mice function - RDocumentation (2024)

Description

The mice package implements a method to deal with missing data.The package creates multiple imputations (replacement values) formultivariate missing data. The method is based on Fully ConditionalSpecification, where each incomplete variable is imputed by a separatemodel. The MICE algorithm can impute mixes of continuous, binary,unordered categorical and ordered categorical data. In addition, MICEcan impute continuous two-level data, and maintain consistency betweenimputations by means of passive imputation. Many diagnostic plots areimplemented to inspect the quality of the imputations.

Generates Multivariate Imputations by Chained Equations (MICE)

Usage

mice( data, m = 5, method = NULL, predictorMatrix, ignore = NULL, where = NULL, blocks, visitSequence = NULL, formulas, blots = NULL, post = NULL, defaultMethod = c("pmm", "logreg", "polyreg", "polr"), maxit = 5, printFlag = TRUE, seed = NA, data.init = NULL, ...)

Value

Returns an S3 object of class mids

(multiply imputed data set)

Arguments

data

A data frame or a matrix containing the incomplete data. Missingvalues are coded as NA.

m

Number of multiple imputations. The default is m=5.

method

Can be either a single string, or a vector of strings withlength length(blocks), specifying the imputation method to beused for each column in data. If specified as a single string, the samemethod will be used for all blocks. The default imputation method (when noargument is specified) depends on the measurement level of the target column,as regulated by the defaultMethod argument. Columns that neednot be imputed have the empty method "". See details.

predictorMatrix

A numeric matrix of length(blocks) rowsand ncol(data) columns, containing 0/1 data specifyingthe set of predictors to be used for each target column.Each row corresponds to a variable block, i.e., a set of variablesto be imputed. A value of 1 means that the columnvariable is used as a predictor for the target block (in the rows).By default, the predictorMatrix is a square matrix of ncol(data)rows and columns with all 1's, except for the diagonal.Note: For two-level imputation models (which have "2l" in their names)other codes (e.g, 2 or -2) are also allowed.

ignore

A logical vector of nrow(data) elements indicatingwhich rows are ignored when creating the imputation model. The defaultNULL includes all rows that have an observed value of the variableto imputed. Rows with ignore set to TRUE do not influence theparameters of the imputation model, but are still imputed. We may use theignore argument to split data into a training set (on which theimputation model is built) and a test set (that does not influence theimputation model estimates).Note: Multivariate imputation methods, like mice.impute.jomoImpute()or mice.impute.panImpute(), do not honour the ignore argument.

where

A data frame or matrix with logicals of the same dimensionsas data indicating where in the data the imputations should becreated. The default, where = is.na(data), specifies that themissing data should be imputed. The where argument may be used tooverimpute observed data, or to skip imputations for selected missing values.Note: Imputation methods that generate imptutations outside ofmice, like mice.impute.panImpute() may depend on a completepredictor space. In that case, a custom where matrix can not bespecified.

blocks

List of vectors with variable names per block. List elementsmay be named to identify blocks. Variables within a block areimputed by a multivariate imputation method(see method argument). By default each variable is placedinto its own block, which is effectivelyfully conditional specification (FCS) by univariate models(variable-by-variable imputation). Only variables whose names appear inblocks are imputed. The relevant columns in the wherematrix are set to FALSE of variables that are not block members.A variable may appear in multiple blocks. In that case, it iseffectively re-imputed each time that it is visited.

visitSequence

A vector of block names of arbitrary length, specifying thesequence of blocks that are imputed during one iteration of the Gibbssampler. A block is a collection of variables. All variables that aremembers of the same block are imputedwhen the block is visited. A variable that is a member of multiple blocksis re-imputed within the same iteration.The default visitSequence = "roman" visits the blocks (left to right)in the order in which they appear in blocks.One may also use one of the following keywords: "arabic"(right to left), "monotone" (ordered low to high proportionof missing data) and "revmonotone" (reverse of monotone).Special case: If you specify both visitSequence = "monotone" andmaxit = 1, then the procedure will edit the predictorMatrixto conform to the monotone pattern. Realize that convergence in oneiteration is only guaranteed if the missing data pattern is actuallymonotone. The procedure does not check this.

formulas

A named list of formula's, or expressions thatcan be converted into formula's by as.formula. List elementscorrespond to blocks. The block to which the list element applies isidentified by its name, so list names must correspond to block names.The formulas argument is an alternative to thepredictorMatrix argument that allows for more flexibility inspecifying imputation models, e.g., for specifying interaction terms.

blots

A named list of alist's that can be usedto pass down arguments to lower level imputation function. The entriesof element blots[[blockname]] are passed down to the functioncalled for block blockname.

post

A vector of strings with length ncol(data) specifyingexpressions as strings. Each string is parsed andexecuted within the sampler() function to post-processimputed values during the iterations.The default is a vector of empty strings, indicating no post-processing.Multivariate (block) imputation methods ignore the post parameter.

