📄 gomphet_ip.ado
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*! version 1.3.0 30aug2004
program define gomphet_ip, sort
version 7, missing
syntax [anything] [if] [in] [, SCores * ]
if `"`scores'"' != "" {
if "`e(shared)'" != "" {
di as err ///
"option scores is not allowed with shared frailty"
exit 322
}
confirm variable `e(dead)'
global EREGd `e(dead)'
confirm variable `e(depvar)'
global EREGt `e(depvar)'
confirm variable `e(t0)'
global EREGt0 `e(t0)'
ml_score `0'
macro drop EREG*
exit
}
syntax newvarname [if] [in] [, ALPHA1 UNCONDitional *]
local 0 `typlist' `varlist' `if' `in', `options'
if "`alpha1'"!="" & "`unconditional'"!="" {
di as error /*
*/ "alpha1 and unconditional can not be specified at the same time"
exit 198
}
if "`alpha1'`unconditional'"=="" {
if "`e(shared)'"!="" {local alpha1 alpha1}
else {local unconditional unconditional}
di as txt "(option `alpha1'`unconditional' assumed)"
}
tempname theta gamma
scalar `theta' = exp(_b[/ln_the])
scalar `gamma' = _b[/gamma]
if "`alpha1'"!="" | `theta' < exp(-20) {
gomper_p `0'
exit
}
/* Step 1:
place command-unique options in local myopts
Note that standard options are
LR:
Index XB Cooksd Hat
REsiduals RSTAndard RSTUdent
STDF STDP STDR noOFFset
SE:
Index XB STDP noOFFset
*/
local myopts /*
*/ "XB Index STDP Time LNTime HAzard HR Surv DEViance CSnell MGale CSUrv CCSnell CMgale OOS MEDian MEAN"
/* Step 2:
call _propts, exit if done,
else collect what was returned.
*/
_pred_se "`myopts'" `0'
if `s(done)' { exit }
local vtyp `s(typ)'
local varn `s(varn)'
local 0 `"`s(rest)'"'
/* Step 3:
Parse your syntax.
*/
syntax [if] [in] [, `myopts' noOFFset]
/* Step 4:
Concatenate switch options together
*/
if "`median'"~="" & "`mean'"~="" {
di as err /*
*/ "options median and mean may not be specified together"
exit 198
}
if "`mean'"~="" {
di as err /*
*/ "unconditional mean predictions for frailty models currently unavailable"
exit 198
}
local type /*
*/ "`xb'`index'`stdp'`time'`lntime'`hazard'`hr'`surv'`deviance'`csnell'`mgale'`csurv'`ccsnell'`cmgale'"
/* Step 5:
quickly process default case if you can
Do not forget -nooffset- option.
*/
/* Step 6:
mark sample (this is not e(sample)).
*/
marksample touse
if "`e(cmd2)'"=="streg" {
st_is 2 full
local is_st yes
local id `_dta[st_id]'
local t `_dta[st_t]'
local t0 `_dta[st_t0]'
local d `_dta[st_d]'
qui replace `touse'=0 if _st==0
}
else {
local t `e(depvar)'
local t0 `e(t0)'
local d `e(dead)'
}
if "`type'"=="" | "`type'"=="time" {
if "`type'"=="" | "`median'"=="" {
di as txt /*
*/ "(option median time assumed; predicted median time)"
}
tempvar xb
qui _predict double `xb' if `touse', xb `offset'
gen `vtyp' `varn'=ln(`gamma'/(2*`theta')* /*
*/ ((1-`theta'*ln(0.5))^2 - 1)*exp(-`xb') + 1) / /*
*/ `gamma' if `touse'
label var `varn' "predicted median `e(depvar)'"
exit
}
if "`type'"=="lntime" {
if "`median'"=="" {
di as txt /*
*/ "(option log median time assumed; predicted median log time)"
}
tempvar xb
qui _predict double `xb' if `touse', xb `offset'
gen `vtyp' `varn'=ln(ln(`gamma'/(2*`theta')* /*
*/ ((1-`theta'*ln(0.5))^2 - 1)*exp(-`xb') + 1) / /*
*/ `gamma') if `touse'
label var `varn' "predicted median ln(`e(depvar)')"
exit
}
if "`median'"!="" { /* I've gone too far */
di as err "median invalid"
exit 198
}
if "`type'"=="xb" | "`type'"=="index" | "`type'"=="stdp" {
_predict `vtyp' `varn' if `touse', `type' `offset'
exit
}
if "`type'"=="hr" {
di as err "unconditional hazard ratios not available"
exit 198
}
if "`type'"=="hazard" {
tempvar xb ff kk
qui _predict double `xb' if `touse', xb `offset'
qui gen double `kk' = exp(`xb'+`gamma'*`t') if `touse'
