Author: kent

If you’re interested in getting an early start, I’ve posted Project #2. You’ll find links to the description of the project, the data files, and the R and JAGS scripts you’ll need for the project on the lecture detail page for Tuesday. You’ll be using JAGS this time, but you won’t have to write any of your own code. Structure will be unfamiliar to you until we cover it in lecture on Tuesday. Those notes will be going up later tonight.

The Prunier et al. paper that provides background on the data was just accepted in <em>American Journal of Botany</em>.

I’ve posted notes on estimating F-statistics. The notes for Tuesday’s lecture are identical to the ones for last Thursday’s lecture. The lecture detail page on both of those days links to the same PDF.

On Tuesday we’ll go over Weir & Cockerham’s approach to estimating F-statistics, and I’ll introduce to a form of stochastic variation that you probably haven’t thought about before. I think you’ll be surprised when you discover how important it can be.

On Thursday (possibly late on Tuesday if we move through Tuesday’s material quickly), we’ll discuss a Bayesian approach to estimating <em>F</em>-statistics. I’ll give you the JAGS code you need, so long as you’re dealing with only two alleles per locus. You can find the code on Thursday’s lecture detail page.

Enjoy the rest of your weekend. I’ll see you bright and early on Tuesday morning.

If you happened to log onto the course website this afternoon between about 4:30 and 5:30, you may have noticed that the lecture schedule and readings pages weren’t working. Not that you should care, but I upgraded the WordPress theme, and I forgot to save a copy of the code that I had to write for those. Luckily, having reconstructed the code once before, it wasn’t too hard to reconstruct it again (and now I have it backed up in two places). I think everything’s back to normal. Let me know if you encounter any problems.

Tonight I was going over the notes on genetic that I posted over the weekend, and I found a couple of small changes I wanted to make. If you’ve already downloaded the older version and printed them, don’t worry about downloading again. I’ll point out the one small error in lecture. The other just changes the heading on a table.

The notes for this week’s lectures are now posted. As usual, you’ll find them linked on the lecture detail page. As a reminder, the Project #1 assignment is also posted. You’ll find it (and a link to a paper you’ll want to refer to) on the lecture detail page for Tuesday.

I’ve posted Project #1. You can find it on the lecture detail page for next Tuesday. If you take a look at it before lab on Tuesday, please try not to freak out. It may look a little daunting, but it should look a little less daunting after lecture and after Nora gives you a little more background (and a few hints). It still won’t be easy, but at least it should be a little less daunting.

The lecture schedule is (finally!) complete. We may tweak it a little bit as the semester goes along, but any changes will be minor.

I have also posted lecture notes for the first week of class. They’re available from the lecture detail page associated with each lecture. As a reminder, to get to the lecture detail page, simply click on the lecture title on the Lecture Schedule page. Once you’re there, you’ll see a brief description of the lecture and you’ll find a link to the associated notes (and sometimes some other resources).

See you bright and early Tuesday morning. Enjoy the rest of your weekend.

I am still working on the course website. The PHP/mySQL interaction is turning out to be a bit more complicated than I remembered.

In the course of getting that running, I just realized that some of the links on the Notes page refer to PDFs that aren’t currently available. In some cases, the notes may no longer be relevant. In other cases, I need to regenerate the PDF. If you click on a link you’re interested in and get a “Not Found” error, let me know.

The process of reconstruction continues. A preliminary version of the Notes page is now available. It includes links to (most of) the notes for the course. Some of the links may be broken. If they are, please let me know. There are also some lectures for which I have notes that don’t have links yet, and some of these are very old lectures that are no longer part of the course. I should have this all sorted out by early next week, and with a little luck, I will also have the Lecture schedule all set.

I’ve also included a link to a single PDF that combines almost everything. Keep in mind that these notes will be revised over the course of the semester, but if you want to download a single PDF file, follow the link at the very top of the page – and keep in mind that it may have some obsolete material and that it is missing some relevant new material.

Happy New Year!

I just finished updating the Resources page for EEB 5348. It includes links to the software we’ll be using during the course. To the extent possible, we’ll do everything in R, JAGS, and Structure, all of which are available for any computer you’re likely to be using (Linux, Mac OS X, or Windows), but we may have to use something else when we get to GWAS.

If you have time and the inclination before classes start, please download and install R and spend some time playing around with it. Unless you are really ambitious, though, I wouldn’t bother with JAGS or Structure yet. Both of them are fairly arcane (but extremely powerful), and I hope you’ll find it easier to use and understand them if we work through them together.