defaultMethod

A vector of length 4 containing the defaultimputation methods for 1) numeric data, 2) factor data with 2 levels, 3)factor data with > 2 unordered levels, and 4) factor data with > 2ordered levels. By default, the method usespmm, predictive mean matching (numeric data) logreg, logisticregression imputation (binary data, factor with 2 levels) polyreg,polytomous regression imputation for unordered categorical data (factor > 2levels) polr, proportional odds model for (ordered, > 2 levels).

maxit

A scalar giving the number of iterations. The default is 5.

printFlag

If TRUE, mice will print history on console.Use print=FALSE for silent computation.

seed

An integer that is used as argument by the set.seed() foroffsetting the random number generator. Default is to leave the random numbergenerator alone.

data.init

A data frame of the same size and type as data,without missing data, used to initialize imputations before the start of theiterative process. The default NULL implies that starting imputationare created by a simple random draw from the data. Note that specification ofdata.init will start all m Gibbs sampling streams from the sameimputation.

...

Named arguments that are passed down to the univariate imputationfunctions.

Functions

The main functions are:

mice()Impute the missing data *m* times
with()Analyze completed data sets
pool()Combine parameter estimates
complete()Export imputed data
ampute()Generate missing data

Vignettes

There is a detailed series ofsix online vignettes that walk you through solving realistic inferenceproblems with mice.

We suggest going through these vignettes in the following order

  1. Ad hoc methods and the MICE algorithm

  2. Convergence and pooling

  3. Inspecting how the observed data and missingness are related

  4. Passive imputation and post-processing

  5. Imputing multilevel data

  6. Sensitivity analysis with mice

#'Van Buuren, S. (2018).Boca Raton, FL.: Chapman & Hall/CRC Press.The bookFlexible Imputation of Missing Data. Second Edition.contains a lot of example code.

Methodology

The mice software was published in the Journal of Statistical Software (Van Buuren and Groothuis-Oudshoorn, 2011). tools:::Rd_expr_doi("10.18637/jss.v045.i03")The first application of the methodconcerned missing blood pressure data (Van Buuren et. al., 1999).The term Fully Conditional Specification was introduced in 2006 to describe a general class of methods that specify imputations model for multivariate data as a set of conditional distributions (Van Buuren et. al., 2006). Further details on mixes of variables and applications can be found in the bookFlexible Imputation of Missing Data. Second Edition.Chapman & Hall/CRC. Boca Raton, FL.

Enhanced linear algebra

Updating the BLAS can improve speed of R, sometime considerably. The detailsdepend on the operating system. See the discussion in the"R Installation and Administration" guide for further information.

Author

Stef van Buuren stef.vanbuuren@tno.nl, KarinGroothuis-Oudshoorn c.g.m.oudshoorn@utwente.nl, 2000-2010, withcontributions of Alexander Robitzsch, Gerko Vink, Shahab Jolani,Roel de Jong, Jason Turner, Lisa Doove,John Fox, Frank E. Harrell, and Peter Malewski.

Details

The mice package contains functions to

  • Inspect the missing data pattern

  • Impute the missing data m times, resulting in m completed data sets

  • Diagnose the quality of the imputed values

  • Analyze each completed data set

  • Pool the results of the repeated analyses

  • Store and export the imputed data in various formats

  • Generate simulated incomplete data

  • Incorporate custom imputation methods

Generates multiple imputations for incomplete multivariate data by Gibbssampling. Missing data can occur anywhere in the data. The algorithm imputesan incomplete column (the target column) by generating 'plausible' syntheticvalues given other columns in the data. Each incomplete column must act as atarget column, and has its own specific set of predictors. The default set ofpredictors for a given target consists of all other columns in the data. Forpredictors that are incomplete themselves, the most recently generatedimputations are used to complete the predictors prior to imputation of thetarget column.

A separate univariate imputation model can be specified for each column. Thedefault imputation method depends on the measurement level of the targetcolumn. In addition to these, several other methods are provided. You canalso write their own imputation functions, and call these from within thealgorithm.

The data may contain categorical variables that are used in a regressions onother variables. The algorithm creates dummy variables for the categories ofthese variables, and imputes these from the corresponding categoricalvariable.

Built-in univariate imputation methods are:

pmmanyPredictive mean matching
midastouchanyWeighted predictive mean matching
sampleanyRandom sample from observed values
cartanyClassification and regression trees
rfanyRandom forest imputations
meannumericUnconditional mean imputation
normnumericBayesian linear regression
norm.nobnumericLinear regression ignoring model error
norm.bootnumericLinear regression using bootstrap
norm.predictnumericLinear regression, predicted values
lasso.normnumericLasso linear regression
lasso.select.normnumericLasso select + linear regression
quadraticnumericImputation of quadratic terms
rinumericRandom indicator for nonignorable data
logregbinaryLogistic regression
logreg.bootbinaryLogistic regression with bootstrap
lasso.logregbinaryLasso logistic regression
lasso.select.logregbinaryLasso select + logistic regression
polrorderedProportional odds model
polyregunorderedPolytomous logistic regression
ldaunorderedLinear discriminant analysis
2l.normnumericLevel-1 normal heteroscedastic
2l.lmernumericLevel-1 normal homoscedastic, lmer
2l.pannumericLevel-1 normal homoscedastic, pan
2l.binbinaryLevel-1 logistic, glmer
2lonly.meannumericLevel-2 class mean
2lonly.normnumericLevel-2 class normal
2lonly.pmmanyLevel-2 class predictive mean matching

