Jabberwocky Ecology

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-webr

Basics

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:
  - webr

Second, create code blocks for webR using (UPDATED to {webr-r} from the old {webr}:

```{webr-r}
# 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.

UPDATE: To add packages directly in Quarto you can (now) add the following to a pages YAML front-matter to install any packages available for web

webr:
  packages: ['dplyr', 'readr']

OLD VERSION: This recently stopped working and I don’t know why.

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.

UPDATE: Copying webr workers is available

The webr workers need to be available, so if you’re rending the site (using quarto render) and then serving it you’ll need to copy those workers into your build directory. You can do this by adding the following under project: in _quarto.yml:

  resources: 
    - "webr-serviceworker.js"
    - "webr-worker.js"

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-corp

UPDATE: The easier way to do this (since quarto render will want to overwrite _headers) is to add a netlify.toml file to your root directory and containing

[[headers]]
  for = "/*"

  [headers.values]
    Cross-Origin-Opener-Policy = "same-origin"
    Cross-Origin-Embedder-Policy = "require-corp"

Other 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.

3See boB Rudis’ speed comparison.

 2 Comments

 Posted on March 13, 2023 by

 data, programming, science

     , , , , ,

Weecology, the Everglades, and Wading Birds, oh my!

A funny thing happened on the way to the pandemic…

In the summer of 2019 a colleague of mine, Dr. Peter Frederick – an expert in the wading birds of the Everglades – emailed me. Peter and I served on some university committees together, so I assumed we were just getting together to chat about changes in graduate student admissions or something else administrative. To my surprise he cracks open his laptop and says, “I want you to think about taking over my long-term study of wading birds in the Everglades.”

Picture of Peter Frederick

Dr. Peter Frederick – UF Emeritus professor and Everglades wading bird expert

It took me a while to stop laughing, then I had to make sure he wasn’t messing with me. But he was serious.

Since the mid 1980s, Peter Frederick has been monitoring wading birds across a large swath of the Everglades ecosystem – specifically Water Conservation Areas 1, 2, and 3. If – like me – those terms are meaningless to you, then let me explain. The Water Conservation Areas comprise ~1350 square miles ( 3,496 sq km) of Everglades marsh habitat that are part of the water supply and flood control system of south Florida.

Image from Google earth showing a white polygon outlining a region of south Florida and a tiny red square in the middle of it

A Google Earth image of part of southern Florida. The white polygon outlines the three water conservation areas. To the north, the southern tip of Lake Okeechobee can be seen. To the east is the Miami Metropolitan area. South of the polygon is the norther edge of Everglades National Park. If you can find the red dot in the photo, it is a scaled representation of the size of my other study area – the Portal Project.

For over 30 years, Peter’s Everglades group has been monitoring all the wading bird breeding colonies across this ~1350 sq mile expanse. This involves an intensive field effort from January to about June (late May-early July is typically the end of the breeding season) to conduct monthly aerial censuses to count nests and weekly visits to a subset of colonies to monitor nest success. How – one might ask – does one accomplish this? Have you seen the movie Planes, Trains and Automobiles? Well, to monitor wading birds in the Everglades its Planes, Trucks, and Airboats.

Planes are used to find colonies across the area and estimate the number of nests in each colony. Trucks are used to move the airboats around to different launching points. Airboats are what get people from the edge of the Everglades out to the tree islands where the colonies are.

Video from an airboat as it moves across the Everglades

Once in a colony, transects are set up and nests are visited weekly to track nest success from egg laying to fledging. Sometimes nests are easy to monitor.

Morgan Ernest standing next to a nest writing on paper

Recording data on nest contents in one of the colonies in the Everglades. Photo from Lindsey Garner

Sometimes, though, they take a little work

Me and Lindsey Garner (my amazing field manager, Everglades guru, and project coordinator) using mirrors on extendable poles to look into nests up in the trees. Photo from Holly Coates

Peter explained all of this to me, showing me pictures and data from the field project, talking about the long-term nature of the project and their recent push into using drones to monitor colonies.

I smiled politely, told him I’d think about it, and then went home to laugh with Ethan about the absurdity of me running a large-scale monitoring program of wading birds in the Everglades that involved planes, airboats, and drones. After all the Venn diagram of my expertise as a small-scale long-term desert rodent field ecologist and the expertise needed for a large-scale, long-term tropical wetland avian ecologist are nearly non-overlapping.

And laugh we did. Laugh and throw out wild ideas. Ideas related to multi-scale spatial and temporal ecology. Ideas related to Artificial Intelligence (AI) and drone-based field ecology. Ideas related to testing large-scale forecasting in a system undergoing unprecedented restoration efforts in the face of unprecedented environmental change.

And then we stopped laughing.

It took a trip to south Florida to visit Everglades National Park and a heart-to-heart conversation with our project manager, Glenda Yenni (who has been with us for so many years now that saying it out loud would force us to confront how old we’ve gotten) for us to finally make a decision.

The trip to Everglades National Park really hit home what we knew intellectually – the Everglades is one of the iconic ecosystems of the world. Unique. Beautiful. And brimming with interesting ecology. Oh, and the big wading birds are super cool.

Great Blue Heron at the water’s edge at Anhinga Trail in Everglades National Park

When we broached the possibility with Glenda, we were braced for her to laugh at us for even thinking about something so outlandish. But it was Glenda’s unbridled enthusiasm for the coolness of the project that finally overcame our reservations. She pointed out how the project really integrated a lot of themes we’d all been invested in (machine learning, ecological dynamics, forecasting) in ways very complementary to those we’d been exploring with Portal. Questions we can address with Portal would be difficult/impossible with the Everglades and vice versa, which meant there was a potential for feedbacks and synergy that our really broad portfolio of research had not been amenable to before.

Of course, all of this was before I knew I would be taking over the project in the middle of a global pandemic. But that’s a story for another day.

Today’s story ends here. With the announcement that Weecology has a brand new bag (and a fleet of airboats and drones). So stay tuned for more stories of our adventures as we learn about wading birds in the amazing and unique landscape of the Everglades.

A foraging flock of large wading birds circling over the Everglades at dawn, as the airboats approach

 5 Comments

 Posted on May 5, 2022 by

 science

Jobs in the US Government for graduate students

Do you have a graduate degree and are looking for a job? The US Government hires thousands of people with your skill set. Here I’ll give a quick overview of the scope of those jobs.
If you’re looking for the exhaustive guide for applying on USAjobs its here.

Why should I work for the federal government?

A career with a federal agency can be just as rewarding, and sometimes extremely similar, as a career in academia. Science, outreach, and land management agencies do a large amount of work that requires the exact skills you learn while in graduate school.

There are numerous perks to working for the government. Job security can be very high as federal employees have a lot of protection against unlawful termination, even when agency funding is cut. If you’re looking to escape academia but don’t want to wander too far, many agencies have research focused institutions where publications are the primary goal. In these cases much less emphasis is placed on outside funding and mentoring students. A lot of these organizations are even located on universities campuses where you can be an adjunct professor if desired. 

For natural resource folk the major land management agencies have numerous monitoring programs where it’s possible to get permanent field positions, or associated management roles. The day to day management of parks, forests, and other public lands also require knowledge of the wildlife and ecosystems in addition to project management and people skills. The positions can pay well too. Someone with a graduate degree could start out making $53k (GS-9) to $76k (GS-12) per year, with cost of living adjustments in most major metro areas. Most years will have a small (1-2%) raise to match inflation. There are also automatic raises at 1-3 year intervals. Other benefits include a 401k, pension, and an array of health insurance plans.

Where can I work with a graduate degree?

