This function plots the penetrance function given the baseline parameter and regression coefficients' values and choices of baseline and frailty distributions.
1 2  penplot(base.parms, vbeta, variation="none", base.dist="Weibull",
frailty.dist="gamma", depend=1, agemin=20)

base.parms 
Vector of parameter values for baseline hazard function.

vbeta 
Vector of regression coefficients for gender and majorgene

base.dist 
Choice of baseline hazard distribution. Possible choices are: 
frailty.dist 
Choice of frailty distribution. Possible choices are 
variation 
Source of residual familial correlation. Possible choices are 
depend 
Variance of the frailty distribution. Dependence within families increases with 
agemin 
Minimum age of disease onset. Default is 20 years of age. 
The penetrance model conditional on the frailty Z and covariates X=(x_s, x_g) is assumed to have the following hazard function
h(tX,Z) = h_0(tt_0) Z \exp(β_s x_s+β_g x_g),
where h_0(t) is the baseline hazard function, t_0 is a minimum age of disease onset, x_s and x_g indicate male (1) or female (0) and carrier (1) or noncarrier (0) of a main gene of interest, respectively.
For example, when using a Weibull distribution for baseline hazard and a gamma distribution for frailty, the penetrance function has the form
1≤ft\{1+\frac{λ^ρ (tt_0)^ρ \exp(β_s x_s+β_g x_g)}{κ}\right\}^{κ} .
The penetrance curve for the second gene model is generated by
1\exp\{λ^ρ (tt_0)^ρ \exp (β_g x_g+β_{g1} x_{g1} + β_{g2} x_{g2})\}
where x_{g1} indicates carrior (1) or noncarrior (0) of a major gene and x_{g2} indicates carrior (1) or noncarrior (0) of a second gene.
Returns plots of the penetrance functions and penetrance estimates by age 70 called pen70
specific to gender and mutationstatus. When plotting with the second gene model, the plot will generate separate curves for mutation carriers and noncarriers, and seperate curves for the second gene carriers and noncarriers.
YunHee Choi
simfam
1 2 3 
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