** HW 2 Solutions 2009 **


** Read in Dataset **
cd "/Users/haley/Dropbox/Desktop/LDA09/data"

infile id infect time gender vitA age using "ICHS.txt"
xtset id time


** fit the model in (a) with independent correlation structure **
xi: xtgee infect time gender age vitA, nolog f(bin) l(logit) corr(ind)

test vitA


** fit the model in (c) using the unstructured correlation **
xtgee infect time gender age vitA, nolog f(bin) l(logit) corr(uns)

estat wcor


** try the exchangeable and ar1 models **
xtgee infect time gender age vitA, nolog f(bin) l(logit) corr(exc)
xtgee infect time gender age vitA, nolog f(bin) l(logit) corr(ar1)

** final model **
xtgee infect time gender age vitA, nolog f(bin) l(logit) corr(exc) robust


** test H0 **
test vitA

** tests in part (f) **
test time
test age
test gender
test age gender


** fit the random intercept model from (g) **
xtlogit infect time gender age vitA

** estimate the probabilities in (i) **
lincom 3*time+3*age+_cons
display exp(-1.49)/(1+exp(-1.49))
display exp(-2.19)/(1+exp(-2.19))
display exp(-0.78)/(1+exp(-0.78))
lincom 3*time+3*age+vitA+_cons

** estimate the same probabilities for the gee model **
xtgee infect time gender age vitA, nolog f(bin) l(logit) corr(exc) robust
lincom 3*time+3*age+_cons
lincom 3*time+3*age+vitA+_cons


** fit a GEE and RE transition model **

** first create the indicator variable for infection at previous visit **
** shift the infection indicator down by 1 row **
gen infect_prev = infect[_n-1]
** drop the first visit of all subjects **
by id: drop if _n==1

xtgee infect infect_prev time gender age vitA, nolog f(bin) l(logit) corr(exc) robust
xtlogit infect infect_prev time gender age vitA