## Announcements

New! Homework 5 solutions posted. User name and password given out in class Mon Sep 28. Subject to revision during grading.

New! Class recordings up to date through Wednesday, December 16.

New! New lecture note on maximum likelihood estimates at infinity.

New! Changed one word in problem 5-3. Calculate their mean values becomes Calculate their expected values.

New! New lecture note on how to draw a graph in R.

New! Version 0.4 of R package `glmbb` has a bug that causes it to report models twice (so they get only half the weight they should have) depending on the order of terms in the formulas you provide R function `glmbb`. The bug has been fixed in version 0.5-1, which is now on the main CRAN site and soon will be on all mirrors. So it is advisable to reinstall this package (or do `update.packages()`) before finishing homework 4.

New! Homework 4 due date changed to Wednesday, November 25. Canvas submission date changed accordingly, and the end of the Canvas discussion group for this assignment also changed accordingly.

New! New erratum posted. Simplified notes on Chapter 8.

New! New erratum posted. Error noticed the notes on model selection and model averaging has been fixed.

New! New reading assignment in Chapters 8 and 9 in Agresti.

Some formulas from office hours Monday and Wednesday.

η = M β
is the relationship between η and β and the log unnormalized posterior density is given by
i (yi + ½) ηieηi
In the course notes for this stuff the R expression `gout\$x` extracts the model matrix from the result returned by R function `glm` (provided the optional argument `x = TRUE` was supplied) and the R expression `gout\$y` extracts the response vector. They are used in R function `logl` in defined in the notes. The line
```eta <- drop(modmat %*% beta)
```
in that function defines η = M β. The rest of the function in the notes is for the binomial rather than the poisson distribution, so you have to figure out how to implement the formula above that calculates the log unnormalized density of the posterior distribution (what you want R function `metrop` to sample).

Mentioned in class, for more on Markov chain Monte Carlo, including an explanation of why the Metropolis algorithm works, one can turn to the introductory chapter of the Handbook of Markov Chain Monte Carlo written by your humble instructor. But everything necessary to do the homework is in the lecture notes for this course. This is only for those who want more info on MCMC.

Reading assignment for Friday, Oct 16 cut. Just read Sections 4.1, 4.2, and 4.3 in Agresti.

Broken link in hw 2 assignment now fixed. The assignment was wrong the file is at

that is, hw2-4.txt rather than h2-4.txt.

New course notes on the Poisson distribution.

New erratum about R function logl in the notes on the binomial distribution.

On Friday, Sep 25, 2020 we depart from categorical data analysis to the reproducibility crisis in science and what statistics done badly has to do with that. Our texts are

This course will use plain R rather than Rstudio.

You can use Rstudio if you want but I don't need anything it does.

There are two R packages designed to be used in this course.

• R package CatDataAnalysis is found at Github. Instructions for installing the package are found on that web page and work on all computers AFAIK.
• R package glmbb will not be used until the middle of the course. It is found on CRAN but one does not normally install the package by going to that web site.

Install the package in R by executing the command

```install.packages("glmbb")
```
at the R command line or, of you prefer, by mousing around in menus of the R app or Rstudio.

New! This web site has no index, so in order to find stuff one needs to use a search engine. Here is how to do that. For example, if you want to find information on the beta distribution, then the search

```"beta distribution" site:www.stat.umn.edu/geyer/5101
```
does that. This works either with Google or with DuckDuckGo. The quotation marks mean find the exact phrase. If they are left off, then the search engine will return results that have the word beta and the word distribution, not necessarily in the same page much less in the same sentence. The magic is the `site:` part, which tells the search engine only to look in that site. The site can be made more restrictive, for example,
```"beta distribution" site:www.stat.umn.edu/geyer/5101/slides
```
says to look only in the slides (this seems to work only in Google, but not in DuckDuckGo even though it is supposed to work in DuckDuckGo).

New! This course is entirely on-line, regardless of what the U does with other courses. It is synchronous in the sense that, if you want to ask questions during lecture, then you must be in the Zoom session at the scheduled time. It is asynchronous in the sense that all Zoom sessions will be recorded and linked on the Canvas site for the course.