iCoxph: Integrative Cox Model for Uncertain Event Times

Description Usage Arguments Value References See Also Examples

View source: R/iCoxph.R

Description

Fit an integrative Cox model proposed by Wang et al. (2020) for right-censored survival data with uncertain event times due to imperfect data integration.

Usage

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Arguments

formula

Survi object specifying the covariates and response variable in the model, such as Survi(ID, time, event) ~ x1 + x2.

data

An optional data frame, list, or environment that contains the covariates and response variables included in the model. If not found in data, the variables are taken from environment(formula), usually the environment from which this function is called.

subset

An optional logical vector specifying a subset of observations to be used in the fitting process.

na.action

An optional function that indicates what should the procedure do if the data contains NAs. The default is set by the na.action setting of options. The "factory-fresh" default is na.omit. Other possible values include na.fail, na.exclude, and na.pass. help(na.fail) for details.

contrasts

An optional list, whose entries are values (numeric matrices or character strings naming functions) to be used as replacement values for the contrasts replacement function and whose names are the names of columns of data containing factors. See contrasts.arg of model.matrix.default for details.

start

A list returned by function iCoxph.start specifying starting values of the parameters to be estimated in the model. Please refer to the arguments of iCoxph.start for the available parameters.

control

A list returned by function iCoxph.control specifying control parameters for the model estimation procedure. Please refer to the arguments of iCoxph.control for the available parameters.

...

Other arguments for future usage. A warning will be thrown if any invalid argument is specified.

Value

An iCoxph-class object, whose slots include

References

Wang, W., Aseltine, R. H., Chen, K., & Yan, J. (2020). Integrative Survival Analysis with Uncertain Event Times in Application to A Suicide Risk Study. Annals of Applied Statistics, 14(1), 51–73.

See Also

iCoxph.start and iCoxph.control, respectively, for starting and controlling iCoxph fitting; summary,iCoxph-method for summary of fitted model; coef,iCoxph-method for estimated covariate coefficients; bootSe for SE estimates from bootstrap methods.

Examples

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library(intsurv)
## generate simulated survival data with uncertain records
set.seed(123)
simuDat <- simData4iCoxph(nSubject = 200)
## fit the integertive Cox model
fit <- iCoxph(Survi(ID, time, event) ~ x1 + x2 + x3 + x4,
              data = simuDat, start = iCoxph.start(methods = "nearest"),
              control = iCoxph.control(tol_beta = 1e-5))
## estimated covariate coefficients
coef(fit)
## get SE estimates by bootstrap
fit <- bootSe(fit, B = 30)
## summary of the fitted model
summary(fit)

intsurv documentation built on Jan. 13, 2021, 3:46 p.m.