The figure below shows the number of employees with graduate degrees for the mainstream science agencies in recent years. The GS and ZP labels indicate different entry pay levels for someone with MS degree (GS-9, ZP-2) and PhD (GS-11/12, ZP3), though they can be obtained with relevant experience too and numerous people without graduate degrees have similar positions. The numbers below also do not include leadership positions (GS-13+, ZP-4+), which for the most part are attainable thru promotion only. Non-permanent positions can be “Term” positions, when someone is brought on for a specific project for 1-4 years, and also post-doc positions. 

What types of jobs are there?

This next series of figures shows the types of positions prevalent across the same agencies. The codes correspond to the different OPM Occupational Series. For example the Food and Drug Administration (FDA) hires numerous chemists, while the U.S. Geological Survey (USGS) hires the majority of hydrologists in the government. The Forest Service (USFS) has a large number of Foresters, but nearly just as many Wildlife Biologists and Archaeologists, as well as Ecologists and Botanists. The most Fish Biologists are employed by NOAA, who is in charge of all endangered and protected ocean animals. The “General” categories are the most common. Agencies use this when a role doesn’t fit precisely into other occupation codes.

Where are the jobs located?

Jobs described above are in every state, though some agencies are more spread out than others. Public land agencies have positions throughout most states, while other agencies are in a handful of locations. For example Centers for Disease Control (CDC) employees are mostly in the Atlanta, GA headquarters.

How do I apply?

Unfortunately finding and applying for federal positions is notoriously difficult. The official jobs site, USAJobs.gov, can have 100’s of open positions for a single occupation type, each one with slightly different requirements. Advice on what exactly should go into an application is also lacking. Numerous people who are extremely qualified aren’t even considered for some roles because they do not meet the exact eligibility requirements, or did not communicate their qualifications well enough. For these reasons I wrote a guide for applying to positions on USAJobs you can find in this post.

Code & Data

Figures above were made with data released monthly by the Office of Personnel Management. The code is available on GitHub.

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 Posted on June 14, 2021 by

 graduate students, jobs, science

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USAJobs Guide for Biologists and Ecologists

Authors: Shawn Taylor, Jessica Burnett

This guide accompanies this post highlighting careers in the US Government. The US federal jobs site, USAJobs, is notoriously difficult to use. This guide aims to clarify much of the process and is geared towards biologists, ecologists, and other natural resources practitioners interested in working for the federal government. Especially in the agencies listed below. It’s especially pertinent to graduate students (Ms & PhD) who are looking for a career outside academia, but a lot of the information also applies toward those with a Bachelor’s degree or in other fields. If you’d like to contribute anything or ask for clarification feel free to comment or add suggestions directly in the google doc version.

Agencies & Types of Jobs

Each of these agencies are like their own corporation. For the most part they all work independently of each other and with their own priorities. Some agencies will interact at the local level, for example when the Forest Service and BLM have land adjacent to each other, or when multiple agencies collaborate on protecting a common endangered species. This list is not all inclusive of every agency and their internal divisions.

U.S. Forest Service (USFS)

The USFS manages the numerous National Forests around the country. A large amount of the USFS budget goes toward firefighting. But outside that agency duties include permitting and administration of logging activities, grazing, mining, and recreation area management. Many positions are centered around large-scale restoration, especially where it concerns endangered species. All major activities must be done under the lens of NEPA and the Endangered Species Act. 

The USFS is hierarchical in structure. The national headquarters is located in Washington D.C, and the country is divided into 9 regions, each containing numerous National Forests (ie. the Gila National Forest, the Flathead National Forest, etc). Each Forest is again divided into districts, which is where much of the on the ground work happens. Each level (National HQ, Regional, National Forest, District) has its own office and staff and usually their own biologists, ecologists, foresters, hydrologists, botanists, geologists, rangeland specialists, soil scientists, etc. 

USFS also has a research division in Forest Research Stations. These are again divided into regions and have numerous offices throughout the country. A lot of research is geared towards better forestry management, restoration, and wildfire research. They run the numerous experimental forests around the country. 

The USFS has their own job board: https://fsoutreach.gdcii.com/, this has listings and outreach notices. All applications must still be listed on, and applied for, through USAJobs.

U.S. Fish and Wildlife Service (USFWS)

Manages the day to day operation of National Wildlife Refuges and National Fish Hatcheries. 

The Ecological Services Program has a number of field stations throughout the country which interact at the local and regional level on conservation issues, especially about listed endangered species. A number of other programs, such as Migratory Birds, Fish and Aquatic Conversation, International Affairs, and Law Enforcement hire graduate level biologists and ecologists. The USFWS also helps administer and enforce the Endangered Species Act, and USFWS biologists are consulted by other agencies who have to consider endangered species in their NEPA planning. Information on USFWS and mailing lists is available here. 

National Park Service (NPS)

NPS manages all National Parks and most National Monuments. Each park unit has an array of biologists across all fields. If a park has locations with significant historical and/or cultural value they will also employ historians, archaeologists, and/or anthropologists. 

The NPS also has the Inventory and Monitoring Network, which is their ecosystem monitoring division. They have regional offices throughout the country, each one doing standardized monitoring at all parks in the area. Each I&M office has various biologists, data people, statisticians, and permanent field crews. 

Bureau of Land Management (BLM)

The BLM manages a large amount of land in the Western U.S. and Alaska. It’s mostly rangeland, but also includes numerous forests (especially in Oregon and Alaska). Instead of regions like in the USFS, management is divided first by state and then subset to districts. Thus most western states have a large State BLM office, usually in the capital city, and several small district offices. Like the USFS all these locations can have a range of science positions which focus on permitting and management of resource extraction, but also recreation and restoration.

U.S. Geological Survey (USGS)

The USGS is a science branch of the Department of Interior, and has two major areas of activity: hazards and environment and natural resources. In the 1990’s many federal biology research positions were moved into the USGS. An array of USGS stations around the country perform research, hazard analysis, mapping, environmental monitoring, education, and scientific outreach encompassing all areas of biology, geography, and natural resources. Some examples include: USGS Coop Units which are located on, and interact heavily with, universities around the country; the Core Science Systems, which has an extremely broad scope in research, modelling, and producing data; the Ecosystems Mission Area which researches numerous things such as land management, habitats, and endangered species. 

U.S. Department of Agriculture (USDA)

Besides the USFS several agencies in the USDA do significant activities in biology and natural resources.

Agricultural Research Service (ARS) – The ARS does an array of research to improve agricultural productivity and sustainability. They have offices throughout the country and focus on genetics, plant breeding, cropping best practices. etc. Research on rangelands and cattle grazing is included under this umbrella, so several western offices have a large focus on rangeland/desert ecology and restoration. 

Natural Resource Conservation Service (NRCS) – This is an outreach organization which provides information on best practices and funding for various activities (eg. soil conservation, restoration, sustainable agriculture) to farmers and other land owners. They run the Plants Database and US Soil Survey. They have offices throughout the country and employ a lot of soil scientists, ecologists, biologists, agronomists, etc.  

Animal and Plant Health Inspection Service (APHIS) – APHIS plays a large role in regulating and monitoring for plant and animal diseases which directly affect agriculture.

National Oceanic and Atmospheric Administration (NOAA)

The NOAA Fisheries division manages marine endangered species under the ESA. This includes whales and other marine mammals, sea turtles, and ocean going salmon. They hire a lot of biologists.

Environmental Protection Agency (EPA)

The EPA administers various sweeping regulations, such as the Clean Water Act, Clean Air Act, and Superfund sites, among many others. They also do research in various areas when it’s relevant to their other goals. For example, EPA scientists do a lot of research on how PCBs and similar pollutants spread through aquatic food webs. 

