epi.surv {SimHap}R Documentation

Epidemiological analysis for survival data

Description

epi.surv is used to fit Cox proportional hazards models to epidemiological survival data.

Usage

epi.surv(formula, pheno, sub = NULL)

Arguments

formula a symbolic description of the model to be fit. The response must be a survival object as returned by the Surv function.
pheno a dataframe containing phenotype data.
sub an expression representing a subset of the data on which to perform the models.

Details

formula should be in the form of response ~ predictor(s). A formula has an implied intercept term. See documentation for the formula function for more details of allowed formulae.

Value

epi.surv returns an object of class epiSurv containing the following items

results a table containing the hazard ratios, confidence intervals and p-values of the parameter estimates.
formula formula passed to epi.surv.
Wald The Wald test for overall significance of the fitted model including SNP parameters.
logLik the log-likelihood for the linear model fit using formula.
fit.coxph an object of class coxph fit using formula1. See coxph.object for details.
rsquared r-squared values for the fitted model.

Author(s)

Pamela A McCaskie

References

Andersen, P., Gill, R. (1982) Cox's regression model for counting processes, a large sample study, Annals of Statistics, 10:1100-1120.

McCaskie, P.A., Carter, K.W, Hazelton, M., Palmer, L.J. (2007) SimHap: A comprehensive modeling framework for epidemiological outcomes and a multiple imputation approach to haplotypic analysis of population-based data, [online] www.genepi.org.au/simhap.

Therneau, T., Grambsch, P., Fleming, T. Martingale based residuals for survival models, Biometrika, 77(1):147-160.

See Also

snp.surv, haplo.surv

Examples


data(survPheno.dat)
mymodel <- epi.surv(formula=Surv(time, status)~age, pheno=survPheno.dat)
summary(mymodel)

# example with subsetting variable
mymodel <- epi.surv(formula=Surv(time, status)~age, pheno=survPheno.dat, 
        sub=expression(sex==1))
summary(mymodel)


[Package SimHap version 1.0.0 Index]