help phenotype
                                                                 (STB-61: dm92)
-------------------------------------------------------------------------------

Title

    phenotype --  Simulate disease status and censored age for family data


Syntax

        phenotype hr [, options]


    options                Description
    -------------------------------------------------------------------------
    Main
      type(d|r)            specifies the type of inheritance
      alpha(#)             specifies the shape parameter of the Weibull
                             distribution
      lambda(#)            specifies the scale parameter of the Weibull
                             distribution
      maxage(#)            specifies the upper bound of age of death
      gamma(#)             specifies the parameter in the log-power density
                             function of death
      sex(b|f|m)           specifies the gender being affected by a disease
      saving(filename)     specifies the name of the file to be saved
    -------------------------------------------------------------------------


Description

    phenotype generates the disease status and censored age based on family
    data created by simuped2 or simuped3 (Cui 2000). A censored age is the
    age at onset of a disease if a person is affected, or the age of death if
    a person has died before developing the disease. Otherwise it is the
    calendar age contained in the original family data. This program expects
    that the genetic hazard ratio, hr, to be specified as a non-negative
    value.  This program is also known as phenotyp in the previous versions.

    Two modes of inheritance, dominant and recessive, are allowed for in this
    program. They are represented by d and r in the type option,
    respectively. Use of other letters will produce an error message.  if a
    disease affects one gender only, the disease status is generated as 0 for
    a person with an opposite gender.  The age of death is determined by a
    log-power density function.  The hazard function of developing a disease
    is assumed to be a Weibull distribution.


Options

        +------+
    ----+ Main +-------------------------------------------------------------

    type(inheritance) specifies the type of inheritance. The option d (the
        default) specifies a dominant inheritance, and r specifies a
        recessive inheritance.

    alpha(#) specifies the shape parameter of the Weibull distribution. The
        default value is 4.21.

    lambda(#) specifies the scale parameter of the Weibull distribution. The
        default value is 9.95e-10.

    maxage(#) specifies the upper bound of age of death. The default value is
        100.

    gamma(#) specifies the parameter in the log-power density function of
        death.  The default value is 15.

    sex(b|f|m) specifies the gender affected by a disease. The option b (the
        default) specifies that both genders are affected, f specifies that
        only females are affected, and m specifies that only males are
        affected.

    saving(filename) specifies the file name of the simulated data. The
        default file name is temp1.dta.


Examples

    clear

    run simuped2.ado

    simuped2 70 10 40 10, reps(1000) sav(output) alle(0.05) sib(5)

    use output, clear

    phenotype 10, type(d) alpha(4.21) lambda(9.95e-10) maxage(100) gamma(15)
        sex(f) sav(output1)

    use output1, clear

    list if famid <= 2, sepby(famid)


Also see

    STB:  STB-58: dm82


References

    Cui J. Simulating two- and three-generation families. Stata Technical
        Bulletin 2000; 58: 2-5.

    Cui J. Simulating disease status and censored age. Stata Technical
        Bulletin 2001; 61: 8-10.

    Cui J and Hopper JL. Why are the majority of hereditary cases of
        early-onset breast cancer sporadic? A simulation study. Cancer
        Epidemiology, Biomarkers & Prevention 2000; 9: 805-812.


Author

    James Cui, Department of Epidemiology and Preventive Medicine, Monash
    University.

    Email: james.cui@med.monash.edu.au


Other Commands I have written:
genhwcci   (if installed)      ssc install genhwcci     (to install this comman
> d)
simuped2   (if installed)      ssc install simuped2     (to install this comman
> d)
simuped3   (if installed)      ssc install simuped3     (to install this comman
> d)
buckley    (if installed)      ssc install buckley      (to install this comman
> d)
qic        (if installed)      ssc install qic          (to install this comman
> d)