Extension Package to 'mice'

Extends and builds on the 'mice' package by adding a functionality to perform multivariate predictive mean matching on imputed data as well as new functionalities to perform predictive mean matching on factor variables.


This package extends and builds on the mice package by adding a functionality to perform multivariate predictive mean matching on imputed data as well as new functionalities to perform predictive mean matching on factor variables.

Installation

The miceExt package can be installed from CRAN as follows:
install.packages("miceExt")

Overview

Overall, miceExt provides three funtions, namely

  • mice.post.matching(),
  • mice.binarize(),
  • mice.factorize(),

out of which the first function post-processes results of the mice()-algorithm by performing multivariate predictive mean matching on a user-defined set of column tuples, and results in imputations that are always equal to already-observed values, which annihilates the chance of getting unrealistic output values. The latter two functions provide a new option to impute categorical data by even extending the functionality of mice.post.matching(). The function mice.binarize() transforms categorical attributes of a given data frame into a binary dummy representation, which results in an exclusively numerical data set that mice can handle well. Inconsistencies within the imputed dummy columns can then be handled by mice.post.matching(), and mice.factorize() finally serves the purpose of retransforming the imputed binary data into the corresponding original categories, resulting in a proper imputation of the given categorical data.

Examples

1 Post-processing of imputated data by multivariate PMM

In this example, we work on a modification of the mammalsleep data set from mice, mammal_data, which is included in the miceExt-package and which has identical missing data patterns on the column tuples (ps,sws) and (mls,gt). We want to post-process the imputations gained from after running mice() on this data by performing multivariate PMM on these tuples. This procedure works in two simple steps:

  1. Run mice() on data set mammal_data and obtain a mids object to post-process:
    mids_mammal <- mice(mammal_data)

  2. Run mice.post.matching(). As column argument blocks has not been specified, it will automatically detect the column tuples with identical missing data patterns and then impute on these:
    post_mammal <- mice.post.matching(mids_mammal)

Now we can look into the resulting imputations via post_mammal$midsobj$imp or analyze the results via the with() function.

2 Imputation of categorical data

In this example, we want to impute the categorical columns gen and phb in the data set boys that is included in the mice-package with the functionalities of the package. This works in three main steps:

  1. Binarize the factor columns in boys the we want to impute on. By default, mice.binarize() will automatically identify all factor columns with missing values and binarize them.
    boys_bin <- mice.binarize(boys)

  2. Run mice() on binarized data and post-process the result with mice.post.matching(), as it is very likely that mice() imputed multiple ones among one set of dummy variables:

    # run mice, note that we need to grab `boys_bin$data` and also use `boys_bin$pred_matrix` as predictor matrix for mice() 
    # to obtain cleaner models
    mids_boys <- mice(boys_bin$data, predictorMatrix = boys_bin$pred_matrix)  
    
    # post_process with mice.post.matching, use output weights from mice.binarize() to avoid imbalanced imputations
    post_boys <- mice.post.matching(mids_boys, weights = boys_bin$weights)
    
  3. Retransform the resulting imputations back into categorical format:
    res_boys <- mice.factorize(post_boys$midsobj, boys_bin$par_list)

Also in this case, we can analyze the resulting imputed dataset via the with() function. If, e.g., we want to take a closer look at the distribution of the values of gen, we can use:
with(res_boys, table(gen))

News

Reference manual

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install.packages("miceExt")

1.1.0 by Tobias Schumacher, a year ago


http://github.com/tobiasschumacher/miceExt


Report a bug at http://github.com/tobiasschumacher/miceExt/issues


Browse source code at https://github.com/cran/miceExt


Authors: Tobias Schumacher [aut, cre] , Philipp Gaffert [aut] , Stef van Buuren [ctb] , Karin Groothuis-Oudshoorn [ctb]


Documentation:   PDF Manual  


GPL-2 license


Imports RANN, RANN.L1

Depends on mice

Suggests testthat


See at CRAN