CaseCohortCoxSurvival-package {CaseCohortCoxSurvival} | R Documentation |
Case-Cohort Cox Survival Inference
Description
This package uses case-cohort data to estimate log-relative hazard, baseline hazards at each unique event time, cumulative baseline hazard in a given time interval and pure risk on the time interval and for a given covariate profile, under the Cox model. For the corresponding variance estimation, it relies on influence functions and follows the complete variance decomposition, to enable correct analysis of case-cohort data with and without stratification, weight calibration or missing phase-two covariate data.
Details
The package provides functions implementing the methods described in Etievant and Gail (2023). More precisely, it includes
a main driver function,
caseCohortCoxSurvival
.one function,
estimatePureRisk
, to estimate pure risks and the corresponding variances with additional covariate profiles.three functions,
estimation
,estimation.CumBH
andestimation.PR
, for parameters estimation.four functions,
influences
,influences.RH
,influences.CumBH
andinfluences.PR
, for influence functions derivation when estimation is with design or calibrated weights and from a case-cohort consisting of the subcohort and cases not in the subcohort (i.e., case-cohort obtained from two phases of sampling).four functions,
influences.missingdata
,influences.RH.missingdata
,influences.CumBH.missingdata
andinfluences.PR.missingdata
, for influence functions derivation when estimation is with design weights and from a case-cohort when covariate information was missing for certain individuals in the phase-two data (i.e., case-cohort obtained from three phases of sampling).two functions,
variance
andvariance.missingdata
, for variance estimation following complete variance decomposition (with design or calibrated weights and without missing phase-two data, or with design weights and missing phase-two covariate data).one function,
robustvariance
, for robust variance estimation.one function,
auxiliary.construction
, to compute the auxiliary variables proposed by Breslow et al. (Stat. Biosci., 2009), Breslow and Lumley (IMS, 2013), and Shin et al. (Biometrics, 2020),.one function,
calibration
, for weight calibration.one function,
estimation.weights.phase3
, for estimating the phase-three weights.
Author(s)
Lola Etievant, Mitchell H. Gail
References
Etievant, L., Gail, M.H. (2023). Cox model inference for relative hazard and pure risk from stratified weight-calibrated case-cohort data. Submitted.