The Business Master (3rd Edition)/The Business Master (3rd Edition).iso/files/business/stata2/survive.kit

Text File | 1988-08-16 | 8.4 KB | 357 lines

set output error

display _new in blue /*
*/ "Loading Survive.Kit Release 2.0  Demonstration Version" _n /*
*/ "Copyright (c) 1987-1988 by ==C=R=C==.  All rights reserved."


/*
  User's wishing to edit Survive.Kit please see comments at end of this file.
*/


* Kaplan-Meier estimates


capture program drop kapmeier
program define kapmeier
    di in blue "not available in demonstration version"
end

* greenwood's formula

capture program drop gwood
program define gwood
    di in blue "not available in demonstration version"
end


cap program drop loglogs
program define loglogs
    if "%_*"=="" {
        di in blu "loglogs survtime deadind [, title(string)]"
        exit
    }
    mac def _options "Title(string) BY(string) *"
    mac def _varlist "req ex"
    mac def _if "opt"
    mac def _in "opt"
    parse "%_*"
    parse "%_varlist", parse(" ")
    capture {
        if "%_title"=="" {
            mac def _title "     Log-Log Survival Check for Weibull"
        }
        if "%_by"!="" {
            mac def _byy "by(%_by)"
        }
        if "%_if`%_in"~="" {
            keep %_if %_in
            }
        _survc %_1 %_2 %_by
        gen _lls = log(-log(_surv))
        gen _lt = log(%_1)
        format _lls %9.0f
        graph _lls _lt, title("%_title") %_options %_byy /*
              */ l1("log(-log(survival))") b2("log(time)")

    }
    cap drop _lt
    cap drop _surv
    cap drop _stds
    cap drop _vlogs
    cap drop _lls
end

/*
    Part 2 - Survival Curve Calculations
*/


capture program drop _survc
program define _survc
    mac def _varlist "req ex"
    mac def _if "opt"
    mac def _in "opt"
    parse "%_*"
    cap drop _xi
    cap drop _surv
    cap drop _stds
    cap drop _vlogs
    capture {
        if "%_3"!="" {
            mac def _byc "by %_3:"
        }
        gen _stds = - %_2
        sort %_3 %_1 _stds /* deaths first */
        gen int _xi = 0
        %_byc replace _xi = 1 %_if %_in
        %_byc replace _xi = sum(_xi)
        %_byc replace _xi = _xi[_N] + 1 - _xi
        gen _surv = 1
        replace _surv = (_xi - %_2) / _xi %_if %_in
        %_byc replace _surv = _surv * _surv[_n-1] if _n>1
        by %_3 %_1: replace _surv = _surv[_N]
        label var _surv "Survival Probability"
        replace _stds = %_2 / _xi / (_xi - 1)
        replace _xi=-1 %if %in /* -1 ==> in the sample */
        replace _stds=0 if _xi!=-1
        %_byc gen _vlogs = sum(_stds)
        by %_3 %_1: replace _vlogs = _vlogs[_N]
        replace _surv=. if _xi!=-1
        replace _vlogs=. if _xi!=-1
        replace _stds = _surv*sqrt(_vlogs)
        label var _stds "Greenwood Survival S.D."
        label var _vlogs "Var(log(_surv))"
        drop _xi
    }
    if _rc {
        di in red "--Break--"
    }
end

capture program drop survcurv
program define survcurv
    if "%_*"=="" {
        di in blu /*
        */ "survcurv time_variable death_indicator[, by(varname)]"
        exit
    }
    mac def _varlist "req ex"
    mac def _options "BY(string)"
    mac def _if "opt"
    mac def _in "opt"
    parse "%_*"
    parse "%_varlist", parse(" ")
    _survc %_1 %_2 %_by %_in %_if
    if _rc==0 {
        di in bl _new "Variables created:"
        desc _stds _surv _vlogs
    }
    if _rc {
        di in red "--Break--"
        BREAK
    }
end

capture program drop survsum
program define survsum
    di in blue "not availble in demonstration version"
end

/*
    Cox Regression Adjunct
*/

capture program drop _coxvar
program define _coxvar
    mac def _varlist "req ex"
    mac def _in "opt"
    mac def _if "opt"
    parse "%_*"
    parse "%_varlist", parse(" ")
    cap drop _rh
    cap drop _temp
    cap drop _rh1
    cap drop baserelh
    cap drop ownsurv
    cap drop basesurv
    cap drop basehaz
    capture {
        predict _rh            /* we'd like to know its cox */
        cap gen _temp = -%_1
        sort _temp %_2
        gen _rh1 = sum(_rh)
        by _temp: replace _rh1=_rh1[_N]
        gen baserelh = 1
        replace baserelh = exp(-%_2/_rh1) %_if %_in
        label var baserelh "Cox Baseline Relative Hazard"
        replace _temp = - %_2
        sort %_1 _temp
        replace _temp = 99 %_if %_in
        gen basesurv = baserelh
        replace basesurv = basesurv * basesurv[_n-1] if _n>1
        label var basesurv "Cox Baseline Survival Prob"
        by %_1: replace basesurv = basesurv[_N]
        replace basesurv=. if _temp!=99
        replace baserelh=. if _temp!=99
        gen ownsurv = basesurv ^ _rh
        label var ownsurv "Survival Probability"
    }
    if _rc==1 {
        di in red "--- Break ---"
        cap drop basesurv
        cap drop basehaz
        cap drop baserelh
        cap drop _rh
        cap drop _temp
        cap drop _rh1
        BREAK
    }
    cap drop _rh
    cap drop _temp
    cap drop _rh1
end