National Environmental Protection Act (NEPA)

NEPA is not an agency of course, but it plays such a big role in the above agencies it deserves an entry here. All major activities on federal land require the local agency to go through the NEPA process. In general this involves gauging the environmental impact of a project, including effects on endangered species and their habitat, determining if those impacts are “worth it”, and outlining any mitigation plans and/or post-project restoration, and soliciting feedback from the public. Of course the actual process is much more in depth and can take years for any single project. You may also see the terms Environmental Assessment (EA) and Environmental Impact Statement (EIS) which are some of the main parts of the NEPA process.

Mines, grazing leases, logging, new roads, new trails, restoration activities, prescribed burns, new buildings, etc. all require a NEPA review. At local BLM and USFS offices many people spend a large amount of their time on NEPA activities. EA and EIS documents usually get input from numerous people (ie. wildlife/fish biologists, botanists, hydrologists, soil scientists, etc.). Some positions are hired exclusively to work on NEPA documents full time. 

If your considering a position where this will be part of your duties it would be good to read some example EA’s or EIS’s. The BLM hosts all of their NEPA projects here. 

On the job/ What to expect

Expectations/Evaluations

Federal employees go through an annual performance review with their immediate supervisors. These are extremely agency specific. At the beginning of every fiscal year (starting in Sep.), or at hiring, these are reviewed and specific goals are laid out. 

Teaching & University affiliations

Some research oriented roles (eg. at some USFS Research Stations, USGS, or ARS locations) are located on a college campus and have the option of having a university affiliation. This can be a staff association which gives access to things like the library. Some people have adjunct professorships which allow them to teach classes, mentor graduate students, or serve on committees while still being a federal employee. 

Benefits

Federal positions have some fairly generous benefits. 

Health Insurance. Plans vary by state. 
Life insurance
Thrift Savings Plan (TSP). This is the equivalent of a 401k and is available to federal employees only. It has up to 5% matching and a few tax benefits beyond what a 401k has. 
Federal Employees Retirement System (FERS). This is the equivalent of a pension. It’s not voluntary, and for anyone hired after 2014 the contribution is 4.4%. The benefits at retirement are calculated with a formula.
Annual Leave. Annual leave accumulates at 4 hours per 80 hour pay period, or slightly more if you’re employed for 3 or more years. It’s “use it or lose it” and past 30 days of leave you do not accumulate anymore. If you leave your position you’ll be paid out any unused annual leave, including at the end of temporary positions.
Sick Leave. Sick leave also accumulates at 4 hours per pay period. There is no limit on the amount of sick leave you can accumulate. If you leave your position you do not get a payout of sick leave, but you do not lose it either. If you are ever employed in a federal position again you can have any prior unused sick leave credited. 
Parental Leave. Federal employees can use sick leave for up to 8 weeks after childbirth or adoption, and are allowed 12 weeks (not necessarily all at once) of unpaid leave for childcare. 

Finding the jobs

USAJobs.gov

This is the primary site for all federal job openings and applications. All other sites point to here.

Job announcements open and close constantly. The opening date is usually decided by an HR specialist, and not necessarily by the hiring supervisor.

Searching USA Jobs

In my experience the best way to see the latest jobs is to search by series. For example as an Ecologist I’ll search for all positions under the 408 and 401 series, filter to only permanent positions, and sort by open date to see the latest openings. This allows me to see all relevant positions regardless of location or agency. A soils person might search with 457 (Soil Conservation), 470 (Soil Science), or 458 (Soil Conservation Technician). Note everyone should also search for 401 Series (General Natural Resources Management and Biological Sciences) since many positions are advertised under it. You can also search the generic 400 series to show open positions in all biology and natural resource series. For more physical science based positions (eg. hydrology, meteorology, geology, etc), you should also search under the 13xx series. Social science positions (eg. archeology, anthropology, geography, etc) can be found under the 01xx series. 

New job announcements are posted every business day. If you open an account on USAJobs you can set up notifications to send a daily,weekly,monthly email whenever new postings match predefined searches. 

Other Websites

All federal jobs have to be advertised somewhere and the posting on USAJobs satisfies that requirement. If a supervisor has an applicant in mind they may not advertise anywhere else, but if they want a large applicant pool they’ll likely post it elsewhere. All ecology/biology job boards are good places to look out for. Some agencies have their own job boards (see above), but they’ll always point you toward the official listing at USAJobs.

Openings with numerous positions and/or locations.

Sometimes an agency will do a *bunch* of hiring all at once, and thus list the same GS Level and series at a number of locations. See this position for an example.

Openings that are open for 1 year.

If you are searching through USAJobs you’ll probably come across positions which have an open and close date one year apart, usually in many locations. These are for positions which are regularly hired, like seasonal technicians. Hiring supervisors, through emails and job ads, will point people toward these positions to apply by a certain date. At the specified date an HR specialist will “pull” all applicants at the relevant locations and go through the selection/interview process as normal while the official job ad remains open. 

This job is open to…

Federal jobs can be restricted so only certain people can apply. This is also known as the Hiring Authority. If you’ve never had a federal job before you’ll likely only qualify for positions that are “Open to the Public”. You may see positions open to only current, or recent federal employees, such as this one. Other options may be available for individuals with disabilities (under Schedule A), tribal members, and others. If you qualify for one of the options, make sure to look at what paperwork is needed and get it ready in PDF format now so it’s available when an announcement opens. Don’t bother applying for a position unless you fit one of the categories listed.
It is common to see the exact same position listed twice, the only difference being who the job is open to. See Hiring Authority for more on this.

Outreach job ads

Sometimes a job will be advertised as an “Outreach”. These are usually circulated via email and ask potential applicants to send a response expressing interest, and potentially sending a resume along as well. The hiring person uses responses to gauge initial interest and what to put into the official ad. Responding to an outreach is not the same as applying for the position.  At some point the official position will be posted on USAJobs. If you responded to the outreach the contact person may or may not notify you when it officially opens. 

Should you respond to outreaches? Yes, especially if it’s a position you’re extremely interested in. It gives an opportunity to connect with the hiring person and/or potential supervisor. Outreaches are also a good source to find more details about the job which may not be in the official USAJobs announcement. If you don’t respond to an outreach you can still apply on USAJobs, when the position opens, and be considered for the position.

Definitions

OPM – Office of Personnel Management

This is the federal agency that dictates all the rules and standards which federal employment must be done. Everything from job advertising, hiring, benefits, promotion, etc, has a rule (and probably an entire handbook) made by the OPM. This is not a human resources department, as you’ll never interact with someone from OPM. Every agency has their own human resources department which handles personal issues, and usually local offices have 1-several people dedicated to this. 

GS Pay Level (eg. GS-5, GS-6, GS-7)

You’ll see these numbers on all job announcements. They designate the salary of a position as well as the experience required to be hired onto that position. Sometimes you’ll see ads with 2+ pay levels (GS 6/7/9, GS 11/12). This means two things: 1) the agency has the option of hiring someone at any of the levels, depending on the person’s experience. 2) If you’re hired at the lower level, then the higher level is usually* the maximum you can achieve through promotion.

*Sometimes an ad will have a higher Promotion Potential listed. 

The exact salary for the same GS level will vary depending on location. Positions in large cities will pay more than those in rural areas. You can see the exact amounts here. These will change slightly every year when congress authorizes a raise for all federal employees (usually around 1%). If the location you are looking to work in is not listed in the table, then the salary is not the “Base Rate”, but the rate listed under “REST OF THE UNITED STATES”. 

If you get an offer the salary is generally non-negotiable. I’ve heard an experience of someone getting an offer for a GS-7, but convincing them they met the qualifications for GS-9 and thus being hired at that. In this case the original announcement was in the range for GS-6/7/9. Someone else has had success negotiating a higher step based on having another offer or existing job with a higher salary. Also you *can* negotiate for some initial leave time. 

