JANUARY 2022
Kyra's Blog
Kyra Bankhead, undergraduate student
1 January 2022
HAPPY NEW YEAR! I got off to a great start and was able to take a lot of time in figuring out how to adequately analyze my data. I have been using GAMM models to analyze the number of harbor seals hauled-out with interactions between air temperature, tide level, noise level and month as fixed factors. I also made sure to include month as a random factor as well. I made separate additive models for the waterfront and the marina so that site wasn’t included as a separate variable. I checked for over dispersion at each site and found that seals hauled-out followed a Poisson distribution. I linked noise level to the response variable seal numbers using a logarithmic function. I also checked for collinearity using the GGally function in R and found Julian date to be correlated with most of the fixed variables so I will make sure to exclude it.
I used R to check for zero inflation and found that both sites had an excess amount of zeros in the response variable of seal numbers. After reading Cambell’s 2021 article on “The consequences of checking for zero-inflation and overdispersion in the analysis of count data,” I realize that I have to use a different distribution for both sites. Since the waterfront does not have overdispersion but is zero inflated, I found that a zero inflated Poisson distribution will work best, whereas a zero inflated negative binomial will be best for the marina.
Kyra Bankhead
Holland's Blog
Holland Conwell, undergraduate student
1 January 2022
Happy New Year! December was admittedly a pretty slow month regarding progress on my project. I enjoyed catching up with family over the holidays and taking a bit of a breather. Despite my slower pace this month during break, I did revisit my efforts to sort the species in the diet dataset into orders. I had envisioned this being a great way to condense and visualize the dataset, and I completed sorting all species mentioned in the diet data by order. However, when it came to sorting the full dataset this way, I ran into some roadblocks. I realized that I might need to switch the dataset back from wide to long format, and I did this through RStudio. Unfortunately, I ended up with a dataset in long format which grouped similar species together instead of grouping individuals by ID. I tinkered around with my code and continued to get this funky format, bringing my work to a halt right before my holiday travels.
I’m still trying to figure out how best to accomplish this task, but I’m now entering the new year with some exciting news! I received word that Zoë finished rerunning the troublesome plates from before. As a result, starting in winter quarter, I believe I should be moving on to some new tasks regarding data analysis, and I’m excited for what’s to come! I’ve been grateful to really become more familiar with the dataset, RStudio, and how I’d like to visualize the data, and I’m ready to dive back into more work on this project in the new year!
Zoë's Blog
Zoë Lewis, graduate student
1 January 2022
Happy New year! December brought the end of fall quarter, a completed DNA metabarcoding data set and many drafts of my general introduction. Before the holidays, I was spending most of my time working on my general introduction to submit before going back to Seattle for a few days. Now, as the holidays have wrapped up, I’ve been spending more time diving into my DNA metabarcoding set, thinking about appropriate groupings for prey species, and digging into the data analysis aspect of this project.
This month I received some very helpful feedback from Adrianne, Dietmar and Alejandro on my general introduction. Having multiple reviewers is so helpful for better streamlining the writing process and developing a stronger draft! I think that with some serious work this week, I’ll have a solid draft to send to my committee and let sit while I start working on other sections of my thesis! Time flies when you are writing a thesis… Although I’m on top of my goals, I want to make sure my final product is as polished as possible. I’m looking forward to taking this quarter to focused on my thesis writing and analysis.
Toward the beginning of December, I had a meeting with Sarah Brown from WDFW and Adrianne, to review the R code used to determine the species percentage. With a few small hiccups, we were able to get a complete summary of each sample, and now I’m able to look into general trends to better inform my future analysis of this dataset.
As my project continues along, I look forward to working with Madison Gard on her independent research to help validate our qPCR methods for sex determination on different species. I look forward to a couple extra days in lab and helping with project that will solidify my understanding of my own methods.
Looking forward to the new year, new quarter, and hopefully in person lab meetings, if omicron permits!
Kathleen's Blog
Kathleen McKeegan, graduate student
1 January 2022
What a crazy end to a crazy year! 2021 was tough due to the tumultuous times we are living in (political turmoil, the pandemic, climate change, civil unrest, etc.). Luckily, this graduate program at Western has been a constant rock throughout the chaos of 2021. I am very grateful that I can dedicate my time and effort to a project that I care deeply about, and that I am surrounded by brilliant and passionate young scientists who inspire me every day. That said, I am very excited to leave 2021 behind and begin a new year.
This past month, I focused mostly on finishing up field observations, processing the remaining 2020 photographs, and preparing for data analysis. Our team of researchers finished up the last drone observation before finals week and the last field observation on December 11th. Kate and I spent finals week working on the difficult to ID photos from 2020. After a few hours of solid work, she and I wrapped up 2020 completely, such that everything was properly IDed, confirmed, and uploaded to the lab computer and hard drives. I also completed another draft of my introduction and methods sections, which was reviewed by Alejandro. At this point, I am feeling comfortable with the state of my introduction, and my methods will become more solid once I complete the data analysis portion of my project.
Kate and I are now focused on processing the 2021 photos. We need to select, crop, and ID photos of each seal in each minute of each observation. I have completed four days of photos so far and am currently working on two more. Luckily, we trained two additional undergraduate research assistants to help us with the ID process, so we hope to have most of the photos completed by the end of Winter Quarter, if not earlier.
Additionally, I found out that my abstract submissions were accepted for two different academic conferences: The Salish Sea Ecosystem Conference and the Whatcom Marine Research Symposium. In both cases, I will be giving a 15-minute presentation with 5 minutes for questions. This will be my first time giving a talk at an academic conference outside of my affiliated school, so I am very excited and a little nervous. I have a lot to do before I present!!
All in all, I was not able to accomplish as much as I had hoped this past month, especially with regards to data analysis. My winter break ended up being quite chaotic (it was a Covid Christmas!) and I therefore found it incredibly difficult to focus on work. But to look on the bright side, I am now well rested and will be able to approach my project with determination and fervor this month. Hopefully I have more to report next time!
Kate's Blog
Kate Clayton, undergraduate student
1 January 2022
Happy holidays! I do not have much to report from this last month. The main accomplishment was our team finishing up the rest of the observations during finals week, bringing an end to the Fall observation schedule. It feels good to have that done!
I have spent most of the break trying to relax and recover from Fall quarter, so I have not been as productive as I had hoped with photo cropping and IDing. I will need to get back into that soon so Kathleen and I can get the 2021 data inputted.
The beginning of Winter quarter will be spent training students on how to photo crop and resuming observations. Once this is completed, the rest of the quarter should be more low-key and allow more time for cropping and IDing. My goal is to complete +6 days of cropping in the next month. Wish me luck!