gFormulaImpute creates multiple imputed synthetic datasets of longitudinal histories under
specified treatment regimes of interest, based on the G-formula.
gFormulaImpute(
data,
M = 50,
trtVars,
trtRegimes,
nSim = NULL,
micePrintFlag = FALSE,
silent = FALSE,
method = NULL,
predictorMatrix = NULL
)an S3 object of class mids (multiply imputed dataset)
The observed data frame
The number of imputed datasets to generate
A vector of variable names indicating the time-varying treatment variables
A vector specifying the treatment regime of interest, or a list of vectors specifying the treatment regimes of interest
The number of individuals to simulate in each imputed dataset. Defaults to number of individuals in observed data
TRUE/FALSE specifying whether the output from the call(s) to mice should be printed
TRUE/FALSE indicating whether to print output to console (FALSE) or not (TRUE)
An optional method argument to pass to mice. If not specified, the default is to impute continuous variables using normal linear regression (norm), binary variables using logistic regression (logreg), polytomous regression for unordered factors and proportional odds model for ordered factors
An optional predictor matrix to specify which variables to use as predictors in the imputation models. The default is to impute sequentially, i.e. impute using all variables to the left of the variable being imputed as covariates
Jonathan Bartlett jonathan.bartlett1@lshtm.ac.uk
gFormulaImpute creates multiple imputed synthetic datasets of longitudinal histories under
specified treatment regimes of interest, based on the G-formula, as described in
Bartlett et al 2023. Specifically, to
the observed data frame, an additional nSim rows are added in which all variables are set to
missing, except the time-varying treatment variables. The latter are set to the values
as specified in the trtRegimes argument. If multiple treatment regimes are specified,
nSim rows are added for each of the specified treatment regimes.
gFormulaImpute uses the mice package to impute the potential outcome values of the
time-varying confounders and outcome in the synthetic datasets. Imputation is performed
sequentially from left to right in the data frame. As such, the variables must be ordered
in time in the input data frame, with the time-varying confounders at each time followed
by the corresponding treatment variable at that time.
For the data argument, gFormulaImpute expects either a fully observed (complete) data frame,
or else a set of multiple imputation stored in an object of class mids (from the mice package).
Unlike with Rubin's regular multiple imputation pooling rules, it is possible
for the pooling rules developed by Raghunathan et al (2003) to give negative
variance estimates. The probability of this occurring is reduced by increasing
M and/or nSim.
gFormulaImpute returns an object of class mids. This can be analysed using the same
methods that imputed datasets from mice can be analysed with (see examples). However, Rubin's standard
pooling rules are not valid for analysis of the synthetic datasets. Instead, the synthetic
variance estimator of Raghunathan et al (2003) must be used, as implemented in the
syntheticPool function.
The development of the gFormulaMI package was supported by a grant from the UK
Medical Research Council (MR/T023953/1).
Bartlett JW, Olarte Parra C, Daniel RM. G-formula for causal inference via multiple imputation. 2023 https://arxiv.org/abs/2301.12026
Raghunathan TE, Reiter JP, Rubin DB. 2003. Multiple imputation for statistical disclosure limitation. Journal of Official Statistics, 19(1), p.1-16.
set.seed(7626)
#impute synthetic datasets under two regimes of interest
imps <- gFormulaImpute(data=simDataFullyObs,M=10,
trtVars=c("a0","a1","a2"),
trtRegimes=list(c(0,0,0),c(1,1,1)))
#fit linear model to final outcome with regime as covariate
fits <- with(imps, lm(y~factor(regime)))
#pool results using Raghunathan et al 2003 rules
syntheticPool(fits)
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