GS stands for General Schedule and is the primary pay schedule used in federal positions, with other pay schedules for positions like law enforcement (GL) or doctors (GP). You might also see pay levels on the ZP/ZT/ZS pay scale (instead of GS). The Z system is used in the Commerce Alternative Personnel System (CAPS) system in the Department of Commerce, thus is seen occasionally in biologist positions for NOAA. Current wiki authors have no experience with this system, but it seems like the main difference is a different promotional structure than the GS pay system. 

Step

The step dictates the pay raises you receive after consecutive years in the same position. Each GS level has 10 steps. New employees are hired at Step 1 and move to Step 2 after one year, and Step 3 after two years. Higher steps require longer waiting times (2 years at steps 4-6, and 3 years at steps 7-9) such that getting to Step 10 pay takes 18 years. 

Read more on pay scales and promotions.

Series (401, 408, 482, etc.)

These designate the type of job being advertised. 4XX is in the Natural Resource/Biology realm, and is one of many job types specified by the OPM (eg. Accountants: 5XX, Transportation: 21XX). You also find other potentially relevant jobs in the Physical Sciences (13XX) or Social Science (01XX) series. 

The main thing the Series dictates is the base experience required for a position. For example an Ecologist (Series 408) requires college coursework in math and ecology. A Wildlife Biologist (Series 486) requires a range of classes in biology. The base requirements dictate what you’ll need to qualify for a GS-5 position using education alone (a Bachelors degree). Higher GS levels require the base requirements in addition to higher degrees and/or more experience. See Eligibility.

Position Types 

These definitions dictate the length of the position and the benefits received. 

  • Permanent positions last indefinitely, have all benefits (retirement, health insurance, sick and vacation leave) and are usually at a GS level of 7/9 or higher. 
  • Temporary positions are used for seasonal technician jobs and end after 6 months to 1 year and have few benefits (only sick and vacation leave). If you work for the same job year after year in a temporary position, you’ll be laid off at the end of each season and will have to go through the hiring process again the next season. You may see these casually mentioned as 1039 or 1040 jobs, as the official limit is Not To Exceed (NTE) 1039 hours, or approximately 6.5 months of 40 hour weeks.
  • Term positions end after 1-4 years but include the full range of benefits during that time, most federal post-doc positions are considered term positions. 
  • Permanent Seasonal. These positions are permanent in that you do not have to re-hired year after year, and you receive all benefits. It is seasonal in that in the off-season you go into non-pay status, where you won’t get a paycheck but you’ll still maintain benefits like health and life insurance. These positions are seen a lot in monitoring programs such as the USFS Forest Inventory and Analysis (FIA) and the NPS Monitoring Network. 
Veterans Preference

If you’re a military veteran you have preference over other applicants. This means that, as long as you meet the experience and/or education requirements for a position, you’ll usually go to the top of the list sent to the Hiring Supervisor. In some cases this means the Hiring Supervisor will receive an applicant list with only one person who has veterans preference, and only if and when they decline a job offer are other applicants considered. Most, but not all, positions consider veterans preference, and it will say so on the USAJobs announcement page. Read more about veterans preference here. Resources for veteran applicants are provided on the EEOC website. 

Competitive & Excepted Service

Most permanent positions are classified as “Competitive”, meaning that you compete with other applicants. There is also the “Excepted” service where the mechanism for hiring is more flexible. Each job announcement states which one it is at the very top. The main thing to know is that if you are hired into an Excepted position, in most cases you are not eligible for future positions which are only open to current Competitive employees (this is also known as Merit Promotion, and will be listed as Competitive Service under “This job is open to”). There is another hiring authority for current federal employees in the Excepted service (listed as Excepted service under “This job is open to”), but is less common. If you have a choice between a Competitive or Excepted position you should take the Competitive one (pay/location/etc. being equal).

Hiring Authorities

This is the set of rules under which the hiring process must follow for any single position. It will align closely with who a job is open to. As the applicant you don’t have to worry about the hiring authority for the most part as long as you are eligible and feel you qualify for a position. Keep in mind that some hiring authorities will give some benefits down the road. For example being hired under a Student Pathway authority, you may be eligible for a permanent position down the road without going through the application process or competing with other applicants. Similar exemptions exist for those with disabilities (See Schedule A hiring below). Take a look at the various hiring authorities, if none of them apply to you then you are limited to positions which are “Open to the Public”.
It is common to see the same job announcement listed twice, the only difference being the Hiring Authorities (as in each has different entries for “This job is open to”). Usually one will be “Open to the Public”, while the other will have more limited options. If you qualify for both announcements absolutely apply for both as there is no penalty for this. This seminar by a NOAA hiring supervisor gives a great overview of this aspect, and many other things.

Schedule A hiring authority

Applicants with disabilities are eligible to apply to positions under the “Schedule A” hiring authority (see here for eligibility criteria). Individuals hired under Schedule A are hired into a “Excepted service” status, meaning that their position is not considered “Competitive.” Although not mandatory, supervisors can recommend individuals hired under Schedule A to be converted into the Competitive status after 2 years of service. Vacancies are sometimes advertised using two listings, one for Schedule A applicants and the other for non-Schedule A. Individuals with disabilities are not limited to Schedule A positions.  If you wish to apply under Schedule A, clearly state your eligibility and interest in your resume and/or cover letter (here is an example). You are not required to disclose details of your disability nor your reasonable accommodations at any point during the application process, however proof of eligibility for Schedule A (e.g., note from a medical professional or a disability agency) is required at the time of application. OPM encourages eligible individuals to reach out to a Disability Program Manager or Selective Placement Program Coordinator (SPPC) for assistance in applying to USAJob vacancies, and to participate in the Selective Placement Program. Resources for Schedule A applicants are provided on the EEOC website.

Applying & Hiring Process

Application Process

The official job portal for all federal jost is USAJobs.gov. To apply you’ll create a resume that has all relevant information. You can create several resume “packages” geared toward different position types, such as a Wildlife Biologist resume or a Restoration Ecology resume. 

People Involved

HR Specialist. This is a person, usually at a regional or higher level office, who handles all HR hiring and on-boarding related activities. In agencies that are constantly hiring new positions year round it can be their full time job. 

Hiring Supervisor. There is no official name for this, but they are basically the person at the local level who is looking for an applicant and will likely be your direct supervisor. As seen below they do not have complete control over who is selected.

Application Steps
  1. Job ad opens on USAJobs and receives a number of applicants.
  2. Job closes and no more applications are allowed. Jobs close at midnight eastern time on the specified closing date. Some will close sooner when they reach a certain number of applications, and if so is specified next to the open/close dates.
  3. An HR Specialist reviews the minimum qualifications and rejects any not meeting them. You may possess the minimum qualifications but if they are not well documented you’ll get rejected here. See Filling Out Your Application
  4. Of those meeting minimum qualification, the HR Specialist reviews the applicants using resume materials and the questionnaire, and chooses top qualified applicants. Top applicants are forwarded to the hiring supervisor for interviews. This is called the “Certification of Eligibles” so you might hear this referred to as “making the cert list”. 
  5. Hiring supervisor conducts interviews and chooses the desired applicant. If the list they receive is long they may not contact every person on it, thus you may not hear from the hiring supervisor even if you were referred.
  6. The decision goes back to the original HR Specialist who goes through the hiring and on-boarding process. Depending on the agency the hiring supervisor can only give a tentative non-binding offer of employment, and might say something like “I’m going to recommend we hire you”. Only the HR Specialist can send the official offer. 

If you don’t meet the initial qualifications (3) or meet them but aren’t among top candidates (4) you’ll get an email stating this. It will be at least several weeks, and potentially a few months, after an announcement closes for this to happen. The messages are automated and won’t give specific reasons for why you did not qualify or were not a top candidate. 

Eligibility for a GS level
By Education

To qualify on education alone you usually need the following for natural resource jobs.

