summary.penmodel function

Summary method for class penmodel

Provides a summary of a fitted penetrance model.

## 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.

Returns

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.

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)

Author(s)

Yun-Hee Choi

See Also

penmodel, penmodelEM, print.penmodel, print.summary.penmodelplot.penmodel