NestedCohort-package {NestedCohort}R Documentation

Survival Analysis of Cohort Studies With Missing Covariate Information ~~ NestedCohort ~~

Description

NestedCohort fits Kaplan-Meier and Cox Models to estimate standardized survival and attributable risks for studies where covariates of interest are observed on only a sample of the cohort. Missingness can be either by happenstance or by design (for example, the case-cohort and case-control within cohort designs).

Details

Package: NestedCohort
Type: Package
Version: 1.0-1
Date: 2007-09-01
License: Unlimited

To fit Kaplan-Meier, use nested.km(). If you only want hazard ratios from a Cox model, used nested.coxph(). If you want standardized survival and attributable risk estimates, used nested.stdsurv().

Author(s)

Author: Hormuzd A. Katki

Maintainer: Hormuzd A. Katki <katkih@mail.nih.gov>

References

Mark, S.D. and Katki, H.A. Specifying and Implementing Nonparametric and Semiparametric Survival Estimators in Two-Stage (sampled) Cohort Studies with Missing Case Data. Journal of the American Statistical Association, 2006, 101, 460-471.

See Also

~~ survival ~~

Examples


# Get zinc dataset
data(zinc)

# Fit and plot Kaplan-Meier
mod <- nested.km(survfitformula="Surv(futime01,ec01==1)~znquartiles",
                 samplingmod="ec01*basehist",data=zinc)
plot(mod,ymin=.6,xlab="Time (Days)",ylab="Survival",main="Survival by Quartile of Zinc",
     legend.text=c("Q1","Q2","Q3","Q4"),lty=1:4,legend.pos=c(2000,.7))

# Fit Cox model, get hazard ratios
coxmod <- nested.coxph(coxformula="Surv(futime01,ec01==1)~
          sex+agepill+smoke+drink+mildysp+moddysp+sevdysp+anyhist+zncent",
          samplingmod="ec01*basehist",data=zinc)
summary(coxmod)

# Fit Cox model, get standardized survivals and attributable risks
mod <- nested.stdsurv(outcome="Surv(futime01,ec01==1)",
                      exposures="znquartiles",
                      confounders="sex+agestr+smoke+drink+mildysp+moddysp+sevdysp+anyhist",
                      samplingmod="ec01*basehist",exposureofinterest="Q4",plot=TRUE,
                      main="Time to Esophageal Cancer by Quartiles of Zinc",data=zinc)


[Package NestedCohort version 1.0-1 Index]