  • GS-5 – Bachelors degree
  • GS-6/7 – 1 year of graduate coursework
  • GS-9 – Masters degree
  • GS-11 – PhD
  • GS-12 – Sometimes just a PhD, but sometimes also a year of GS-11 (or equivalent) experience depending on the position and agency.
  • GS-13 and higher. Only experience can qualify for these positions.

*While GS-8 and GS-10 are possible they’re rarely seen. 

You’ll need to prove your education and scanned transcripts are the best option for this. A good practice is to request official copies of all relevant transcripts now and have them sent to yourself, then scan them as PDFs so they’ll be available when an announcement opens that you want to apply to. Unofficial transcripts are fine for the application but they will likely request official transcripts if you are offered a position. As long as it states somewhere you have a degree awarded then that is sufficient. You’ll also need your transcripts in most instances to prove you meet minimum coursework requirements. See More on Education below.
If you are still in school and graduating soon you may still be able to apply. Look for text in the announcement to the effect of “Only experience and education obtained by XX date will be considered”. They are very strict about the dates. Some positions state that a degree must be earned by the start date. The HR specialist may ask for proof that you’ll attain a degree If you have yet to graduate. Generally some “official looking document” from your advisor or department head stating you’ll have a degree by a certain date will suffice, though this is at the discretion of the HR Specialist. Also the minimum education requirement for some positions is 1-2 years of graduate course work, so if you are 2+ years into your graduate program and graduating soon you can qualify without having the degree in hand yet.

By Experience.

You can qualify for a GS level without the above education by having 1+ years of work experience at the prior level. For example you can qualify for a GS-9 by having 1 year as a GS-7, or qualify for a GS-11 with 1 year as a GS-9. This can be equivalent work if it was not a federal position. For example 1 year of experience as field tech in an academic lab should be equal to GS-5 work and will qualify you for a GS-6 job. GS-6-9 are usually crew leaders or permanent biology positions, and GS-11 are usually doing research/analysis, or are the lead person managing various programs year round. Sometimes a year at GS-5 will qualify for GS-7 and the qualifications will say this.

To an extent, previous positions must match the one you’re applying for. For example having experience as a GS-9 Hydrologist won’t necessarily qualify you for a GS-11 Soil Scientist. Though skills and duties vary widely nowaday so it won’t hurt to try, as long as your experience meets the required specialized experience. See Filling out your application.

To qualify with non-federal job experience you need to lay out the job description of your prior job. It should match as close as possible to the “specialized experience” described in the job announcement. This can be done on your resume, don’t be afraid to make it as long as possible. In your application I also recommend having a letter specifically outlining each point of the specialized experience and referencing the prior job duty that matches it. See the Appendix for examples of this. Whether it counts or not is up to the discretion of the HR Specialist. 

By Education and Experience

It’s possible to combine education and experience if you’re falling short on one. The important thing is the total experience *time* must add up accordingly. If you have 1 semester of graduate coursework (approximately 5-6 months) and 4 months of GS-5 level experience, that will not qualify for a GS-6 position. 1 semester of graduate coursework and 6 or more months of GS-5 experience will. OPM guidelines for this are here, there are some stipulations for doing this with GS-9 or higher. The UGSS also has a detailed breakdown for combining experience and education. The final calculation is up to the discretion of the HR Specialist.

Any experience you have from your coursework (eg. graduate field or lab work) likely will not count as experience. See the Paragraph i Education and experience gained concurrently, here.

More on education

If qualifying by education you will need to meet specific coursework requirements. Each series has its own specifications. For example to qualify for a position under the Wildlife Biology Series, 486* you need:

  • 9 hours of wildlife courses
  • 12 hours of zoology related courses
  • 9 hours of botany or plant science courses

These are strict requirements and a lot of applicants miss qualifying by not considering this or being a few courses short. You need to provide transcripts to show that you took these courses, so always upload transcripts with your application. Also consider adding a letter in addition to your cover letter outlining all your courses. See the Example education qualification letter.

*You can still be a Wildlife Biologist if you do not have botany courses. Many of these positions are hired under the more general 401 series. For example see this large hire by the USFWS.

Multiple Job Series

Many announcements have multiple series listed. For example this one is advertised for either a 401, 408, 415, or 1301. In this case you must meet the minimum requirements for at least one of these series. In the questionnaire you’ll be asked about each series and whether you feel you qualify for it. It is possible to qualify for more than one series and it is ok to say you are qualified for more than one. Don’t forget about specialized experience, which in these cases is usually the same regardless of which series you qualify for. 

Filling Out your application

The hardest part about USAJobs applications is proving that you meet the minimum qualification. Therefore always read the Qualifications sections of the announcement. This is how the initial application pool is screened and HR Specialists will be looking at the exact wording of the announcement to match to your resume and experience. Especially look at the “specialized experience” as this is how specialties are defined at the higher grade levels (GS9+). For example an announcement for a GS-9 Hydrologist might have specialized experience as “management of streamflow data; evaluation and/or application of watershed hydrology models; operation of streamflow measurement equipment” and you must have these skills listed in your resume to qualify. Consider having a separate qualification letter, in addition to your resume, to highlight things. See the example in the appendix.

Resume/CV

Most people recommend uploading a pdf resume/cv instead of using the USAJobs resume builder. A word doc is also acceptable and may have better results with the resume scanning software, but make sure to remove any attached comments. Near the end of each announcement you’ll find the “Required Documents” section which outlines the minimum details which need to be included in your resume. One of the most important things is putting the start and end dates of prior positions (down to the month) and hours worked for each job in your resume. This is because meeting the qualifications with prior experience is based on total time worked. When they say “At Least one year” they mean at least 52 weeks of 40 hours/week. Someone should be able to quickly look at the prior experience on your resume and do the math to make sure it meets the minimum.

Under each prior position list duties and accomplishments. This is where you should match the wording and specifics of the qualifications (and the questionnaire, see below) to your past experience and accomplishments. Don’t be afraid of being too detailed, especially for listing experience to match to the specifics of the announcement. Prior experience can also be freelance or volunteer work, but you still need to list the time frame and total hours per week worked. 

References

You can include references in your resume if you like but they are not required. The HR Specialist will not contact them for the initial screening. If your application makes it to the final application pool the hiring supervisor will request them if needed.

Cover letter

Absolutely include cover letters tailored to each position. These can be geared toward the hiring supervisor who will be doing interviews. Here all general advice about cover letters applies. If applying for a research position this can be treated similar to a university professor application package, where your cover letter highlights how you’re a great fit and a separate research statement highlights past accomplishments and future work and goals.

Questionnaire 

You should also read through the application questionnaire. You can find this linked in the “How you will be evaluated” section of the announcement. You’ll fill this out during the application after you upload documents. It will have some bureaucratic questions like what, if any, federal positions you’ve had before or your veterans status. Most, but not all, positions will also have a series of experience questions where you rate yourself on a scale from no experience to expert. In addition to the qualifications, details about these experience ratings are things you should highlight in your resume. The HR Specialist probably will not fact check anything beyond comparing it against your resume. The hiring supervisor (likely your future boss) may call references to verify things, or will be knowledgeable enough to know when experience has been overstated. Some embellishment is fine but outright lies (ie. saying you supervised technicians when you never did) can be justification to not hire you. 

Job/Application Questions

If there is a contact person on the announcement who looks like the hiring person (usually listed near the top), then consider emailing them asking for more details about the job, duties, location, etc. They can potentially tell you more in depth details about the position and it will also put you on their radar. Due to hiring rules there are many things they cannot say or discuss with you, so don’t be surprised if you get very vague answers. If the only contact person is in HR (usually listed near the bottom) don’t contact them unless you have a legitimate application question. This is likely 1 of 100’s of positions on their plate and they cannot tell you any specific job details beyond what is in the announcement. The HR contact can answer questions like what special forms may be needed or whether past federal experience falls under one of the special hiring authorities.

