summary.penmodel: Summary method for class 'penmodel'

In FamEvent: Family Age-at-Onset Data Simulation and Penetrance Estimation

Summary method for class penmodel

Description

Provides a summary of a fitted penetrance model.

Usage

## S3 method for class 'penmodel'
summary(object, correlation=FALSE, ...)

Arguments

object	An object class of 'penmodel', a fitted model by penmodel or penmodelEM functions.
correlation	Logical; if TRUE, returns the correlation matrix of the estimated parameters. Default is FALSE.
...	Further arguments passed to or from other methods.

Value

Returns the object of class 'summary.penmodel', including the following summary values:

estimates	List of parameter estimates of transformed baseline parameters and regression coefficients, their standard errors, their robust standard errors if robust=TRUE was selected when fitting the penetrance model, t-statistics and corresponding two-sided p-values.
varcov	Variance-covariance matrix of the parameter estimates.
varcov.robust	Robust variance-covariance matrix of the parameter estimates if robust = TRUE was selected when fitting the penetrance model.
correlation	Correlation matrix obtained from the variance-covariance matrix.
correlation.robust	Correlation matrix obtained from the robust variance-covariance matrix if robust = TRUE was selected when fitting the penetrance model.

Author(s)

Yun-Hee Choi

See Also

penmodel, penmodelEM, print.penmodel, print.summary.penmodel plot.penmodel

Examples

# Simulated family data 

set.seed(4321)
fam <- simfam(N.fam = 200, design = "pop+", variation = "none", base.dist = "Weibull", 
       base.parms = c(0.01, 3), vbeta = c(-1.13, 2.35), agemin = 20, allelefreq = 0.02)
 
# Penetrance model fit for the simulated family data

fit <- penmodel(Surv(time, status) ~ gender + mgene, cluster = "famID", 
       parms=c(0.01, 3, -1.13, 2.35), data = fam, design = "pop+", base.dist = "Weibull")

# Summary of the model parameter and penetrance estimates from model fit

summary(fit)

## Not run: 
Estimates: 
            Estimate Std. Error t value Pr(>|t|)  
log(lambda)   -4.531    0.08583 -52.793  0.01206 *
log(rho)       1.113    0.04688  23.737  0.02680 *
gender        -1.302    0.19233  -6.768  0.09339 .
mgene          2.349    0.23825   9.859  0.06436 .
Signif. codes:   0 '***'  0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 

## End(Not run)

FamEvent documentation built on Nov. 17, 2022, 5:06 p.m.