Jabberwocky Ecology

2017 Summer Plant Census

Someone (**cough** **cough** Morgan) fell down on their job rebloging the Portal Project 40th anniversary posts to Jabberwocky. But that means this week is the week o’ Portal as we reblog the various posts from the past few weeks. First up, what happens when we go out in the summer to count plants?

The Portal Project

Twice a year the Portal crew gets a little larger, and spends a few extra days, and we count plants on all 384 quadrats. Despite some of us being in our second decade of visiting the site, and everyone on the plant crew being intimately familiar with most of the species at the site, and that the rodent RA has been watching the plants grow and giving us monthly updates, we still never really know what we’re going to find once we get out there. The desert does what it wants.

The uncertainty seems especially high for the summer plant community. Some years we arrive to an ocean of grass, waving in the breeze. Those are the years we spend a lot of ‘quality time’ with each quadrat. Other years we arrive to a dustbowl. We walk around the site laying our PVC quadrat down and picking it back up…

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Ode to six-legged wonder

While the Portal Project focuses primarily on rodents and plants, there is more to our ecosystem than just those taxa. This week’s Portal Project post focuses on some insect work at the site.

The Portal Project

If four legs are great, six legs are better. Right? For forty years now, the Portal Project has primarily focused on two-legged creatures trapping, studying, and sometimes cuddling small, furry four-legged creatures. But we haven’t ignored the six-legged inhabitants of our long-term research site, and I am going to tell you more about them now.

roachantmouse Which one of these is least like the other?

I am the Ernest lab entomologist, who doesn’t consider herself an entomologist. I am interested in biodiversity, community, and macroecological patterns like those studied by generations of Portal rodent researchers. I just happen to study them using bees. There are over twenty thousand species of bees in the world, and about four thousand in North America. My research so far has focused on the community ecology of native bees in a global hotspot of bee diversity in California. But as fate or luck would have it…

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The Spectabulous Spectabs of Portal

The latest installment from the Portal Project Blog on the watch for Banner-tailed Kangaroo Rats

The Portal Project

Much beloved by those who have worked at the Portal Project, the banner-tailed kangaroo rat (Dipodomys spectabilis) is one of the most charismatic rodents at the site (for us smammal lovers who think rodents can be charismatic, anyway). The fact that they have a nickname—spectabs—attests to this fondness. Look at that mighty tufted tail! Those giant, majestic furred feet! Weighing in at over 100 grams as adults, they are twice the size of our other kangaroo rat species (D. ordii and D. merriami). What’s not to love?

8067256761_6ab7d78602_zDipodomys spectabilis

As avid readers of the Portal blog might recall, the site used to be much grassier back in the day. At the start of the project in 1977, spectabs were running the show at Portal; we even had some plots that excluded only D. spectabilis because they were so dominant! For the spectabs, this was a desert…

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Portal Phenocam

How did we get those daily pics of the desert turning green in a week? Meet Portal’s new toy: the Phenocam.

The Portal Project

You may have noticed the super-cool daily images featured in last week’s post. They’re from our new network camera.

For starters, it allows us to do things like watch our desert field site turn from brown to green in no time flat (and back to brown again this winter).

But even cooler, our camera is part of the PhenoCam Network. They’re organizing a network of near-surface remote sensing images from sites all over the world. This creates a time series of images, in RGB and infrared, that can be used for phenology monitoring by the PhenoCam folks, us, or anyone who’s interested.

The PhenoCam folks make all the imagery freely available to download. From installation and configuration to image analysis, they provide awesome support. And their R package phenopix provides a quickstart to using phenocam imagery.

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How fast can a desert turn green?

Ever wondered how fast the desert can turn green when the rains get going? There’s a Portal blog post on that (with pics)!