Hiring Process

If you accept an offer there will be plenty of communication between yourself and your new supervisor. You’ll likely be put in touch with the HR Specialist who will send you a bunch of on-boarding forms to fill out, though it’s also possible a local HR Person will handle this.

Background checks. All positions (except for seasonal ones*) will require a background check. Most positions are “non-sensitive”, so you’ll fill out form SF85. This involves writing down all your jobs, addresses, and schooling for the prior 10 years and 3 non-family personal references. Most of the time Letters *do* get sent to your personal references for them to fill out. 

*Seasonal positions that last 6 months or less usually don’t require a background check. But most seasonal positions have the option to extend an additional 6 months or longer, and if the agency/supervisor extends your position then you’ll probably be required to complete the background check then.

Other Resources
Record Seminars
Appendix

This PDF contains three example letters outlining specific qualifications for job announcements.

Appendix PDFDownload

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 Posted on June 14, 2021 by

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Supporting and managing academic labs during a pandemic, some thoughts

Adjust expectations, be flexible, support your groups

Research will be different from normal for a while and even in the best cases it will also be slower. The shift to working remotely will limit the kinds of work we can do and everyone doing research is experiencing a dramatic disturbance to their lives. This means the people in our labs will need flexibility and support.

Talk to your lab members to understand their needs: Recognize that these needs will be different for different people. Many will have new responsibilities and stresses that preclude working normally, but some may use work as a coping mechanism.

Make it clear that moving more slowly and delaying things is expected and 100% OK. Push back project timelines, understand that some folks will make little to no progress for a while, consider delaying stressful graduate activities like qualifying exams.

Provide financial reassurance: If true, ensure your team that their current funding won’t be cut. If possible, offer extensions on funding. This will help alleviate stress and uncertainty.

Recognize power dynamics when offering flexibility: Make sure that team members are comfortable opting-out of “optional” choices and don’t feel pressured to be productive, to work on-campus, or work at certain times.

Provide access to university resources: Inform group members about university programs related to mental health, expanded sick leave, and other forms of support for well being.

Give your team the resources they need to work from home:  Encourage your group to move things from campus that they need to work at home including computers, books, and chairs. Universities typically allow this for remote work (there may be a form to fill out). If possible, purchase additional supplies needed for remote work (e.g., headsets).

Adopt & adapt tools and approaches for managing remote teams

Remote management recommendations focus on good communication, breaking projects into manageable pieces, keeping everyone on the same page with clear next steps, and tracking progress. This will make your group more efficient and inclusive when working remotely.

Use video conferencing to replace in-person interactions: Do this for any regular meetings you have (e.g., one-on-one meetings, lab group meetings) and also informal interactions (like popping into an advisors office or chatting science with labmates). Communicate your availability and how to set up meetings.

Use a group-based discussion tool (e.g., Slack or Microsoft Teams) : This supports asking questions and working on group projects and facilitates interactions among lab members with different work hours (important for those with responsibilities like child care). It can also provide an outlet for social interactions. Text does lose subtle social cues so video or audio is still best for delicate conversations. Check out the getting started documentation for Slack or Microsoft Teams.

Read up on managing remote teams: There are some unique skills to remote management, but there is lots of information on how to do this including: How to overcome your worries about letting people work remotely, How to oversee a remote team’s work, Ten simple rules for a successful remote postdoc.

Use project management and collaboration tools: These tools help you use good remote management practices. Most labs will benefit from a tool for writing and a tool for project management. Labs that write code (including for analyzing data) will also benefit from a code collaboration platform. Check out getting started guides for Google Docs (for writing) and Trello (for project management). Learning version control for managing code is a bigger commitment, but the Software Carpentry lessons are a good starting point.

Help identify research that can be done remotely, but understand the limits

It’s important to prioritize the safety of your team over research. This may mean changing your research plans to support social distancing and reduce or eliminate travel.

Focus on analyzing and writing up existing data and ideas: This is the easiest adjustment because it minimizes shifts in research area and need for new skills. Existing data isn’t just what a specific student has already collected, but can include previous data collection from your lab.

Synthesize existing knowledge: Writing reviews lets your team use their expertise to synthesize existing knowledge.

Conduct research on open data: There are increasingly large amounts of openly available data in many fields. There may be data that can be used to address questions similar to those you are studying using field or lab based approaches.

Collaborate when extending into new research areas: Computational research, working with large datasets, systematic reviews and metaanalyses all take expertise. To pivot into new methods or topics consider finding someone with the associated expertise to collaborate with. There may well be experts on your students’ committees or in your department or university.

Develop new skills/expertise to expand your groups’ research horizons: Instead of jumping into a new project requiring new skills support your team taking this time to learn new skills (e.g., computing methods or statistical approaches) or develop new expertise (reading up on new areas of the literature) to serve as the foundation for future research.

Initially prepared for the UF/IFAS Faculty Forum: Living, Working, and Adapting to the New Normal of COVID-19. Led by Ethan White (@ethanwhite) (who is responsible for anything bad) with contributions from SK Morgan Ernest (@skmorgane), Hao Ye (@Hao_and_Y), Brandon S. Cooper (@brandonscooper), JJ Emerson (@JJ_Emerson), Katy Huff (@katyhuff), Russell Neches (@ryneches), Auriel Fournier (@RallidaeRule), Jessica Burnett (@TrashBirdEcol), Melissa Rethlefsen (@mlrethlefsen), Eric Scott (@LeafyEricScott), Kathe Todd-Brown (@KatheMathBio), itati en casa (@itatiVCS), Alexey Shiklomanov (@ashiklom711) (who are responsible for anything awesome). A lot of the thinking in “Adopt & adapt tools and approaches for managing remote teams” was influenced by “Ten simple rules for a successful remote postdoc” by Kevin Burgio, Caitlin McDonough MacKenzie, Stephanie Borrelle, Morgan Ernest, Jacquelyn Gill, Kurt Ingeman, Amy Teffer, and me.

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 Posted on April 27, 2020 by

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Tips for an effective remote defense

Zoom works great: I’ve seen up to ~50 folks attending the talk remotely and slides with video. Everything connection wise worked well except for a single committee member with some minor freezing during the private defense.

Have backup options: Give yourself time and backups in case things go wrong. Set up the connection early (15+ minutes) and ask the committee to show up early to check everything is working. Have one of more backups including a phone based conference call.

Call manager should not be the person defending: Have someone else, ideally a committee member, set up and manage the Zoom (or other system) call. This means that the student doesn’t need to deal with that on top of everything else and can focus on the defense.

Mute everyone for the presentation: Either ask all participants to mute themselves at the start or (better yet) have whoever is managing the call mute them all centrally. It’s easy for the audience to forget they aren’t muted and accidentally interrupt the presentation.

Audience, show you engagement: Leave your video on (unless bandwidth is an issue). If you’ve ever given a remote talk the lack of normal audience engagement is really challenging. A bunch of live video faces really helps. Also, consider exaggerating your positive responses. With lots of folks everyone is small so clear head nods, thumbs ups, and big smiles can all help mimic normal positive audience feedback.

Use a multi-monitor setup: Having two monitors will let you see folks attending the talk plus your slides and notes. Of course if it’s easier for you to not see the audience, then definitely take the opportunity of defending remotely to not have to see them. You’ll need to setup zoom to work with dual monitors for this to work properly https://support.zoom.us/hc/en-us/articles/201362583-Using-Dual-Monitors-with-the-Zoom-Desktop-Client Alternatively you can share your screen from one computer and join the call from another computer to see all the participants.

