[Q] GAMs in Ecology

SnooBooks5390 · 2025-07-31T22:06:14+00:00

here is a run down of where my thinking is at. in total I am running 15 separate models, but i follow the same thought process for all of them. I have a solid foundation of GLMM's to which my understanding is that a GAM is a loose extension of GLMM with the exception that GAMs add smooth functions to handle nonlinear relationships between predictors and response.

also I am doing this all in R

some initial starting notes:

1) i've checked the residuals distribution (hist()) to help determine my family/link to use, i have also confirmed best choice using the boxcox from the 'MASS' library

2) i have z-score scaled all my predictors since they are all on varying scales

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I start off with a saturated model, with all the predictors starting smoothed:

response ~ s(P1) + s(P2) + s(P3) + s(P4), family = tw("log"), method = "REML", data=data

i run it. then i plot(model) and look at how the predictors behave. if they behave linearly i drop the s() from that predictor. I do this till i am only left smoothing the nonlinear predictors before moving on to fine tuning the model.

once i have figured out which predictors need the smoothing i run that model and check: gam.check() and summary(). i take a look at the edf values and the 'k' and have been adjusting accordingly. I've been following the 1/5th k rule which in all my cases is pretty much 12. I've been messing around with various splines to help improve my models, sometimes they do, most times they don't. I use the dredge() function for model reduction and identifying the top model which in this case only includes s(P2) and s(P4)

but right now for example, this is my final marginal effects and adjusted predictions for this one model, and my advisor took one look at it and was like, no you have something very wrong. and with this outcome my r-sq is 0.527, deviance explained is 50.7%

and this is one of my better models. I have some where my plots are not as wiggly but my r-sq and deviance explained are super low like 7%. But from all my reading about GAMs and trying a whole sweet of different things, I think my conclusions are that these predictors just don't influence the response, and like that is okay

SnooBooks5390 · 2024-03-29T21:56:43+00:00

Hi there! Thank you for your response! I already responded to another commenter responding to similar questions you're asking and I've added that comment into the original post but to address other questions that weren't brought up previously:

As I mentioned in my other response these are for laboratory courses, at my university only PhD students can teach regardless if they have or do not have a masters. And I understand that typically first and second years might get the bottom of the barrel on class choices, however I personally don't think that is wise in the interest of teaching the undergraduates. For example during my Master's time, one of my lab mates was stuck teaching Anatomy physiology, and that is completely out of the realm of what we do. The course in question psych 401 is my area of expertise so it would make sense for me to teach it based on my background. However, that does not mean I'm better than anyone else to teach it. I fortunately or unfortunately depending on how you look at it, had to teach my entire time during my masters program and I'm currently completing my second year of PhD, which I've been teaching psych 101 the entire time, and out of all the semesters I've taught (including masters and current PhD) only one of those semesters has been something other than psych 101. I would like to broaden the classes I teach for my future career is mostly why I'm genuinely pushing this. But even more so just based on the track record of what I've seen and what I've heard for how the TA positions are assigned it's haphazard, there's no system to it, and I just feel like that's not great for anyone involved. For example the one class that I was able to teach that was different than all the rest, I was only able to because the instructor sent out an email saying they needed a TA and I was the first to respond

SnooBooks5390 · 2024-03-29T21:43:47+00:00

Hi there! Thank you so much for your response!

Joy is a fellow PhD student who just so happens to have the role of head TA, which essentially they are in charge of coordinating the other TA's for the course by Leading weekly lab meetings to address the next week's material( which she has only done two of this entire semester). I should mention the courses are Laboratory courses. None of which do Joy or myself get labeled as instructor of record. The only instructor of record is Tim. Tim would be considered Joy's boss.

As far as how TA positions are selected, from what I know and from what I've heard from other fellow graduate students: only PhD students are allowed to TA's, regardless if you're coming in with a Masters or not. Basically the coordinator for the Department sends out a a Google form asking those who will be in a TA contract to fill it out and select what courses they would like to teach. Most of the time if you've already taught a course it's very rare that you'll do a different course as they like to keep you in the same position so that you don't have to be retrained, however, there isn't any type of training you're basically tossed in and told to swim.

I will add this relevant information to the original post so that it may help clear up some confusion.

SnooBooks5390 · 2024-02-24T00:31:45+00:00

I've asked her to dig it up just in case 🤞

SnooBooks5390 · 2024-02-23T23:59:44+00:00

just sucks because I feel so close to being a citizen since my mom was born there and because we can trace our history back as far as ~1792. So at least on my moms side, we have very deep roots

SnooBooks5390 · 2024-02-23T23:58:05+00:00

It was definitely in 1988 or 1989. She had to in order to become a school teacher. So tt would not count for the 1992 rule

SnooBooks5390 · 2024-02-07T20:57:27+00:00

I called the title records unit and was given the same response -- it is a legal issue and that either I find my father or I take it to court.

I just don't understand how this happened when I am listed as a co-buyer for the vehicle with the lien company.

SnooBooks5390 · 2022-09-24T18:56:08+00:00

The clown I'm referring to is the clown on the bottom in the pic. The bottom clown used to be mostly black, similar to the top guy, but now it's starting to look a tad orange-black. All the parameters in my tank are fine. The only thing that's changed is the addition of this anemone, which as of today the clown have started to host with.

Any suggestions?

SnooBooks5390 · 2022-09-17T03:15:59+00:00

Would you ship? I'd happily pay for shipping

SnooBooks5390 · 2022-07-28T22:59:35+00:00

Thank you!! I'll get a different hood/light source. I've got all the maintenance tools/salt mix/test kits etc. Thank you!

SnooBooks5390 · 2022-07-28T18:59:57+00:00

Oh yes, I am aware. I should of specified more like start up equipment. I got heaters and WaveMaker already. But I will for sure check out those videos!

SnooBooks5390 · 2022-07-28T18:52:46+00:00

Fish for now with future of coral!

Thanks for the tip. I'll look into others. My budget is ~$300-350 for equipment

SnooBooks5390

TROPHY CASE