Jabberwocky Ecology

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:

  1. Run retriever reset scripts from the command line
  2. Uninstall the old version of the EcoData Retriever
  3. Install the new version
  4. Run retriever update from 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.

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

EcoData Retriever logoWe 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.

bbs_install_animated

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")

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

Retreiver Logo
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

Four basic skill areas for a macroecologist [Guest post]

This is a guest post by Elita Baldridge (@elitabaldridge), a graduate student in Ethan White’s lab in the Ecology Center at Utah State University.

As a budding macroecologist, I have thought a lot about what skills I need to acquire during my Ph.D. This is my model of the four basic attributes for a macroecologist, although I think it is more generally applicable to many ecologists as well:

  • Data
  • Statistics
  • Math
  • Programming

Data:

  • Knowledge of SQL
  • Dealing with proper database format and structure
  • Finding data
  • Appropriate treatments of data
  • Understanding what good data are

Statistics:

  • Bayesian
  • Monte Carlo methods
  • Maximum likelihood methods
  • Power analysis
  • etc.

Math:

  • Higher level calculus
  • Should be able to derive analytical solutions for problems
  • Modelling

Programming:

  • Should be able to write programs for analysis, not just simple statistics and simple graphs.
  • Able to use version control
  • Once you can program in one language, you should be able to program in other languages without much effort, but should be fluent in at least one language.

General recommendations:

Achieve expertise in at least 2 out of the 4 basic areas, but be able to communicate with people who have skills in the other areas.  However, if you are good at collaboration and come up with really good questions, you can make up for skill deficiencies by collaborating with others who possess those skills.  Start with smaller collaborations with the people in your lab, then expand outside your lab or increase the number of collaborators as your collaboration skills improve.

Gaining skills:

Achieving proficiency in an area is best done by using it for a project that you are interested in.  The more you struggle with something, the better you understand it eventually, so working on a project is a better way to learn than trying to learn by completing exercises.

The attribute should be generalizable to other problems:  For example, if you need to learn maximum likelihood for your project, you should understand how to apply it to other questions.  If you need to run an SQL query to get data from one database, you should understand how to write an SQL query to get data from a different database.

In graduate school:

Someone who wants to compile their own data or work with existing data sets needs to develop a good intuitive feel for data; even if they cannot write SQL code, they need to understand what good and bad databases look like and develop a good sense for questionable data, and how known issues with data could affect the appropriateness of data for a given question. The data skill is also useful if a student is collecting field data, because a little bit of thought before data collection goes a long way toward preventing problems later on.

A student who is getting a terminal master’s and is planning on using pre-existing data should probably be focusing on the data skill (because data is a highly marketable skill, and understanding data prevents major mistakes).  If the data are not coming from a central database, like the BBS, where the quality of the data is known, additional time will have to be added for time to compile data, time to clean the data, and time to figure out if the data can be used responsibly, and time to fill holes in the data.

Master’s students who want to go on for a Ph.D. should decide what questions they are interested in and should try to pick a project that focuses on learning a good skill that will give them a headstart- more empirical (programming or stats), more theoretical (math), more applied (math (e.g., for developing models), stats(e.g., applying pre-existing models and evaluating models, etc.), or programming (e.g. making tools for people to use)).

Ph.D. students need to figure out what types of questions they are interested in, and learn those skills that will allow them to answer those questions.  Don’t learn a skill because it is trendy or you think it will help you get a job later if you don’t actually want to use that skill.  Conversely, don’t shy away from learning a skill if it is essential for you to pursue the questions you are interested in.

Right now, as a Ph.D. student, I am specializing in data and programming.  I speak enough math and stats that I can communicate with other scientists and learn the specific analytical techniques I need for a given project.  For my interests (testing questions with large datasets), I think that by the time I am done with my Ph.D., I will have the skills I need to be fairly independent with my research.

Postdoc in Evolutionary Bioinformatics [Jobs]

There is an exciting postdoc opportunity for folks interested in quantitative approaches to studying evolution in Michael Gilchrist’s lab at the University of Tennessee. I knew Mike when we were both in New Mexico. He’s really sharp, a nice guy, and a very patient teacher. He taught me all about likelihood and numerical maximization and opened my mind to a whole new way of modeling biological systems. This will definitely be a great postdoc for the right person, especially since NIMBioS is at UTK as well. Here’s the ad:

Outstanding, motivated candidates are being sought for a post-doctoral position in the Gilchrist lab in the Department of Ecology & Evolutionary Biology at the University of Tennessee, Knoxville. The successful candidate will be supported by a three year NSF grant whose goal is to develop, integrate and test mathematical models of protein translation and sequence evolution using available genomic sequence and expression level datasets. Publications directly related to this work include Gilchrist. M.A. 2007, Molec. Bio. & Evol. (http://www.tinyurl/shahgilchrist11) and Shah, P. and M.A. Gilchrist 2011, PNAS (http://www.tinyurl/gilchrist07a).

The emphasis of the laboratory is focused on using biologically motivated models to analyze complex, heterogeneous datasets to answer biologically motivated questions. The research associated with this position draws upon a wide range of scientific disciplines including: cellular biology, evolutionary theory, statistical physics, protein folding, differential equations, and probability. Consequently, the ideal candidate would have a Ph.D. in either biology, mathematics, physics, computer science, engineering, or statistics with a background and interest in at least one of the other areas.

The researcher will collaborate closely with the PIs (Drs. Michael Gilchrist and Russell Zaretzki) on this project but potentiall have time to collaborate on other research projects with the PIs. In addition, the researcher will have opportunties to interact with other faculty members in the Division of Biology as well as researchers at the National Institute for Mathematical and Biological Synthesis (http://www.nimbios.org).

Review of applications begins immediately and will continue until the position is filled. To apply, please submit curriculum vitae including three references, a brief statement of research background and interests, and 1-3 relevant manuscripts to mikeg[at]utk[dot]edu.