I am thrilled to announce that I succesfully passed my PhD Defense last Friday, now I just need to address a few edits from my committee and my dissertation and PhD will be complete.
I am thrilled to announce that I have accepted a two year post doc at Mississippi State University, based in Biloxi, MS working as part of the Gulf of Mexico Avian Monitoring Network.
I’ve had this conversation with several people over the past few weeks, so like most things I talk to people frequently about I figured it was a good idea to write it up.
SUCCESSFULLY DEFEND MY PHD (the rest of this will just be gravy if that happens)
Lists of things
One of the challenges of working with rails is we know so little about them, and what we do know is often scattered in small data points here from the 1960s, and here from the 2000s. There is little data that has been collected in a deliberate way over a long period. The first place I looked was The Birds of North America, which provides detailed species accounts for each species. These graphs showed me some data, with literal question marks on it, that didn’t provide a lot of guidance as to when Virginia Rails were migrating (Conway 1995)
As a result of these fairly uninformative graphs I often end up digging into some literature to find data. Over the past two years I’ve tracked down almost all the issues of The Bluebird, journal of the Audubon Society of Missouri, and compiled all the spring and autumn migration data contained therein Data available here on figshare. These data are opportunistic at best (someone saw a rail, and decided to report it) but when looking at pre-eBird times (eBird being a very large online database of citizen science bird observations, which really took over after 2000) these kind of state by state resources can be vital.
I targeted Missouri because that is where my own field work takes place and I was seeking data to compare to my own. In five years and over 1000 hours of surveys I hadn’t seen very many Yellow or Virginia Rails (<100 in each case). This made quantifying their migration difficult especially because I am assuming some level of year to year variability in migration, which is common among birds.
So I sought out this other data, from the state Audubon Society. I also downloaded all August-November eBird.org observations for Missouri, Illinois, Indiana, Kentucky and Ohio (roughly the same latitude as Missouri and within the same adminsitrative flyway). These represent another type of opportunistic data, where members of the public go out birding, record what they see, and submit their observations. More data points were available here but eBird data can be biased because people tend to bird where they live, meaning effort is not evenly distributed across the landscape. So I sought out a third type of data, building strikes.
When I tell people rails hit buildings they are often surprised, but many many bird species have been recorded striking buildings. Many species of birds migrate at night and the lights on tall structures in large cities (and even in less urban situations) can disorient them and lead to collisions. In many large cities there are building strike monitoring programs where people walk the same route each morning and record what is found on the sidewalk (in many cases the dead birds are also collected and given to a museum, YAH MUSEUMS!). These data could be another interesting source since they are being collected each day in the same place, though this is only occurring in large cities. I obtained these data points from Loss et al (2014), Thanks Scott!
So I have these three kinds of data, and my own data, and I want to figure out what on earth they can tell me about the migration of two of the least studied birds in North America.
I thought about doing this a few different ways, first trying histograms, and line graphs, even scatter plots. None of these seemed to work. All the sample sizes were different and whatever the story was it was lost.
Then I tried box plots, with the idea this would help take out the highly variable y axis due to different sample sizes, and allow us to compare the duration and median date of migration.
This was ok. I only had one data point for building strikes of Yellow Rails, so I excluded it, and this figure is fine. But I wasn’t really happy with it, I was still wrestling back and forth with if I should be describing each data type on its own, or if they should all be lumped together, and I found this graph deceptive, it did a good job of making it clearer because the sample size was hidden, but that hidden element bugged me.
|Data Type||Yellow Rail||Virginia Rail||Citation|
|The Bluebird||20||20||(Fournier 2016)|
|eBird||53||261||(Sullivan et al. 2009)|
|Building Strikes||1||3||(Loss et al. 2014)|
|My Surveys||77||114||Fournier et al. Unpublished Data|
So I tried some other methods, again and again.
Finally I settled on this one.
