mice: mice.impute.panImpute – R documentation

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mice.impute.panImpute

Impute multilevel missing data using pan

Description

This function is a wrapper around the panImpute function from the mitml package so that it can be called to impute blocks of variables in mice. The mitml::panImpute function provides an interface to the pan package for multiple imputation of multilevel data (Schafer & Yucel, 2002). Imputations can be generated using type or formula, which offer different options for model specification.

Usage

mice.impute.panImpute(
  data,
  formula,
  type,
  m = 1,
  silent = TRUE,
  format = "imputes",
  ...
)

Arguments

`data`	A data frame containing incomplete and auxiliary variables, the cluster indicator variable, and any other variables that should be present in the imputed datasets.
`formula`	A formula specifying the role of each variable in the imputation model. The basic model is constructed by `model.matrix`, thus allowing to include derived variables in the imputation model using `I()`. See `panImpute`.
`type`	An integer vector specifying the role of each variable in the imputation model (see `panImpute`)
`m`	The number of imputed data sets to generate.
`silent`	(optional) Logical flag indicating if console output should be suppressed. Default is to `FALSE`.
`format`	A character vector specifying the type of object that should be returned. The default is `format = "list"`. No other formats are currently supported.
`...`	Other named arguments: `n.burn`, `n.iter`, `group`, `prior`, `silent` and others.

Value

A list of imputations for all incomplete variables in the model, that can be stored in the the imp component of the mids object.

Note

The number of imputations m is set to 1, and the function is called m times so that it fits within the mice iteration scheme.

This is a multivariate imputation function using a joint model.

Author(s)

Stef van Buuren, 2018, building on work of Simon Grund, Alexander Robitzsch and Oliver Luedtke (authors of mitml package) and Joe Schafer (author of pan package).

References

Grund S, Luedtke O, Robitzsch A (2016). Multiple Imputation of Multilevel Missing Data: An Introduction to the R Package pan. SAGE Open.

Schafer JL (1997). Analysis of Incomplete Multivariate Data. London: Chapman & Hall.

Schafer JL, and Yucel RM (2002). Computational strategies for multivariate linear mixed-effects models with missing values. Journal of Computational and Graphical Statistics, 11, 437-457.

Examples

blocks <- list(c("bmi", "chl", "hyp"), "age")
method <- c("panImpute", "pmm")
ini <- mice(nhanes, blocks = blocks, method = method, maxit = 0)
pred <- ini$pred
pred["B1", "hyp"] <- -2
imp <- mice(nhanes, blocks = blocks, method = method, pred = pred, maxit = 1)

mice

Multivariate Imputation by Chained Equations

v3.13.0

GPL-2 | GPL-3

Authors

Stef van Buuren [aut, cre], Karin Groothuis-Oudshoorn [aut], Gerko Vink [ctb], Rianne Schouten [ctb], Alexander Robitzsch [ctb], Patrick Rockenschaub [ctb], Lisa Doove [ctb], Shahab Jolani [ctb], Margarita Moreno-Betancur [ctb], Ian White [ctb], Philipp Gaffert [ctb], Florian Meinfelder [ctb], Bernie Gray [ctb], Vincent Arel-Bundock [ctb]

Initial release

2021-01-26