window push log using 5.20.EsophagealCa.ClassVersion.log, replace
window push set more on
window push *  5.20.EsophagealCa.ClassVersionlog
window push *
window push *  Regress esophageal cancers against age and dose of alcohol 
window push *  and tobacco using a multiplicative model.
window push *
window push use 5.5.EsophagealCa.dta, clear
window push sort tobacco
window push by tobacco: tabulate cancer alcohol [freq=patients] , column
window push *
window push *  Combine tobacco levels 2 and 3 in a new variable called smoke
window push *
window push generate smoke = tobacco
window push recode smoke 3=2 4=3
window push label variable smoke "Smoking (gm/day)"
window push label define  smoke 1 "0-9" 2 "10-29" 3 ">= 30"
window push label values smoke smoke
window push table smoke tobacco [freq=patients], row col
window push *
window push *  Regress cancer against age, alcohol and smoke 
window push *  using a multiplicative model
window push *
window push logistic cancer i.age i.alcohol i.smoke [freq=patients]
window push lincom 2.alcohol + 2.smoke, or
window push lincom 3.alcohol + 2.smoke, or
window push lincom 4.alcohol + 2.smoke, or
window push lincom 2.alcohol + 3.smoke, or
window push lincom 3.alcohol + 3.smoke, or
window push lincom 4.alcohol + 3.smoke, or
window push *
window push *  Regress cancer against age, alcohol and smoke. 
window push *  Include alcohol-smoke interaction terms.
window push *
window push logistic cancer i.age alcohol##smoke [freq=patients]
window push lincom 2.alcohol + 2.smoke + 2.alcohol#2.smoke, or
window push lincom 2.alcohol + 3.smoke + 2.alcohol#3.smoke, or
window push lincom 3.alcohol + 2.smoke + 3.alcohol#2.smoke, or
window push lincom 3.alcohol + 3.smoke + 3.alcohol#3.smoke, or
window push lincom 4.alcohol + 2.smoke + 4.alcohol#2.smoke, or
window push lincom 4.alcohol + 3.smoke + 4.alcohol#3.smoke, or
window push * 
window push *   Calculate delta deviance
window push *
window push display 2*( 351.96823   -349.29335   )
window push display chi2tail(6, 5.34976)
window push more
window push *
window push *  Perform Pearson chi-squared and Hosmer-Lemeshow tests of 
window push *  goodness of fit.
window push *
window push lfit
window push lfit, group(10) table
window push *
window push *  Perform residual analysis
window push *
window push predict p, p
window push label variable p 						///
window push     "Estimate of {&pi} for the j{superscript:th} Covariate Pattern"
window push predict dx2, dx2
window push predict rstandard, rstandard
window push generate dx2_pos = dx2 if rstandard >= 0
window push generate dx2_neg = dx2 if rstandard <  0
window push label variable dx2_pos "Positive residual"
window push label variable dx2_neg "Negative residual"
window push predict dbeta, dbeta
window push scatter        dx2_pos p [weight=dbeta]			///
window push       , msymbol(Oh) mlwidth(medthick) mcolor(red)  		///
window push     || scatter dx2_neg p [weight=dbeta]			///
window push       , msymbol(Oh) mlwidth(medthick) mcolor(blue) 		///
window push     ||, ylabel(0(1)8, angle(0)) 				///
window push         ymtick(0(.5)8) yline(3.84, lwidth(medthick)) 		///
window push         xlabel(0(.1)1) xmtick(0(.05)1)  				///
window push         ytitle("Squared Standardized Pearson Residual") 	///
window push         xscale(titlegap(2))
window push more
window push save temporary, replace
window push drop if patients == 0
window push generate ca_no = cancer*patients
window push collapse (sum) n = patients ca = ca_no, by(age alcohol smoke dbeta dx2 p)
window push *
window push *  Identify covariate patterns associated with large squared residuals
window push *
window push list n ca age alcohol smoke dbeta dx2 p if dx2 > 3.84, nodisplay
window push *
window push *  Rerun analysis without the covariate pattern A
window push *
window push use temporary, clear
window push drop if age == 4 & alcohol ==4 & smoke == 1
window push logistic cancer i.age i.alcohol##i.smoke [freq=patients]
window push lincom 2.alcohol + 2.smoke + 2.alcohol#2.smoke, or
window push lincom 2.alcohol + 3.smoke + 2.alcohol#3.smoke, or
window push lincom 3.alcohol + 2.smoke + 3.alcohol#2.smoke, or
window push lincom 3.alcohol + 3.smoke + 3.alcohol#3.smoke, or
window push lincom 4.alcohol + 2.smoke + 4.alcohol#2.smoke, or
window push lincom 4.alcohol + 3.smoke + 4.alcohol#3.smoke, or
window push *
window push *  Rerun analysis without the covariate pattern B
window push *
window push use temporary, clear
window push drop if age == 4 & alcohol ==1 & smoke == 3
window push logistic cancer i.age i.alcohol##i.smoke [freq=patients]
window push lincom 2.alcohol + 2.smoke + 2.alcohol#2.smoke, or
window push lincom 2.alcohol + 3.smoke + 2.alcohol#3.smoke, or
window push lincom 3.alcohol + 2.smoke + 3.alcohol#2.smoke, or
window push lincom 3.alcohol + 3.smoke + 3.alcohol#3.smoke, or
window push lincom 4.alcohol + 2.smoke + 4.alcohol#2.smoke, or
window push lincom 4.alcohol + 3.smoke + 4.alcohol#3.smoke, or
window push log close