This graph does a few things I really like. It separates out the Birds of North America data, which isn’t really data so much as my visualization of the information on the graph in the Birds of North American Accounts. It also lumps the data in a way I am comfortable with. All the data I gathered from other sources, Audubon Society of Missouri, eBird and the building strike data, are lumped into ‘Opportunistic Observations’ which I think is the most conservative way of looking at them. My data, which were collected through nightly regular surveys are separated for two main reasons 1) they are my data and I wanted to compare my data to other data, 2) they were collected under one standardized protocol, unlike the other data types.
I think this data does a better job of showing the story. Yellow Rail migration, in my study and in the opportunistic data is occurring in two strong peaks which are near each other. Why they aren’t the same could be related to a variety of biases and assumptions in the data set. These also overlap well with the Birds of North America account range though they start earlier, which could be a big deal.
Virginia Rail migration is clearly a different beast. Opportunistic observations have two peaks, one of which strongly overlaps with my data, and migration is starting earlier and continuing much later than it does in the Birds of North America Account.
One thing I don’t like about this figure is I don’t have a good way of showing the yearly variation in the data, which is probably asking too much of what is still a pretty limited data set, but a ornithologist can dream!
I’m still working on this manuscript, and still trying to decide if this is the best way to visualize this kind of data. If you have ideas I’d love to hear them, firstname.lastname@example.org or @RallidaeRule.
Conway, Courtney J. (1995). Virginia Rail (Rallus limicola), The Birds of North America (P. G. Rodewald, Ed.). Ithaca: Cornell Lab of Ornithology; Retrieved from the Birds of North America: https://birdsna.org/Species-Account/bna/species/virrai DOI: 10.2173/bna.173
Fournier, Auriel (2016): The Bluebird Rail Data. figshare. https://dx.doi.org/10.6084/m9.figshare.2760913.v2 Retrieved: 21 50, Dec 05, 2016 (GMT)
Loss, S. R. S. S., T. Will, P. P. Marra, S. R. S. S. Loss, and P. P. Marra. 2014. Bird–building collisions in the United States: Estimates of annual mortality and species vulnerability. Condor 116:8–23. http://www.bioone.org/doi/abs/10.1650/CONDOR-13-090.1%5Cnhttp://dx.doi.org/10.1650/CONDOR-13-090.1.
Sullivan, B. L., C. L. Wood, M. J. Iliff, R. E. Bonney, D. Fink, and S. Kelling. 2009. eBird: A Citizen-based Bird Observation Network in the Biological Sciences. Biological Conservation 142:2282–2292.
2016 numbers followed by (all time project total)
Presented one of my dissertation chapters at the North American Ornithological Conference this past week. Using species distribution models from marshbird monitoring data to inform bayesian assignment of migratory rails during autumn migration.
Rebecca Heiseman, Beth Ross, Desiree Narango, Jordan Rutter and myself did a short workshop at the North American Ornithological Conference Tuesday, highlighting the many ways twitter can be used by scientists.
Building off the success of the workshop Matt Boone and I taught at AOU in 2015 I taught a full day R workshop on programming, functions, data management and how to build an R package at the North American Ornithological Conference this year. Had 60+ participants and everyone learned a ton. Hoping to tweak it again, improve it some more and teach it again at AOU in 2017.
New Paper - Combining citizen science species distribution models and stable isotopes reveals migratory connectivity in the secretive Virginia rail
Just returned from a great meeting in Corpus Christi, Texas and the annual meeting of the Society of Wetland Scientists. I’ve never been to SWS before and it was a wonderful and informative meeting and great chance to break out of my often very bird focused bubble and think about wetlands in some new ways.
There are pictures of me geeking out about birds since I was quite small. Those who knew me even in passing as a kid are unsurprised where I ended up. I have been incredibly fortunate along the way to be guided mentored and at time shoved by some very key people in my life.
Sometime around American Thanksgiving I was asked on Twitter to recommend a few historic women in ornithology for someone’s kid to research for a school paper. I sat there, stared at my screen and then hung my head.
Last fall I tweeted from @RealScientists and @BioTweeps as part of the outreach for my fall field work (#MORails). I choose to do this during my field work since live tweeting rail captures is WAY more exciting then live tweeting running R code or writing which is what I do the other 9 months of the year.
