smcfcs (version 2.0.0)

smcfcs.casecohort: Substantive model compatible fully conditional specification imputation of covariates for case cohort studies

Description

Multiply imputes missing covariate values using substantive model compatible fully conditional specification for case cohort studies.

Usage

smcfcs.casecohort(originaldata, smformula, method, sampfrac, in.subco, ...)

Arguments

originaldata

The case-cohort data set (NOT a full cohort data set with a case-cohort substudy within it)

smformula

A formula of the form "Surv(entertime,t,d)~x", where d is the event (d=1) or censoring (d=0) indicator, t is the event or censoring time and entertime is equal to the time origin (typically 0) for individuals in the subcohort and is equal to (t-0.001) for cases outside the subcohort [this sets cases outside the subcohort to enter follow-up just before their event time. The value 0.001 may need to be modified depending on the time scale.]

method

A required vector of strings specifying for each variable either that it does not need to be imputed (""), the type of regression model to be be used to impute. Possible values are "norm" (normal linear regression), "logreg" (logistic regression), "brlogreg" (bias reduced logistic regression), "poisson" (Poisson regression), "podds" (proportional odds regression for ordered categorical variables), "mlogit" (multinomial logistic regression for unordered categorical variables), or a custom expression which defines a passively imputed variable, e.g. "x^2" or "x1*x2". "latnorm" indicates the variable is a latent normal variable which is measured with error. If this is specified for a variable, the "errorProneMatrix" argument should also be used.

sampfrac

The proportion of individuals from the underlying full cohort who are in the subcohort

in.subco

The name of a column in the dataset with 0/1s that indicates whether the subject is in the subcohort

...

Additional arguments to pass on to smcfcs

Author

Ruth Keogh

Jonathan Bartlett

Details

This version of smcfcs is designed for use with case cohort studies but where the analyst does not wish to, or cannot (due to not having the necessary data) impute the full cohort. The function's arguments are the same as for the main smcfcs function, except for smformula, in.subco, and sampfrac - see above for details on how these should be specified.

Examples

#the following example is not run when the package is compiled on CRAN
#(to keep computation time down), but it can be run by package users
if (FALSE) {
  #as per the documentation for ex_cc, the sampling fraction is 10%
  imps <- smcfcs.casecohort(ex_cc, smformula="Surv(entertime, t, d)~x+z", sampfrac=0.1,
                            in.subco="in.subco", method=c("", "", "norm", "", "", "", ""))
  library(mitools)
  impobj <- imputationList(imps$impDatasets)
  models <- with(impobj, coxph(Surv(entertime,t,d)~x+z+cluster(id)))
  summary(MIcombine(models))
}