smcfcs (version 2.0.0)

smcfcs.nestedcc: Substantive model compatible fully conditional specification imputation of covariates for nested case control studies

Description

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

Usage

smcfcs.nestedcc(originaldata, smformula, method, set, event, nrisk, ...)

Arguments

originaldata

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

smformula

A formula of the form "Surv(t,case)~x+strata(set)", where case is case-control indicator, t is the event or censoring time. Note that t could be set to the case's event time for the matched controls in a given set. The right hand side should include the case control set as a strata term (see example).

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.

set

variable identifying matched sets in nested case-control study

event

variable which indicates who is a case/control in the nested case-control sample. Note that this is distinct from d.

nrisk

variable which is the number at risk (in the underlying full cohort) at the event time for the case in each matched set (i.e. nrisk is the same for all individuals in a matched set).

...

Additional arguments to pass on to smcfcs

Author

Ruth Keogh

Jonathan Bartlett

Details

This version of smcfcs is designed for use with nested case control studies. The function's arguments are the same as for the main smcfcs function, except for smformula, set, event and nrisk - 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) {
  predictorMatrix <- matrix(0,nrow=dim(ex_ncc)[2],ncol=dim(ex_ncc)[2])
  predictorMatrix[which(colnames(ex_ncc)=="x"),c(which(colnames(ex_ncc)=="z"))] <- 1

  imps <- smcfcs.nestedcc(originaldata=ex_ncc,set="setno",nrisk="numrisk",event="d",
                          smformula="Surv(t,case)~x+z+strata(setno)",
                          method=c("", "", "logreg", "", "", "", "", ""),
                          predictorMatrix=predictorMatrix)
  library(mitools)
  impobj <- imputationList(imps$impDatasets)
  models <- with(impobj, clogit(case~x+z+strata(setno)))
  summary(MIcombine(models))
}