qui gen double `ff'= `kk'/sqrt(1+2*`theta'/`gamma'* /*
*/ (`kk'-exp(`xb'))) if `touse'
gen `vtyp' `varn'= `ff' if `touse'
label var `varn' "predicted hazard"
exit
}
if "`type'" =="surv" {
tempvar xb ff ff0
qui _predict double `xb' if `touse', xb `offset'
qui gen double `ff'=1+2*`theta'/`gamma'*exp(`xb')* /*
*/ (exp(`gamma'*`t')-1) if `touse'
qui gen double `ff0'=1+2*`theta'/`gamma'*exp(`xb')* /*
*/ (exp(`gamma'*`t0')-1) if `t0'>0 & `touse'
qui replace `ff' = exp((1-sqrt(`ff'))/`theta') if `touse'
qui replace `ff0' = exp((1-sqrt(`ff0'))/`theta') /*
*/ if `t0'>0 & `touse'
qui replace `ff' = `ff'/`ff0' if `t0'>0 & `touse'
gen `vtyp' `varn' = `ff' if `touse'
if "`t0'"=="0" {
label var `varn' "S(`t')"
}
else label var `varn' "S(`t'|`t0')"
exit
}
if "`type'"=="csnell" {
tempvar mg
qui predict double `mg' if `touse', mgale `offset'
gen `vtyp' `varn' = (`d'!=0) - `mg' if `touse'
if "`id'"!="" { local part "partial " }
label var `varn' "`part'Cox-Snell residual"
exit
}
if "`type'"=="mgale" {
tempvar xb ff
qui _predict double `xb' if `touse', xb `offset'
qui gen double `ff'= /*
*/ (`d'!=0)+(1/`theta')* /*
*/ (1-sqrt(1+2*`theta'/`gamma'*exp(`xb')* /*
*/ (exp(`gamma'*`t')-1))) if `touse'
qui replace /*
*/ `ff'=`ff'-(1/`theta')* /*
*/ (1-sqrt(1+2*`theta'/`gamma'*exp(`xb')* /*
*/ (exp(`gamma'*`t0')-1))) if `t0'>0 & `touse'
gen `vtyp' `varn' = `ff' if `touse'
if "`id'"!="" { local part "partial " }
label var `varn' "`part'Martingale-like resid."
exit
}
/* Step 7:
handle options that take argument one at a time.
Comment if restricted to e(sample).
Be careful in coding that number of missing values
created is shown.
Do all intermediate calculations in double.
*/
/* Step 8:
handle switch options that can be used in-sample or
out-of-sample one at a time.
Be careful in coding that number of missing values
created is shown.
Do all intermediate calculations in double.
*/
if "`is_st'"=="yes" {
if "`type'"=="deviance" {
tempvar cmg
qui predict double `cmg' if `touse', cmgale `offset' /*
*/ `oos'
gen `vtyp' `varn' = sign(`cmg')*sqrt( /*
*/ -2*(`cmg' + (`d'!=0)*(ln((`d'!=0)-`cmg')))) /*
*/ if `touse'
label var `varn' "deviance residual"
exit
}
if "`oos'"=="" {
tempvar es
qui gen byte `es' = e(sample)
}
else local es "`touse'"
if "`type'"=="csurv" {
if "`_dta[st_id]'" == "" {
predict `vtyp' `varn' if `touse' & `es', /*
*/ surv `offset'
exit
}
tempvar surv
qui predict double `surv' if `es', surv `offset'
sort `es' `_dta[st_id]' `t'
qui by `es' `_dta[st_id]': replace /*
*/ `surv'=`surv'*`surv'[_n-1] if _n>1 & `es'
gen `vtyp' `varn' = `surv' if `touse'
label var `varn' "S(`t'|earliest `t0' for subj.)"
exit
}
if "`type'"=="ccsnell" {
if "`_dta[st_id]'" == "" {
predict `vtyp' `varn' if `touse' & `es', /*
*/ csnell `offset'
exit
}
tempvar cs
qui predict double `cs' if `es', cs `offset'
sort `es' `_dta[st_id]' `t'
qui by `es' `_dta[st_id]': replace /*
*/ `cs'=cond(_n==_N,sum(`cs'),.) if `es'
gen `vtyp' `varn' = `cs' if `touse'
label var `varn' "cum. Cox-Snell residual"
exit
}
if "`type'"=="cmgale" {
if "`_dta[st_id]'" == "" {
predict `vtyp' `varn' if `touse' & `es', /*
*/ mgale `offset'
exit
}
tempvar mg
qui predict double `mg' if `es', mg `offset'
sort `es' `_dta[st_id]' `t'
qui by `es' `_dta[st_id]': replace /*
*/ `mg'=cond(_n==_N,sum(`mg'),.) if `es'
gen `vtyp' `varn' = `mg' if `touse'
label var `varn' "cum. Martingale-like resid."
exit
}
}
/* Step 9:
handle switch options that can be used in-sample only.
Same comments as for step 8.
*/
* qui replace `touse'=0 if !e(sample)
/* Step 10.
Issue r(198), syntax error.
The user specified more than one option
*/
error 198
end
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