My latest post as the science/math editor for Science Borealis is up. Talking about the role of hunting and statistics in wetland conservation, especially as it relates to migratory birds.
I’m already into my second week as the Teaching Assistant for the Undergrad/Graduate Biometry course here at UA. I am really excited to be teaching again this semester (I always forget how much I enjoy it) and doubly so since I get to teach people about R. I’m working on moving all the course materials over from systat to R, since this is the first time its being taught in R. If you are curious what we cover check out the repo.
Submit 4 of 5 chapters for publication (multiple times if necessary!!)
Lists of things
If you are a regular reader the topic of my most recent paper won’t be too surprising. Dr. Alex Bond and I have written an editorial in The Wildlife Society Bulletin entitled Volunteer Field Technicians Are Bad for Wildlife Ecology.
Here are the best photos and tweets of the 2015 #MORails season. https://storify.com/amv_fournier/morails-2015
The fall migration part of my project was highlighted recently in the University of Arkansas Research Blog Field Notes. Check it out here
30 treatment wetlands
10,700 miles driven in the truck
~1200 miles driven on ATV
169 hours of surveying
1063 Sora (don’t do the math for miles/dollar per Sora, just don’t)
7 Virginia rails
12 Yellow rails
62 rails captured (3 Virginia, 5 Yellow, 54 Sora)
62 sets of feathers gathered for migratory connectivity research (these will be combined with feathers from previous years, the 60 from Canada this summer and hunter feathers from all over the central US!!!)
120 hours of nighttime go pro video footage (videos will be posted once I get time to process them)
5 fouled spark plugs
3 carburetors cleaned
2 spotlights held together with electrical tape and hope
1 new air filter
5 oil changes on ATVs
1 flat tire (ON THE FIRST DAY)
5 seasons of Breaking Bad watched
+/- 1000 cups of tea and coffee consumed
0 times running out of gas on the ATVS
0 times losing wallets
0 times putting ATVs into way to deep water
0 King Rails (sadly)
0 Black Rails (still not sure they exist….)
many hours sprawled out in random parking lots trying to figure out what was wrong with the atvs
many hours of laughing and brownies and cooking together
In response to a request from a friend who is just starting her PhD, here is what I wish I could tell my first year PhD Student self, and what advice I can give to other graduate student Women in STEM. This was written during the first week of my field season, so the thoughts are short, but I am happy to discuss them more if folks have questions or comments.
My work in Saskatchewan this summer was highlighted in the University of Arkansas Research Blog Field Notes recently.
Monday August 10th begins my fourth field season. Just saying that makes me pause, I’m a fourth year PhD Student, a PhD Candidate, man time has flown.
I’m pleased to say I am joining the Science Borealis team as a Math & Statistics Editor. I’ll be writing posts and helping in other ways to spread the job of Math and Statistics. So far they are graciously ignoring the fact that I am not in fact Canadian.
Matt Boone and I have compiled our notes and resources from the workshop we taught at the 2015 meeting of the American Ornithologists Union/Cooper Ornithological Society. If you are interested check out the repo here
I gave a presentation at the American Ornithologists Union/Cooper Ornithological Society meeting in Norman, OK this past week highlighting some work that I started in my undergraduate and which I hope to soon have accepted for publication.
I’m giving a presentation today at the Association of Field Ornithology / Society of Canadian Ornithologists / Wilson Ornithological Society Joint Meeting in Wolfville, Nova Scotia today.
I’ve been on both sides of the problem for several years now. I spent years applying for field technician positions, interviewing, and snagging a few, now I just finished hiring for my fourth field season of my PhD fieldwork. I’m something of a questioner, I’m always asking people for their thoughts on how to do things, and I’ve picked many brains about how to apply for field jobs and here are my take aways, for those who are coming up in the ranks.