Manage bandwidth and adjust accordingly: Test streaming quality in advance in the same place and time of day you’ll be defending. If viewers notice bandwidth issues (blurry or dropping frames) try moving the laptop closer to the WiFi router or plugging directly into the router or a wired Ethernet port. If there are still bandwidth issues you may want to have the audience stop their video. Since the presenter often can’t tell if there are connection issues the person managing the call should either ask viewers to turn off their video via chat or turn off video centrally to avoid interrupting the presenter if possible.

Mimic “step out of the room”: The committee should have a plan for having the student “step out of the room. In Zoom this can be done by using a breakout room for the committee to talk and then return to the main room when done (which is made possible by having a committee member manage the Zoom call). You can also put the defending student “on hold” https://support.zoom.us/hc/en-us/articles/201362813-Attendee-On-Hold

Committee members should use video: Committee members should definitely use video if possible during the private portion of the defense. This is an inherently stressful activity and a lot of the usual positive encouraging social cues get lost with voice only communication. That said, if you’re freezing when asking questions it’s probably because of your local wireless/upload bandwidth and so you can probably help this by turning off your video so that you can communicate clearly.

Committee members should be kind and supportive: Frankly you should always be doing this, but it’s even more important now because everyone is under a ton of extra stress. This doesn’t mean you can’t probe the work, just do it in a positive way focused on helping the student. Also, consider minimizing required changes for the thesis. Most of us aren’t focusing well right now and revisions are often due on a tight timeline. Clearly distinguish recommendations for changes prior to submitting papers from changes required for the thesis.

Communicate excitement about a student passing clearly/effusively: This is a big deal even if you’re stressed and can’t celebrate it in the usual ways. Make really clear how big a deal this is to try to overcome the different feel of a video interaction vs. an in person congratulations.

Celebrate: New MS/PhDs – This may not be how you envisioned the conclusion of years work happening, but that doesn’t change that it’s a huge accomplishment. Celebrate in whatever (publicly responsible) way you can. One option is a video-based celebration. They’re surprisingly fun!

If you like this in another format there is a PDF or you can get the text from a Google Doc.

This post is based on a Twitter thread by Ethan White (https://twitter.com/ethanwhite/status/1240336385896316928) with ideas contributed to that thread by @echoechoR, @JosephLo16, @michaelhoffman, @kimpy79, and @ellelnutter. This document is released under the CC0 publication domain declaration (https://creativecommons.org/share-your-work/public-domain/cc0/) so that you can share and modify without restriction or need to provide credit. Thanks to @adanianscience for motivating me to put it up in formats useful for folks not on Twitter.

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 Posted on March 31, 2020 by

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Data science competition: Converting remote sensing into trees

Understanding and managing forests is crucial to understanding and potentially mitigating the effects of climate change, invasive species, and shifting land use on natural systems and human society. However, collecting data on individual trees in the field is expensive and time consuming, which limits the scales at which this crucial data is collected. Remotely sensed imagery from satellites, airplanes, and drones provide the potential to observe ecosystems at much larger scales than is possible using field data collection methods alone.

We running the second in a series of data science competition where multiple groups attempt to use the same remote sensing data from low flying airplanes to infer the locations, sizes and species identities of millions of trees. This kind of collaborative data analysis challenge has proven highly effective in other fields for quickly improving methods for converting image data to useful information. This round of the competition focuses on exploring how methods generalize beyond a single forest.

There are two tasks in the current competition: 1) identifying individual trees in remote sensing images; and 2) classifying trees into species.

Panel 1: Identify - RGB image of trees from above showing trees outlined by blue polygons. Panel 2: Classify - polygons from Panel 1 color coded by species identity

Teams (or individuals) can participate in either or both tasks. Task 1 requires working with remote sensing data (RGB, LIDAR, and Hyperspectral). Task 2 can either leverage this raw remote sensing data or use simplified tabular data provided by the organizers. Details of the different tasks will be available starting March 1st. To read more and sign up check out the competition website:

IDTreeS data science challenge

You can learn about the results of the first round of this competition in the summary paper and full PeerJ paper collection. We plan to write up the results of this round of the competition in a similar way, with a synthetic paper covering the competition, data, and comparison of different methods, and with each team given the opportunity to write up and publish associated short papers on the methods they used and results they produced.

This challenge is supported by the Gordon and Betty Moore Foundation’s Data-Driven Discovery Initiative through grant GBMF4563 and the National Science Foundation through grant DEB-1926542. It uses data from the National Ecological Observatory Network in addition to data collected by the organizers. It is being organized by the Weecology lab, Machine Learning and Sensing lab, Data Science Research lab, and Stephanie Bohlman and Aditya Singh‘s labs all at the University of Florida and the Environmental Observation & Informatics program at the Nelson Institute for Environmental Studies at the University of Wisconsin.

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 Posted on February 3, 2020 by

 science

Ph.D Student Opening in Weecology

PH.D STUDENT POSITION IN COMMUNITY ECOLOGY

The Ernest Lab at the University of Florida has an opening for a Ph.D student interested in research in the area of community ecology, forecasting, and/or temporal dynamics to start fall 2020.  The student will participate in the collection of small mammal and plant data at our long-term site in southeastern Arizona which will be used as part of our recently funded NSF grant to tackle challenges associated with ecological forecasting under novel conditions. While participation in the field data collection at the long-term site is expected, students in the Ernest Lab are free to develop their own research projects depending on their interests. The Ernest lab is interested in general questions about the processes that structure communities, with a particular focus on understanding when and how ecological communities change through time and how we can forecast those changes. Examples of research that students in the Ernest lab have pursued as part of their dissertation include: Does long-term change in communities occur through gradual species replacements or rapid reorganization events?, Are biodiversity patterns sensitive to changes in biotic interactions?, Do disturbances impact species populations and community-level properties similarly?, and How does the colonization of new species impact habitat patch preferences?

The Ernest Lab is part of the Weecology research group, 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 quantitatively 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, at teaching-focused colleges, and as postdocs in major research groups. 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 LGBTQIA+ community, military veterans, people with disabilities, and students who are the first generation in their family to go to college. We work hard to create a supportive and inclusive lab environment and expect all members of Weecology to abide by the lab code of conduct.

More information about the Ernest lab and Weecology research group is available at: (https://weecology.org). You can also check out the blog for our long-term study (https://portalproject.wordpress.com) and our lab blog (https://jabberwocky.weecology.org; if you’re reading the ad here, you’ve found it already!).

Interested students should contact Dr. Morgan Ernest (skmorgane@ufl.edu) by Oct 15th, 2019 to start a dialogue about the position and receive further information about the next steps in the application process.

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 Posted on September 11, 2019 by

 science

Way too many examples of graduate students not getting their paychecks

It’s not uncommon to hear stories of mistakes resulting in graduates students missing paychecks. This is a major problem because most students live month-to-month and can’t wait for a missed check to be fixed in the next pay cycle. Despite the commonness and dramatic impact of missed pay in graduate school*, it’s common to see these issues written off as isolated incidents and not part of a more systematic problem. As a counterpoint to this idea, here are just some of the responses to a single tweet about this problem.

If you’d like to add your own experiences either post them to Twitter (responding to or quote tweeting the original tweet or tagging me @ethanwhite; I’ll keep updating this post as new experiences come in) or post a comment on this blog post.

https://twitter.com/LongNP4/status/1035923345668169729

 

*As a number of folks have noted this issue is also a real challenge for lots of folks both at universities (adjuncts, postdocs, and even professors) and beyond. I couldn’t agree more. That said I think there are some unique things related to graduate students that make the occurrence of these mistakes more common (like the fact that at many universities they are “hired” at least once and often 2-3 times/year; more on this soon) and I also think it’s OK to highlight and attempt to fix general issues within specific populations.

