cd "/Users/dave/UCSF/Projects/Teaching/Teaching 12/Lecture 8"
use "lecture class.dta", clear

mkspline agesp = age, cubic nknots(5)
mkspline agedonsp = age_don, cubic nknots(5)
mkspline yearsp = year, cubic nknots(5)

logistic txtype prevtx prevtx##c.yearsp* prevtx##c.agesp* prevtx##c.agedonsp* i.hla 
predict prop
xtile group=prop, nq(5)
tab group txtype
/*

	Overlap

*/
kdensity prop if txtype==1, generate(dens1 x1) nograph
kdensity prop if txtype==0, generate(dens0 x0) nograph
twoway (line x0 dens0, sort) (line x1 dens1, sort), yscale(off)  xtitle(Probability of Cadaveric Kidney) scheme(s1color) legend(order(1 "Living" 2 "Cadaveric"))

table txtype group, c(mean prevtx) format(%9.2f)
/*
	
	Quintile

*/
cc death txtype, by(group)
logistic death i.txtype i.group
tabulate death txtype if group==1
tabulate death txtype if group==5
/*

	Likelihood Ratio Test for Interaction

*/
logistic death txtype##i.group
est store A
logistic death txtype i.group
lrtest A
/*

	Linear in Propensity

*/
logistic death i.txtype prop

/*

	Splines

*/
mkspline prop_sp = prop, cubic nknots(3)
logistic death txtype prop_sp*
/*

	Quintile

*/
logistic death i.txtype i.group
margins txtype
. margins, dydx(txtype)
/*

	RR based on Quintile

*/
logistic death i.txtype i.group
margins txtype, post
nlcom (logRR: log(_b[1.txtype]) - log(_b[0.txtype]))
/*

	(log) RR based on Quintile

*/
logistic death i.txtype i.group
margins txtype, post
nlcom (logRR: log(_b[1.txtype]) - log(_b[0.txtype]))
/*

	(log) OR based on Quintile

*/
logistic death i.txtype i.group
margins txtype, post
nlcom (OR: log(_b[1.txtype])+log(1-_b[0.txtype])-log(_b[0.txtype])-log(1-_b[1.txtype]) )
/*

	Regression

*/
logistic death i.txtype prevtx year age age_don i.hla
logistic death i.txtype prevtx prevtx##c.yearsp* prevtx##c.agesp* prevtx##c.agedonsp* i.hla 
/*

	(log) OR based on Logistic Regression for Death

*/
margins txtype, post
nlcom (OR: log(_b[1.txtype])+log(1-_b[0.txtype])-log(_b[0.txtype])-log(1-_b[1.txtype]) )
/*

	20 Strata

*/
xtile group3=prop, nq(20)
logit death txtype, i.group3