| CaseCohortCoxSurvival-package {CaseCohortCoxSurvival} | R Documentation |
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.
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 and
estimation.PR, for parameters estimation.
four functions, influences, influences.RH,
influences.CumBH and influences.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 and influences.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 and variance.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.
Lola Etievant, Mitchell H. Gail
Etievant, L., Gail, M.H. (2023). Cox model inference for relative hazard and pure risk from stratified weight-calibrated case-cohort data. Submitted.