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 Posted on September 3, 2018 by

 science

Weecology at #ESA2018 [updated]

The weecology group is coming in force to the annual meeting of the Ecological Society of America which is being held in New Orleans next week. We’ve been up to a quite diversified list of things over the past year ranging from temporal dynamics of communities to forecasting and remote sensing. We also have people involved in a number of outreach or training events this year. We’re super proud of all the work everyone has been doing – both on the science end of things and the culture of science end of things. The Weecologists involved with each presentation/event are highlighted in electric blue with links to either their web page or google scholar profile so you can learn more about them. Talk or event titles link to the relevant listing in the ESA program.

Schedule

Monday

10:15-11:30 Special Session: Path to being a strong ally in science. Location: Convention Center 238-239. (Juniper Simonis is involved in this session)

11:30-1:15 Workshop: NEON Resources for Your Research. Location: Convention Center 238-239 (Ethan White is on the panel).

1:50-2:10 Weak impacts of climatic factors on intraspecific body size variation in endothermic species. Kristina Riemer, Narayani Barve, Brian Stucky, Stephen Mayor, Robert Guralnick, Ethan White. Location: Convention Center Rm 356.

3:20-3:40 The influence of data type, functional traits, and ecoregion on native bee phenology. Joan Meiners, Michael Orr, Kristina Riemer, Shawn Taylor, Terry Griswold. Location: Convention Center – R05

3:30-5:00 INSPIRE Session on Rapid Ecological Transitions: Synthesizing Concepts about Abrupt State Changes in Nature. Organized by SK Morgan Ernest, Christie Bahlai, Kendi Davies, and Sarah Elmendorf. Location: Convention Center – Rm 243

3:30 Rapid Ecological Transitions: A state space of concepts and ideas. SK Morgan Ernest. Location: Convention Center – Rm 243

4:40-5:00 Prediction and forecasting of Portal fauna via particle filtration. Juniper Simonis, Glenda Yenni, Shawn Taylor, Erica Christensen, Ellen Bledsoe, Ethan White, SK Morgan Ernest. Location: Convention Center Rm 355.

Tuesday

2:00-2:30 Evidence of rapid transitions in long-term community data. Erica Christensen, David Harris, Renata Diaz, SK Morgan Ernest. Location: Marriott – River Bend 1

3:10-3:40 Dynamic indicators of ecosystem resilience. Hao Ye, Erica Christensen, SK Morgan Ernest, Juniper Simonis, Ethan White. Location: Marriott – River Bend 1

5:00-6:00 during the poster session Juniper Simonis will hold an informal chat for those interested in knowing more about starting your own consulting business (likely in the poster hall, assuming there’s room). For more information, contact Juniper on Twitter @DapperStats

6:30-8:00 Long-term Studies and Paleoecology Mixer. Location: Rusty Nail Bar (SK Morgan Ernest is the chair of the Long-term Studies Section. If you like talking about temporal dynamics or want to learn more about paleoecology, come join us!).

Wednesday

10:50-11:10 Heterogeneity in competitors affects patch preference in the same extrinsic environment. Ellen Bledsoe, SK Morgan Ernest. Location: Convention Center Rm 356.

11:30-12:30 during lunch Juniper Simonis will hold another informal chat for those interested in knowing more about starting their own consulting business (location not yet determined). For more information, contact Juniper on Twitter @DapperStats

3:30-5:00 Software skills for reproducible data-intensive research. Ethan White. Location: Convention Center Rm 243.

4:20-4:40 Scaling up remote sensing fundamental unit: from pixels to crowns. Sergio Marconi, Sarah Graves, Stephanie Bohlman, Jeremy Lichstein, Aditya Singh, Ethan White. Location: Convention Center 338

Thursday

1:30-2:30 Getting a handle on your data with the dplyr R Package. Shawn Taylor . At the Data Help Desk in the Poster/Exhibit Hall.

4:30-6:30 Evaluating a near-term ecological forecast of plant phenology. Shawn Taylor, Ethan White. Location: Poster 110, Exhibit Hall

 

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 Posted on August 3, 2018 by

 science

A Julia Package for the Data Retriever

We are excited to announce the first release of a new Julia package that let’s you run our Data Retriever software with a native Julia interface.

For those of you not familiar with Julia it is a new programming language that is similar to R and Python, has a central focus on data analysis, and is designed from the ground up to be fast. It is an emerging scientific programming and data analysis language. Tim Poisot and his lab have been leaders in introducing Julia to the ecology community (thanks to them you can access GBIF data, analyze ecological networks, and more) and we’re pleased to start following his lead.

After installing the Python package getting your favorite dataset into Julia involves opening Julia and running:

julia> Pkg.add("Retriever")
julia> using Retriever
julia> iris_data = Retriever.install_csv("iris")
julia> iris_data = readcsv("iris_Iris.csv")

Like the Python and R versions of the retriever the Julia version also lets you install into a number of different database management systems and formats to meet your needs including PostgreSQL, MySQL, SQLite, JSON, and XML. So if you need to install a large dataset and access if from the database you can do that:

julia> Pkg.add("SQLite")
julia> using SQLite
julia> Retriever.install_sqlite("breed-bird-survey", file="bbs.sqlite")
julia> db = SQLite.DB("bbs.sqlite")
julia> SQLite.query(db, "SELECT * FROM breed_bird_survey_counts LIMIT 10")

We use the PyCall package to directly run the Python code from the main retriever package. Cross-language support like this is really useful for letting difficult to develop core code be easily used in different languages and it’s great that this is a core feature of Julia.

The development of this package was lead by Shivam Negi, a fantastic Google Summer of Code student with us last year, and our amazing senior software developer Henry Senyondo.

This is our first Julia package and so there are sure to be lots of things to improve (starting with the documentation). If you use Julia, or are interested in experimenting with it, we’d love feedback, issues, and pull requests. We’re always enthusiastic to have new contributors and help everyone get started, especially if they’re just learning. For more information see:

 

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 Posted on April 5, 2018 by

 science

Data science competition for converting remote sensing to ecological data

Scaling-up ecological patterns and processes is crucial to understanding the effects of environmental change on natural systems and human society. We are piloting a Data Science Challenge where multiple groups attempt to use the same remote sensing data from low flying airplanes to infer the location and type of trees in forests. This will allow forests to be studied in detail at much larger scales than is currently possible. This kind of collaborative data analysis challenge has proven highly effective in other fields for quickly improving methods for converting image data to useful information.

There are three sets of tasks: 1) identifying individual trees in remote sensing images; 2) aligning ground data with remote sensing data; and 3) classifying trees into species.

Screen Shot 2017-11-06 at 10.33.22 AM

Teams (or individuals) can participate in all of them or just pick the tasks they are most interested in. Tasks 2 and 3 can be accomplished using just tabular data. Task 1 requires working directly with spatial data. Details of the different tasks and links to the data are available at the challenge website:

https://www.ecodse.org/

We plan to write a general paper about the competition, the data, and the performance of the different methods used. Individual participants will be invited to write and publish associated short papers on the methods they used and results they produced. We already have a journal that has agreed to publishing all of these related contributions together into a collection (pending review of course).

The challenge is already open and the deadline for submissions is December 15th. Once you sign up on the website you will receive an email with some additional details. If you have any questions feel free to respond to that email or checkout the FAQ to see if they have already been answered.

This challenge is sponsored by the National Institute of Standards Technology as part of it’s Data Science Evaluation series and is also partially supported by he Gordon and Betty Moore Foundation’s Data-Driven Discovery Initiative through grant GBMF4563.It uses data from the National Ecological Observatory Network in addition to data collected by the organizers. It is being organized by the Data Science Research lab, the Weecology lab, and Stephanie Bohlman’s lab all at the University of Florida.

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 Posted on November 7, 2017 by

 science

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