penplot function

Plot penetrance functions

Plots the penetrance functions given the values of baseline parameters and regression coefficients and choices of baseline and frailty distributions.

penplot(base.parms, vbeta, cuts = NULL, variation = "none", base.dist = "Weibull", 
frailty.dist = NULL, depend = 1, agemin = 20, agemax = 80, print = TRUE, 
col = c("blue","red","blue","red"),  lty = c(1, 1, 2, 2), add.legend = TRUE, 
add.title = TRUE, x = "topleft", y = NULL, xlab = "Age at onset", ylab = "Penetrance", 
ylim = NULL, main = NULL, ...)

Arguments

• base.parms: Vector of parameter values for the specified baseline hazard function: base.parms = c(lambda, rho) should be specified for base.dist = "Weibull", "loglogistic", "Gompertz", "gamma", and "lognormal", c(lambda, rho, eta) for base.dist = "logBurr", or interval constant hazard values for the intervals produced by cuts for base.dist = "piecewise".
• vbeta: Vector of regression coefficients for gender and majorgene, vbeta = c(beta.s, beta.g). If variation = "secondgene", regression coefficients for gender, major gene and second gene, vbeta = c(beta.s, beta.g1, beta.g2), should be specified.
• cuts: Vector of cut points defining the intervals where the hazard function is constant. The cuts should be specified when base.dist = "piecewise" and must be strictly positive and finite. Default is NULL.
• variation: Source of residual familial correlation. Possible choices are: "frailty" for frailty shared within families, "secondgene" for second gene variation, or "none" for no residual familial correlation. Default is "none".
• base.dist: Choice of baseline hazard distribution. Possible choices are: "Weibull", "loglogistic", "Gompertz", "lognormal", "gamma", or "piecewise". Default is "Weibull".
• frailty.dist: Choice of frailty distribution. Possible choices are "gamma" for gamma distribution or "lognormal" for log normal distributions when variation = "frailty". Default is NULL.
• depend: Variance of the frailty distribution. Dependence within families increases with depend value. Default value is 1.
• agemin: Minimum age of disease onset. Default is 20 years of age.
• agemax: Maximum age of disease onset. Default is 80 years of age.
• print: Logical; if TRUE, prints the penetrance values by age 70 obtained from the assumed model for male carriers, female carriers, male noncarrers, and female noncarriers. Default is TRUE.
• col: Colors of lines for male carriers, female carriers, male noncarrers, and female noncarriers. Default is c("blue", "red", "blue", "red").
• lty: Types of lines for male carriers, female carriers, male noncarriers, and female noncarriers. Default is c(1, 1, 2, 2).
• add.legend: Logical; if TRUE, displays legend in the plot. Default is TRUE.
• add.title: Logical; if TRUE, displays title in the plot. Default is TRUE.
• x, y: Position of legend; see legend . Defaults are x = "topleft", y = NULL.
• xlab: Title for the x-axis. Default is "Age at onset".
• ylab: Title for the y-axis. Default is "Penetrance".
• ylim: Limits of the y-axis. Default is NULL. If NULL, ylim will be automatically determined.
• main: Main title of the plot. Default is NULL. If NULL, the title will be automatically created.
• ...: Other parameters to be passed through to plotting functions.

Details

Proportional hazard models

The penetrance model conditional on the covariates is assumed to have the following hazard function:

where is the baseline hazard function, is a minimum age of disease onset, and indicate male (1) or female (0) and carrier (1) or non-carrier (0) of a main gene of interest, respectively.

The penetrance function for the penetrance model has the form,

where is the cumulative baseline hazard function.

Shared frailty models

The penetrance model conditional on the frailty $Z$ and covariates is assumed to have the following hazard function:

where is the baseline hazard function, is a minimum age of disease onset, and indicate male (1) or female (0) and carrier (1) or non-carrier (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

Two-gene models

The penetrance curve for the two-gene model is generated by

where is the cumulative baseline hazard function, indicates carrior (1) or non-carrior (0) of a major gene and indicates carrior (1) or non-carrior (0) of a second gene. When plotting with the two-gene model, the plot will generate separate curves for mutation carriers and noncarriers, and separate curves for the second gene carriers and noncarriers.

Returns

Displays plots of the penetrance functions and returns the following values:

• pen70: Penetrance estimates by age 70 specific to gender and mutation-status subgroups.

• x.age: Vector of ages of onset ranging from agemin to agemax years

• pen: Penetrance estimates computed at each age of x.age; if variation = "none" or "frailty", it includes subgroups specific to gender and mutation status for major gene. If variation = "secondgene", it includes subgroups specific to gender and both mutation statuses for major gene and second gene.

Author(s)

Yun-Hee Choi

See Also

simfam, plot.penmodel

Examples

# Penetrance function curves based on Weibull baseline hazard function

penplot(base.parms = c(0.01,3), vbeta = c(0.5, 2), variation = "none", base.dist = "Weibull", 
                agemin = 20, ylim = c(0,1))