## ----setup, message=FALSE, warning=FALSE,include=TRUE-------
library(lme4)
library(lmerTest)
library(gee)    # for generalized estimating equations
library(MASS)   # For confidence limits for parameters


## ----data---------------------------------------------------
depress <- read.table(file="D:/Dropbox/edps587/lectures/10 logreg/depression_data_long.txt", header=TRUE)

head(depress)


## ----logreg-------------------------------------------------
# standard logistic regression

model1a <- glm(y ~ severe +  Rx + time + Rx*time, data=depress, family=binomial)
summary(model1a)


## ----gee----------------------------------------------------
model.gee <- gee(y ~ severe  + Rx + time + Rx*time, id, data=depress, family=binomial, corstr="exchangeable")
summary(model.gee)


## ----laplace------------------------------------------------
model2 <- glmer(y ~ severe +  Rx + time + Rx*time + (1 |id ), data=depress, family=binomial)
summary(model2)


## ----agq----------------------------------------------------
model3 <- glmer(y ~ severe +  Rx + time + Rx*time + (1 |id ), data=depress, family=binomial, nAGQ=10)
summary(model3)


## ----extractR, eval=FALSE-----------------------------------
## setwd("D:/Dropbox/edps587/lectures/10 logreg")
## knitr::purl("R_markdown_depression_example.Rmd","R_script_depression_example.txt")
## 
##