https://github.com/cran/rstpm2
Tip revision: 3344f17ec3e85d100ce183c2559fe953aca48c9b authored by Mark Clements on 05 November 2019, 22:00:05 UTC
version 1.5.1
version 1.5.1
Tip revision: 3344f17
test.do
* stata
clear
webuse brcancer
stset rectime, f(censrec==1)
cap program drop dopredictions
program define dopredictions
preserve
predict hr, hrnumerator(hormon 1) ci
predict haz, hazard ci
predict surv, surv ci
predict sdiff, sdiff1(hormon 1) ci
list hr* in 1/5
list haz* surv* in 1/5
list sdiff* in 1/5
restore
end
* basic model
stpm2 hormon, df(3) scale(h)
dopredictions
* logit model
stpm2 hormon, df(3) scale(odds)
dopredictions
* normal model
stpm2 hormon, df(3) scale(normal)
dopredictions
* tvc
stpm2 hormon, df(3) tvc(hormon) dftvc(3) scale(h)
dopredictions
* delayed entry
preserve
gen entry = 0
replace entry = rectime*0.5 if hormon==0
stset rectime, f(censrec==1) enter(entry)
stpm2 hormon, df(3) scale(h)
dopredictions
restore
* delayed entry and tvc
preserve
replace _t0 = rectime*0.5 if hormon==0
stpm2 hormon, df(3) scale(h) tvc(hormon) dftvc(3)
dopredictions
restore
* cure
stpm2 hormon, df(3) scale(h) cure
dopredictions
* relative survival
preserve
gen rate0=10^(-5+x1/100)
stpm2 hormon, df(3) scale(h) bhazard(rate0)
dopredictions
restore
* robust variance
preserve
gen wt = 1
replace wt = 10 if hormon==0
stset rectime [pw=wt], f(censrec==1)
stpm2 hormon, df(3) scale(h) vce(robust)
dopredictions
restore
* test speed
clear all
set mem 100m
webuse brcancer
stset rectime, f(censrec==1)
expand 500
timer clear
timer on 1
stpm2 hormon, df(3) scale(h)
timer off 1
timer list
** Cure
* http://www.pauldickman.com/survival/solutions/q37.do
clear
use "http://www.pauldickman.com/survival/colon.dta"
stset surv_mm, failure(status=1 2) scale(12) exit(time 120.5)
gen _age = min(int(age + _t),99)
gen _year = int(yydx + _t)
sort _year sex _age
merge m:1 _year sex _age using "http://www.pauldickman.com/survival/popmort.dta", keep(match master)
** Cure model using stpm2 **
stpm2 year8594, df(6) bhazard(rate) scale(hazard) cure
predict surv, surv ci
list surv surv_lci surv_uci in 1/6
stpm2 year8594, df(6) bhazard(rate) scale(hazard)
stpm2 year8594, df(6) scale(hazard)
preserve
clear
set obs 101
gen x=_n-1
gen y=(x-50)^2
replace y=0 if _n==20 | _n==30
rcsgen x, knots(0 25 50 75 95 100) gen(rcs) reverse
return list
quietly su y
di `r(sum)'
regress y rcs*
quietly predict yhat
scatter x yhat
restore
use http://fmwww.bc.edu/repec/bocode/s/stmixed_example2, clear
// stset the data:
stset stime, f(event=1)
// stmixed treat || trial: , dist(fpm) df(3) gh(20) nonadapt nohr nolog
timer clear 1
timer on 1
stmixed treat || trial: , dist(fpm) df(3) gh(20) nohr nolog
timer off 1
timer list 1
matrix list e(vcv)
tab trial, gen(trialvar)
timer clear 1
timer on 1
stmixed treat trialvar2-trialvar15 || trial: treat, nocons dist(fpm) df(3)
timer off 1
timer list 1
stpm2 treat i.trial, df(3) scale(hazard)
* delayed entry
webuse brcancer, clear
preserve
gen entry = 0
replace entry = rectime*0.5 if hormon==0
stset rectime, f(censrec==1) enter(entry)
staft hormon, df(3)
restore
use "http://www.pauldickman.com/survival/ew_breast.dta", clear
codebook agegroup
keep if agegroup==1
stset survtime, failure(dead==1) exit(time 5)
tab dep, gen(dep)
staft dep2 dep3 dep4 dep5, df(5)
staft dep2 dep3 dep4 dep5, df(5) tvc(dep2 dep3 dep4 dep5) dftvc(2)
preserve
replace survtime=5
cap drop af1
predict af1, af at(dep2 0 dep3 0 dep4 0 dep5 1)
list in 1/1
restore