grants, and reputation, and I think that sharing at least increases one’s chances of getting tenure indirectly.
UPDATE: Added missing link to Titus Brown’s post: http://ivory.idyll.org/blog/2014-eli-conversation.html
Jabberwocky Ecology 