The Portal Project

In the desert, water is life. Without it, the desert is brown and dusty. At our site, the rains come twice a year – once during the ‘winter’ (I put that in quotes for our readers where winter means snow and/or extended periods below freezing) and once during the summer. Water in the summer and water in the winter don’t have the same effect on the desert, though. Plants need both warmth and water to grow. When rain falls in the desert in the winter, growth is slow and typically waits until the warmer temperatures of spring. In the summer, though, the high temperatures and the rain from Arizona’s monsoons make for an explosive combination. How fast can the desert turn green? Here’s a series of photos from our site – one per day for a week that we think conveys this better than words. Enjoy the slide show:

You…

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Pregnancy in Kangaroo rats

A guest post from last week on the Portal Blog about studying Kangaroo rat placentas!

The Portal Project

~While everyone’s busy at ESA this week, we’d like to keep the 40th anniversary ball rolling with a guest post from a visiting researcher at Portal. Jess Dudley has been using the Portal area to compare pregnancy in kangaroo rats and Australian marsupials. We’ll be featuring other guest posts through the rest of the year. (If you’d like to do something similar, please send us your info!)~

In July 2015 I travelled the 24+ hours from Sydney, Australia to the beautiful town of Portal to research pregnancy in Kangaroo rats. To everyone’s astonishment we do not have Kangaroo rats in Australia! I am sure I don’t need to explain my fascination with Kangaroo rats with this audience but in terms of pregnancy they have some unique features which differ from most rodents. This finding by King and Tibbitts in the 1960’s led me to wonder how the placenta forms during pregnancy…

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Weecology at ESA

We have a modest sized group of current folks at ESA this week presenting on all the cool things they’ve been doing. We’re also around and always happy to try to find time to grab a coffee or just a few minutes to chat science.

Our schedule for the week is:

Monday

Get a double dose of rapid change in ecological communities from the Portal Project with Morgan Ernest and Erica Christensen.

02:50 PM – 03:10 PM in C120-121. Erica Christensen (w/Dave Harris & Morgan Ernest). Novel approach for the analysis of community dynamics: Separating rapid reorganizations from gradual trends.

03:20 PM – 03:40 PM in C120-121. Morgan Ernest (w/Erica Christensen). Do existing communities slow community reorganization in response to changes in assembly processes?

Tuesday

Find out what we can learn about how natural systems may change in response to climate from looking at large datasets with Ethan White and Kristina Riemer.

01:50 PM – 02:10 PM in D139. Kristina Riemer (w/Rob Guralnick & Ethan White). No general relationship between mass and temperature in endotherm species.

02:30 PM – 02:50 PM in Portland Blrm 256. Ethan White (w/Dave Harris & Shawn Taylor). Data-intensive approaches to forecasting biodiversity.

Thursday

Check out a new project with a new and exciting research tool for us (metabarcoding) at the poster session.

04:30 PM – 06:30 PM in the Exhibit Hall. Ellen Bledsoe (w/Sam Wisely & Morgan Ernest). DNA metabarcoding of fecal samples provides insight into desert rodent diet partitioning.

Collaborations

There are also plenty of weecology collaborations being presented this week:

We’re really looking forward to catching up with old friends and meeting new people this week.

The Portal Project 40th Anniversary

The Portal Project turns 40 this year! In celebration, we will be regularly posting about the history of the site, new things going on, natural history of the desert, and other fun things over at the Portal Blog.

The Portal Project

Funded by the National Science Foundation to study the importance of competition and granivory in desert ecosystems, the Portal Project first started collecting data in the summer of 1977. The initial grant was just for 5 years, yet 40 years later the site is still collecting data on plants, rodents, and weather.

To our friends who study paleoecology, 40 years is an eyeblink but in the span of a human life, 40 years is a long time. As you might expect, much has changed on the project. For one thing, after 40 years, the team running the site has changed. The original team of scientists, Jim Brown, Dinah Davidson, and Jim Reichman have all retired from the daily challenges of training students and writing grants, though some are still doing science. In their place, Tom Valone and I do our best to keep things running, studying the mysteries of the…

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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:

  1. We already cite lots of non-peer reviewed things in ecology
  2. Lots of fields already do this and they are doing just fine.
  3. 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:

  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.