capture program drop coxvar
program define coxvar
    if "%_*"=="" {
        di in blu "coxvar survtime deadind"
        exit
    }
    mac def _varlist "req ex"
    mac def _in "opt"
    mac def _if "opt"
    parse "%_*"
    parse "%_varlist", parse(" ")
    capture _coxvar %_1 %_2 %_if %_in
    if _rc==0 {
        di in bl _new "Variables created:"
        desc baserelh basesurv ownsurv
    }
end

cap program drop coxbase
program define coxbase
    if "%_*"=="" {
        di in blu "coxbase survtime deadind [, title(string)]"
        exit
    }
    mac def _options "Title(string) *"
    mac def _varlist "req ex"
    mac def _in "opt"
    mac def _if "opt"
    parse "%_*"
    parse "%_varlist", parse(" ")
    capture {
        if "%_title"=="" {
            mac def _title "     Baseline Survival Curve"
        }
        if "%_offset"=="" {
            mac def _myaxis "noaxis xline(0) yline(0)"
        }
        _coxvar %_1 %_2 %_if %_in
        graph basesurv %_1, c(l) title("%_title") /*
         */  ysca(0,1) xsca(0,.) ytic(0,.25,.5,.75,1) %_options
    }
    cap drop basesurv
    cap drop baserelh
    cap drop ownsurv
end

cap program drop coxhaz
program define coxhaz
    if "%_*"=="" {
        di in blu "coxhaz survtime deadind [, title(string)]"
        exit
    }
    mac def _options "Title(string) *"
    mac def _varlist "req ex"
    mac def _in "opt"
    mac def _if "opt"
    parse "%_*"
    parse "%_varlist", parse(" ")
    capture {
        if "%_title"=="" {
            mac def _title "     Baseline Hazard Function Estimate"
        }
        _coxvar %_1 %_2 %_if %_in
        gen _b1 = %_1==%_1[_n-1]
        replace _b1 = 1 if basesurv==basesurv[_n-1]
        gen _t1 = 1
        replace _t1 = 0 %_if %_in /* work across deleted obs */
        replace _b1 = 1 if _t1==1
        replace _t1 = %_1
        replace _t1 = 0 if _n==1
        replace _t1 = _t1[_n-1] if _b1
        gen _t2 = basesurv
        replace _t2 = 1 if _n==1
        replace _t2 = _t2[_n-1] if _b1
        gen basehaz = (_t2[_n-1]-_t2)/_t2[_n-1]/(_t1-_t1[_n-1]) if !_b1
        label var basehaz "Cox Baseline Hazard Rate"
        graph basehaz %_1, title("%_title") /*
               */ ysca(0,.) xsca(0,.) xlabel ylabel %_options
        drop _b1 _t1 _t2
        di in blu _new "Variables created:"
        noisily desc baserelh basesurv ownsurv basehaz
        exit
    }
    di in red "--Break--"
    cap drop _b1
    cap drop _t1
    cap drop _t2
    cap drop basrelh
    cap drop basesurv
    cap drop ownsurv
    cap drop basehaz
end

/*
   Part 3: Log Rank Test(s)
*/


capture program drop logrank
program define logrank
    di in blue "not available in demonstration version"
end


capture program drop mantel
program define mantel
    di in blue "not available in demonstration version"
end


capture program drop wilcoxon
program define wilcoxon
    di in blue "not available in demonstration version"
end


di
di in gr "The following new commands are now available:"
di "   coxbase        gwood          loglogs        mantel        survsum"
di "   coxhaz         kapmeier       logrank        survcurv      wilcoxon"
di "   coxvar"
di _n in gr "See " in wh "help survive.kit" in gr "."
exit

Notes to User's wishing to edit this file:

These comments are placed at the end of the file, after the exit, so that
Stata does not have to read through them every time the user types "run
Survive.Kit"

Feel free to edit this file and delete programs in which you have no interest.
Before editing this file, however, make sure the the original is BACKED UP.
Please do not remove the copyright notice at the top of this file.

If you do edit the file, you should add a display command at the top of this
file indicating that you have edited the file.  You should change the display
just above these comments that lists the new commands now available.

All utility programs start with an underscore '_'.

Some programs use other programs in achieving the desired result.  Review the
table below carefully before deleting programs.

        Program         Requires
        --------------------------
        coxbase         _coxvar
        coxhaz          _coxvar
        coxvar          _coxvar
        gwood           _survc
        kapmeier        _stemp1  _survc
        loglogs         _survc
        logrank
        mantel
        survcurv        _survc
        survsum         _survc
        wilcoxon

For instance, if you deleted the _coxvar program, you would break coxbase,
coxhaz, and coxvar.

<end of Survive.Kit>