📄 gamma_p.ado
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*! version 6.2.0 10sep2004
program define gamma_p, sort
version 7, missing
syntax [anything] [if] [in] [, SCores * ]
if `"`scores'"' != "" {
marksample touse, novarlist
confirm variable `e(dead)'
global EREGd `e(dead)'
confirm variable `e(t0)'
global EREGt0 `e(t0)'
ml_score `0'
macro drop EREG*
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 "`time'"~="" & "`lntime'"~="" {
di as err /*
*/ "options time and lntime may not be specified together"
exit 198
}
local type /*
*/ "`xb'`index'`stdp'`time'`lntime'`hazard'`hr'`surv'`deviance'`csnell'`mgale'`csurv'`ccsnell'`cmgale'"
local type2 "`type'`mean'`median'"
/* 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 _caller() < 7 {
if "`type'"=="" {
local flag 6
di as txt "(option time assumed; predicted time)"
}
if "`type'"=="lntime" {
local flag 7
}
}
else {
local flag 0
if "`type'"=="" { local flag 1 }
if "`type2'"=="median" { local flag 2 }
else if "`type2'"=="mean" { local flag 3 }
else if "`type2'"=="time" { local flag 4 }
else if "`type2'"=="lntime" { local flag 5 }
if `flag'==1 | `flag'==2 | `flag'==4 {
local type="time"
local median="median"
di as txt /*
*/ "(option median time assumed; predicted median time)"
}
else if `flag'==5 {
local type="lntime"
local median="median"
di as txt /*
*/ "(option median log time assumed; predicted median log time)"
}
else if `flag'==3 {
local type="time"
local median
local mean="mean"
di as txt /*
*/ "(option mean time assumed; predicted mean time)"
}
}
tempvar sigma kappa
qui _predict double `sigma' if `touse', xb eq(#2)
qui replace `sigma'=exp(`sigma') if `touse'
qui _predict double `kappa' if `touse', xb eq(#3)
if "`type'"=="time" & "`median'"=="median" {
tempvar xb sgn
qui _predict double `xb' if `touse', xb `offset' eq(#1)
qui gen double `sgn'=cond( `kappa'<0,-1,1) if `touse'
gen `vtyp' `varn'= /*
*/ invgammap((1/((`kappa')^2)),0.5)*((`kappa')^2) if `touse'
qui replace `varn'= `sgn'*log(`varn')*`sigma' /*
*/ +(abs(`kappa')*`xb')
qui replace `varn'= exp(`varn'/(abs(`kappa'))) if `touse'
label var `varn' "predicted median `e(depvar)'"
exit
}
if "`type'"=="xb" | "`type'"=="index" | "`type'"=="stdp" {
_predict `vtyp' `varn' if `touse', `type' `offset' eq(#1)
exit
}
if "`flag'"=="6" {
tempvar lt
version 6: qui predict double `lt' if `touse', lntime mean
gen `vtyp' `varn'=exp(`lt') if `touse'
label var `varn' "predicted `e(depvar)'"
exit
}
if "`flag'"=="7" { /* note _caller()<7, so correct */
tempvar xb
tempname nkappa
scalar `nkappa'=abs(e(kappa))
qui _predict double `xb' if `touse', xb `offset'
gen `vtyp' `varn'=`xb' /*
*/ + e(sigma)/ `nkappa'*(digamma(`nkappa'^-2) /*
*/ -log(`nkappa'^-2)) if `touse'
label var `varn' "predicted ln(`e(depvar)')"
exit
}
if "`type'"=="lntime" & "`mean'"~="" {
tempvar xb sgn nkappa
qui gen double `sgn'=cond( `kappa'<0,-1,1)
qui gen double `nkappa'=abs( `kappa') if `touse'
qui _predict double `xb' if `touse', xb `offset' eq(#1)
gen `vtyp' `varn'=`sgn'*(`xb' /*
*/ + `sigma'/ `nkappa'*(digamma(`nkappa'^-2) /*
*/ -log(`nkappa'^-2))) if `touse'
label var `varn' "predicted mean ln(`e(depvar)')"
exit
}
if "`type'"=="lntime" & "`median'"=="median" {
tempvar elnt
qui predict double `elnt' if `touse', time median
gen `vtyp' `varn'= ln(`elnt') if `touse'
label var `varn' "predicted median log `e(depvar)'"
exit
}
if "`type'"=="time" & "`mean'"=="mean" {
tempvar xb aa bb cc
qui _predict double `xb' if `touse', xb `offset' eq(#1)
capture assert `kappa'>0 if `touse'
if _rc {
di as txt "note: mean time prediction not available" _c
di as txt " when estimated kappa < 0;"
di as txt " one or more observations set to missing"
}
qui gen double `aa' = cond(`kappa'>0,(1/`kappa')^2,.) if `touse'
qui gen double `bb' = `aa'^(-`sigma'*sqrt(`aa'))*exp(`xb') /*
*/ if `touse'
qui gen double `cc' = `sigma'*sqrt(`aa') /*
*/ if `touse'
gen `vtyp' `varn' = `bb'*exp(lngamma(`aa'+`cc') - /*
*/ lngamma(`aa')) if `touse'
label var `varn' "predicted mean `e(depvar)'"
exit
}
if "`type'"=="hr" {
di as err /*
*/ "Hazard ratios only available for those models with a natural"
di as err /*
*/ "proportional-hazards parameterization"
exit 498
}
if "`type'"=="hazard" {
tempvar xb ff z s sgn l
qui gen double `sgn'=cond( `kappa'<0,-1,1) if `touse'
qui gen double `l'= (abs(`kappa'))^(-2) if `touse'
qui _predict double `xb' if `touse', xb `offset' eq(#1)
qui gen double `z'= `sgn'*(ln(`t')-`xb')/ `sigma' if `touse'
qui gen double `s'= gammap(`l',`l'*exp(`z'/sqrt(`l'))) /*
*/ if `touse'
qui replace `s'=cond(`sgn'==1,1-`s',`s') if `touse'
qui gen double `ff'=((`l'-0.5)*ln(`l')) /*
*/ + (`z'*sqrt(`l'))-`l'*exp(`z'/sqrt(`l')) /*
*/ -lngamma(`l') - ln(`t'* `sigma') if `touse'
qui replace `ff'= exp(`ff') if `touse'
gen `vtyp' `varn'= `ff'/`s' if `touse'
label var `varn' "predicted hazard"
exit
}
if "`type'" =="surv" {
tempvar xb ff z z0 ff0
tempname sgn l
qui gen double `sgn'=cond( `kappa'<0,-1,1) if `touse'
qui gen double `l'= (abs(`kappa'))^(-2) if `touse'
qui _predict double `xb' if `touse', xb `offset' eq(#1)
qui gen double `z' = `sgn'*(ln(`t')-`xb')/ `sigma' /*
*/ if `touse'
qui gen double `z0' = `sgn'*(ln(`t0')-`xb')/ `sigma' /*
*/ if `t0'>0 & `touse'
qui gen double `ff'= gammap(`l',`l'*exp(`z'/sqrt(`l'))) /*
*/ if `touse'
qui gen double `ff0'= gammap(`l',`l'*exp(`z0'/sqrt(`l'))) /*
*/ if `t0'>0 & `touse'
qui replace `ff'=cond(`sgn'==1,1-`ff',`ff') if `touse'
qui replace `ff0'=cond(`sgn'==1,1-`ff0',`ff0') /*
*/ 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 `ff' if `touse',surv
gen `vtyp' `varn' = (`d'!=0)+ln( `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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