Marsh Bird Field Technician: Missouri
This post was originally peeked by a thread on reddit about lab safety horror stories, and is in fact horrifying. My experience lies in a different realm, field work, where safety is often also a big issue, though the guidelines around it are often missing, or totally ignored. I chatted very briefly with a few folks about this on twitter a week or so ago and my initial wanting to write this post was dampened by the realization that like the reddit post, this may spark a string of ‘oh you did that dangerous thing, mine was so much more dangerous’ and further fuel the masochistic dangerous mindset that often hangs over fieldwork and is very alienating to many, and dangerous for everyone.
In March I coordinated a Software Carpentry workshop here at the University of Arkansas. We did a two-day workshop on R, the Unix Shell and Git and it was very well received. A few people have asked me to write up my thoughts on planning the workshop, the workshop itself, etc, so here it goes.
I originally wanted to call this ‘why I love birds’ but I realized that my urge to write this comes not really from my love of all things with feathers, but from my passion for what I do, and the sadness I sometimes feel when others try to tell me my passion is bad, or don’t have passion of their own towards their own science.
beware, this is something I feel VERY passionately about
At The Wildlife Society National Conference this year in Pittsburgh I presented a poster summarizing our results from the first year of our crossover experiment. If you would like to check it out, it’s on figshare.
Every year of fieldwork I do seems like an additional argument for Murphy’s Law and Long-Term Research. No two years are alike, and this year was the year of thunderstorms and rain. 2012 was a drought and 2013 was drought-like (it rained earlier in the year, but not much during the season). Despite the weather’s best efforts we were able to get in all the surveys we needed to complete and picked up on some weird patterns along the way. This year had no clear peak in migration (unlike the previous two field seasons) though we saw essentially the same number of birds, they just came through at a more steady rate throughout the year.
Somehow the 2014 field season is already half over, and once again the weather and the birds are throwing a totally different suite of challenges our way.
Each season of my project is broken down into four rounds of surveys. We visit each region of the state four times and we’ve just finished up our first set of visits to each region.
Since I’m now on the other side of comps I’ve had a few people ask me for suggestions on how to prepare for their own. Here’s a few thoughts.
My comps are coming up fast (8 days!!) and the end of the semester is finally past, FINALLY. The past two months have been a bit of a wake up call about how I need to take care of myself as well as my work. In the spirit of taking care of myself, I’m carving out a few minutes to breathe and share a bit more of my comps process.
Can you see the tiny clear antennae sticking out from between his feathers, that is the geolocator
Marla showing a cardinal to some kids
Staying focused is hard, being productive perhaps even more challenging. In grad school the challenge of focus is especially true because there are SO many things pulling for your attention. Your research, your classes, any teaching you do, writing grants, writing papers, presenting at conferences, and all the other tasks. It makes it easy to be very busy without actually doing anything.
Science is all about discovering new things, whether its information new to humanity as a whole or just to yourself. The moment of discovery is what drives many of us in science. As I’m studying for my comprehensive exams I am having a lot of these moments. Things are clicking together. I am forming connections between papers and ideas which had never occurred to me before. Constant discovery is what makes all my studying so addictive, even when it takes me two hours to get through a paper because I’m going to Google every other paragraph for another explanation.
A few weeks back I had a series of conversations with some other scientists who decided to tell me different variations of ‘birds aren’t important’ ‘people who work on birds lack creativity’ ‘you aren’t as good of a scientists because you work on a charismatic animal’.
Pass my Comprehensive Examinations - If I accomplish nothing else this year but this it will be a huge success.
I love science because the idea a bird can FLY from continent to continent twice a year and come back to the same place, amazes me. I love things with wings, with feathers, with elaborate songs and displays. I love birds, and I have since I was young, (granted I still am, so lets just say, younger). I love how many different ways there are to move from place to place throughout the year. So many different strategies and ideas. I love the fact that migration has captured the human imagination for millenia and connects people across languages and cultures.
2013 was a very good year, both personally and professionally.
