******************************************************
************************ALL MEN***********************
******************************************************


******************Descriptive tabeller******************
use "E:\workdata\706364\Terese\Data\Nyt\alle_DCD_var.dta", clear
tab c_age if c_age <19
mean c_age
tab demens_samlet, m

*crosstab
tab IQ10cat demens_samlet, m row
tab edu4cat demens_samlet, m row
tab cohort demens_samlet, m row
tab c_district_ny demens_samlet, m row

summarize(c_height)

sort IQ10cat
tab IQ10cat, summarize(c_height)

sort edu4cat
tab edu4cat, summarize(c_height)

sort cohort
tab cohort, summarize(c_height)

sort c_district_ny
tab c_district_ny, summarize(c_height)

gen entry_age = (entry - bdate)/365.25

mean entry_age

*********COX ANALYSER*********
stset exit, failure(demens_samlet) id(pnr) origin(bdate) entry(entry) scale(365.25)

stsum

*Model 1
stcox height_SD y c_age i.c_district_ny, strata(y) cluster(v_mor_pnr)


*Model 2a
stcox height_SD i.edu4cat y c_age i.c_district_ny, strata(y) cluster(v_mor_pnr)

*Model 2b
stcox height_SD i.IQ10cat y c_age i.c_district_ny, strata(y) cluster(v_mor_pnr)

*Model 3
stcox height_SD i.IQ10cat i.edu4cat y c_age i.c_district_ny, strata(y) cluster(v_mor_pnr)

**********************
***Test of assumptions
**********************
stcox height_SD, schoenfeld(sch*) scaledsch(sca*)
stphtest, plot(height_SD) msym(oh)

stcox c_age, schoenfeld(sch*) scaledsch(sca*)
stphtest, plot(c_age) msym(oh)

stphplot, by(IQ10cat)
stphplot, by(edu4cat)

***************************
***Over and below 60 years
***************************
stsplit nyalder2, at(60)

tab demens_samlet if nyalder2 == 0
tab demens_samlet if nyalder2 == 60

replace demens_samlet = 0 if demens_samlet == .

*Model 3
stcox height_SD i.IQ10cat i.edu4cat c_age i.c_district_ny if nyalder2 == 0, strata(y) cluster(v_mor_pnr) 

*Model 3
stcox height_SD i.IQ10cat i.edu4cat c_age i.c_district_ny if nyalder2 == 60, strata(y) cluster(v_mor_pnr) 


**********
*Splines
**********
use "E:\workdata\706364\Terese\Data\Nyt\alle_DCD_var.dta", clear
stset exit, failure(demens_samlet) id(pnr) origin(bdate) entry(entry) scale(365.25)

stsum

rc_spline height_SD, nknots(4)

stcox _Sheight_SD1 _Sheight_SD2 _Sheight_SD3 i.IQ10cat i.edu4cat c_age i.c_district_ny, strata(y)

splinecenter , firstvar(height_SD) firstcovs(3) ref(0.0) alpha(0.975) exp(1)


twoway (rarea lo hi height_SD, color(gs13)) (line bv height_SD, lcolor(black) lpattern(solid) xlabel(-2 -1 0 1 2,tposition(inside)) yscale(log) yline(1) graphregion(color(white)) ytitle(HR))	 if height_SD >-2 & height_SD<2



******************************************************
************************BROTHERS**********************
******************************************************

use "E:\workdata\706364\Terese\Data\Nyt\brothers_DCD.dta", clear

******************Descriptive tabeller******************
sort IQ10cat
tab IQ10cat, summarize(c_height)

sort edu4cat
tab edu4cat, summarize(c_height)

sort cohort
tab cohort, summarize(c_height)

sort c_district_ny
tab c_district_ny, summarize(c_height)


***********************COX ANALYSER******************
stset exit, failure(demens_samlet) id(pnr) origin(bdate) entry(entry) 

*Model 3
stcox height_SD i.IQ10cat i.edu4cat y c_age i.c_district_ny, cluster(v_mor_pnr)

*Model 3
stcox height_SD i.IQ10cat i.edu4cat y c_age i.c_district_ny, strata(v_mor_pnr)

**Test of assumptions
stcox height_SD, schoenfeld(sch*) scaledsch(sca*)
stphtest, plot(height_SD) msym(oh)

stcox c_age, schoenfeld(sch*) scaledsch(sca*)
stphtest, plot(c_age) msym(oh)

stphplot, by(IQ10cat)
stphplot, by(edu4cat)

************************************************
*********************TWINS**********************
************************************************

use "E:\workdata\706364\Terese\Data\Nyt\twins_DCD.dta", clear

******************Descriptive tabeller******************

tab IQ10cat demens_samlet, m row
tab edu4cat demens_samlet, m row
tab cohort demens_samlet, m row


summarize(c_height)

sort IQ10cat
tab IQ10cat, summarize(c_height)

sort edu4cat
tab edu4cat, summarize(c_height)

sort cohort
tab cohort, summarize(c_height)

sort c_district_ny
tab c_district_ny, summarize(c_height)

tab demens_samlet


***********************COX ANALYSER******************
stset exit, failure(demens_samlet) id(pnr) origin(bdate) entry(entry) 

stcox height_SD i.IQ10cat i.edu4cat y c_age i.c_district_ny, cluster(twinpairno)
stcox height_SD i.IQ10cat i.edu4cat y c_age i.c_district_ny, strata(twinpairno)

**Test of assumptions
stcox height_SD, schoenfeld(sch*) scaledsch(sca*)
stphtest, plot(height_SD) msym(oh)

stcox c_age, schoenfeld(sch*) scaledsch(sca*)
stphtest, plot(c_age) msym(oh)

stphplot, by(IQ10cat)
stphplot, by(edu4cat)