**Logistic regression for binary data****NEPAL DATA****
***generate obs no representing equally spaced times****

egen newid=group(id)
summ newid
drop id
ren newid id
sort id age
by id: gen obsno=_n
tab obsno
tsset id obsno

***Generate binary breastfeeding variable***
xttab bf
** label list
gen bfbin=1*(bf==1|bf==2)
tab bf bfbin


***Explore marginal mean model wrt age
ksm bfbin age, lowess bw(.4) xlab ylab(0(.2)1) nograph gen(bfbinsm) 
sort age
gr bfbin bfbinsm age, c(.L) s(oi) ylab

gen bfbinjg=bfbin+.1*(uniform()-.5)
sort age
gr bfbinjg bfbinsm age, c(.L) s(oi) ylab
 

*** logistic regression in STATA ***
gen agesex=age*sex
logit bfbin age sex agesex
logistic bfbin age sex agesex

predict prob

*** sensitivity and specificity from 2 by 2 table ***
gen c = .5
gen bfhat = 1 if prob > c
replace bfhat = 0 if bfhat == .
tab bfbin bfhat

*** test for statistical significance ***
test agesex
test sex agesex


***FIT GEE w/ AR(1)***
xtgee bfbin sex age agesex, f(bin) link(logit) corr(ar1) 
test sex agesex
xtgee bfbin  age, f(bin) link(logit) corr(ar1) 
xtcorr, compact
xtcorr


***Assess the model fit****
predict bffitar1
sort age
gr bfbinjg bfbinsm bffitar1 age,c(.ll) s(oii) ylab


****Fit GEE with uniform corr model ****
xtgee bfbin sex age agesex, f(bin) link(logit) corr(exc) nolog
   ** display exponential of coefficient ***
xtgee bfbin age , f(bin) link(logit) corr(exc) nolog 
xtgee bfbin age , f(bin) link(logit) corr(exc) nolog eform
predict bffitexc
gr bfbinjg bfbinsm bffitar1 bffitexc age,c(.lll) s(ooip) ylab


***Fit an unstructured correlation structure***

xtgee bfbin age , f(bin) link(logit) corr(unst) nolog 
xtcorr