Looking at the numbers can be really discouraging as a woman in STEM. It often seems like the cards are stacked against us and I must be very crazy to think that I am the exception to all of it. That is probably another discussion for another time. This post for The Lab and Field got me thinking about my own work and how I can help change those statistics myself, more then just being a female in STEM. That post references an article in nature that encourages us each to calculate our own gender gap. Or the ratio of Females to Males in our own work. It’s easy to talk about these gaps as national wide, or international problems and brush them off, but when you look at your own numbers, it’s pretty sobering.
One of the things I greatly enjoy and also find really challenging as a grad student is serving as a mentor to others, both undergraduates and the technicians that work for me during my field seasons. I love getting to know people, offering up my experiences and things that I’ve done and helping them understand the many many confusing paths that they might be able to take through their professional careers. After my techs work for me they of course go on to other jobs and opportunities and I get calls for references for them. I’ve been really lucky and had some fantastic techs so I am more then happy to pass that along to whatever their up to next, be that grad school or more field jobs. I’m just finishing up my third round of writing a letter of recommendation for one of my techs for graduate school. I find this a lot more challenging then just talking to someone on the phone. On the phone I know that I can better communicate the excitement that I feel about my techs and can give the person as much or as little detail as they want, a letter is totally one sided and I don’t’ want to come across and unenthusiastic. I want to communicate the strengths of each one of them, the reasons that they were such valuable members of my team and why I think they would be fantastic grad students. And that is hard.
Field Season 2013 By The Numbers
So most people never see rails, and when they find out I work with rails they have a million questions. Most people are frustrated by rails, even the ones that are easier to see like Sora. I’ve had several people tell me that they don’t actually exist.
Not alot of birds out here at the end of October but the wetlands are beautiful as they go through their fall colors.
So the federal shutdown ended, thank goodness, just in time so that my fourth round of surveys was not destroyed. The state properties are only available to us to survey through october 15th so all of our surveys after that date are just on the National Wildlife Refuges, which were closed during the shutdown, thankfully though they are open now and we are back in business.
So I’ve finally had a chance to get my final copy of the poster up on figshare, if you’re interested in taking a closer look at it follow this link.
I’ve been really lucky in the past 10 years to experience a wide variety of leadership styles, some really inspiring and some really frustrating bosses. I’ve learned a lot from both and last fall I got my first real chance to implement them.
So I’ve started on another side project (yes I realize I haven’t written much on my other side projects yet but I am really pumped about this one so this one first). Photo by Justin Lehman my awesome tech Yellow Rails have quickly become my favorite of the rails over the past few months. Between there extra sneaky habits and the fact that they are just so pretty I am pretty solidly addicted to Yellow Rails. Those of you who have been subjected to listening about my senior project of my undergrad know a bit about the morphometric model I worked on for the Virginia Rail (my second favorite rail). We were actually pretty successful with that (currently working on getting it published waiting to hear back from a journal!). So now I’m working on getting a group of people together to try and do the same thing for the Yellow Rail.Basically a morphometric model is a statistical model and in our case we’re trying to take morphometrics (that is body measurements such as wing length bill length etc) and use discriminant analysis to predict the sex of the bird.So this past week I’ve sent out dozens of emails to anyone that anyone has ever told me works with Yellow Rails trying to get together a great group of collaborators and the biggest sample size that we can. So far I’ve received some great positive responses and if you do Yellow Rail research by any chance and are interested in working on this and I haven’t emailed you shoot me a line (email@example.com) the more the merrier!
So now that I’ve managed to get into graduate school and am having a pretty good time thus far I’ve been getting lots of questions on what method I used to go about getting the position I did. This is a complex question, there is a lot that you need to do and think about and just about as many ideas on how to go about it. But since I keep getting asked here is my take, what I did, and what I’ve been told can help you along the way. Keep in mind, I’m still in my first year, so while I was successful in getting in only time will tell if I end up successful all the way around.
So this year I’m trying to set some ambitious and varied goals, both professional and personal, just to set out what I hope this year will bring. I know that likely all of this won’t happen, and that new adventures and things will present themselves as well, and I am excited for all of them.
Being in grad school makes me even more statsitic centered then I already was, the need to quantify things has led me to put together things list of different numbers for 2012.