Hi class,
Here is the script for Chapter 11, Chapter11_jtf.r , plus a paper by Potts and Elith (2006) that helps explain what all that crazy code at the end is. Look at Appendix B for the algorithm that Zuur implemented. I still haven’t gotten it to run correctly, but I’m working on it.
Jack
Hi Class –
The script for today is Chapter10_jtf.r , but I may also have time to include an example from “R in a Nutshell”.
Jack
Hi class,
The new scripts are up:
Also, in Chapter 8, I forgot to talk about the likelihood functions for each distribution. That is what R uses to figure out the likelihood of each observation given the parameters.
Jack
Hi class,
I went over Chapter 7 again, and made a few changes. The new script is Chapter7_jtf_v2.r
Jack
Hi class,
The script for Chapter 7 is now online ( Chapter7_jtf.r ). Lots of stuff going on in this chapter. Enjoy!
Jack
Hi All,
Here is the script ( Chapter6_jtf.new.r ) I ended up with at the end of class today (I was trying to plot a smoother through the residuals of the M3.gls model, but it didn’t actually work until after class) . I have also uploaded the slides I did to explain ARMA models. Tomorrow, we’ll work with some of your data and try to diagnose what to do with the random part of the model (fix heterogeneous variances, add random effects, add autocorrelation, or something else we haven’t gotten to yet).
Jack
Hi class-
Here is the script for Chapter 6 (Chapter6_jtf.r ). I may get the simulation script working soon, but don’t hold your breath.
Jack
Hi class –
Be sure to read the protocol that appears on page 90 for gls models, as Zuur uses it for mixed effect models in general. A shorter version of it is in chapter 5 (bottom of p. 121).
Tomorrow we’ll start on Chapter 5 – Mixed Effects Models. The main script I’ll be following is Chapter5_jtf.r . I’ll also spend a little time simulating the M.lm and M2.lm models for the owls in the simulation script – Chapter5_Simulation.r . This is the key chapter in the whole book, so be sure to ask questions if you don’t understand something.
Jack
Hi,
Here is today’s script: Chapter4_jtf.r . Be careful of the identify command. You are supposed to click on the point you want to identify (the outlier) and then press the “Finish” button in the upper left corner of the plot window. It will then tell you which record is the outlier (it should be 26).
Also, I didn’t get to it, but I have a script to simulate a dataset for chapter 4 ( Chapter4_Simulation.r ). Run through it, if you want.
Jack
Hi class,
I will put the scripts that I go through in class up here, as I change them some from what is in the book or on Zuur’s website. So far, I have the ones for Chapter 2 and Chapter 3 up. I tried to comment stuff that I added, but let me know if you can’t figure out why I am doing something.
Jack