These corresponding functions are coded in the mice library undernames mice.impute.method, where method is a string with thename of the univariate imputation method name, for example norm. Themethod argument specifies the methods to be used. For the j'thcolumn, mice() calls the first occurrence ofpaste('mice.impute.', method[j], sep = '') in the search path. Themechanism allows uses to write customized imputation function,mice.impute.myfunc. To call it for all columns specifymethod='myfunc'. To call it only for, say, column 2 specifymethod=c('norm','myfunc','logreg',...{}).

Skipping imputation: The user may skip imputation of a column bysetting its entry to the empty method: "". For complete columns withoutmissing data mice will automatically set the empty method. Setting the empty method does not produce imputations for the column, so any missingcells remain NA. If column A contains NA's and is used aspredictor in the imputation model for column B, then mice produces noimputations for the rows in B where A is missing. The imputed datafor B may thus contain NA's. The remedy is to remove column A fromthe imputation model for the other columns in the data. This can be doneby setting the entire column for variable A in the predictorMatrixequal to zero.

Passive imputation: mice() supports a special built-in method,called passive imputation. This method can be used to ensure that a datatransform always depends on the most recently generated imputations. In somecases, an imputation model may need transformed data in addition to theoriginal data (e.g. log, quadratic, recodes, interaction, sum scores, and soon).

Passive imputation maintains consistency among different transformations ofthe same data. Passive imputation is invoked if ~ is specified as thefirst character of the string that specifies the univariate method.mice() interprets the entire string, including the ~ character,as the formula argument in a call to model.frame(formula,data[!r[,j],]). This provides a simple mechanism for specifying deterministicdependencies among the columns. For example, suppose that the missing entriesin variables data$height and data$weight are imputed. The bodymass index (BMI) can be calculated within mice by specifying thestring '~I(weight/height^2)' as the univariate imputation method forthe target column data$bmi. Note that the ~ mechanism worksonly on those entries which have missing values in the target column. Youshould make sure that the combined observed and imputed parts of the targetcolumn make sense. An easy way to create consistency is by coding all entriesin the target as NA, but for large data sets, this could beinefficient. Note that you may also need to adapt the defaultpredictorMatrix to evade linear dependencies among the predictors thatcould cause errors like Error in solve.default() or Error:system is exactly singular. Though not strictly needed, it is often usefulto specify visitSequence such that the column that is imputed by the~ mechanism is visited each time after one of its predictors wasvisited. In that way, deterministic relation between columns will always besynchronized.

#'A new argument ls.meth can be parsed to the lower level.norm.draw to specify the method for generating the least squaresestimates and any subsequently derived estimates. Argument ls.methtakes one of three inputs: "qr" for QR-decomposition, "svd" forsingular value decomposition and "ridge" for ridge regression.ls.meth defaults to ls.meth = "qr".

Auxiliary predictors in formulas specification: For a given block, the formulas specification takes precedence overthe corresponding row in the predictMatrix argument. Thisprecedence is, however, restricted to the subset of variablesspecified in the terms of the block formula. Anyvariables not specified by formulas are imputedaccording to the predictMatrix specification. Variables withnon-zero type values in the predictMatrix willbe added as main effects to the formulas, which willact as supplementary covariates in the imputation model. It is possibleto turn off this behavior by specifying theargument auxiliary = FALSE.

References

van Buuren, S., Boshuizen, H.C., Knook, D.L. (1999) Multipleimputation of missing blood pressure covariates in survival analysis.Statistics in Medicine, 18, 681--694.

van Buuren, S., Brand, J.P.L., Groothuis-Oudshoorn C.G.M., Rubin, D.B. (2006)Fully conditional specification in multivariate imputation. Journal ofStatistical Computation and Simulation, 76, 12, 1049--1064.

van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice:Multivariate Imputation by Chained Equations in R. Journal ofStatistical Software, 45(3), 1--67. tools:::Rd_expr_doi("10.18637/jss.v045.i03")

Van Buuren, S. (2018).Flexible Imputation of Missing Data. Second Edition.Chapman & Hall/CRC. Boca Raton, FL.

Van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice:Multivariate Imputation by Chained Equations in R. Journal ofStatistical Software, 45(3), 1-67.tools:::Rd_expr_doi("10.18637/jss.v045.i03")

Van Buuren, S. (2018).Flexible Imputation of Missing Data. Second Edition.Chapman & Hall/CRC. Boca Raton, FL.

Van Buuren, S., Brand, J.P.L., Groothuis-Oudshoorn C.G.M., Rubin, D.B. (2006)Fully conditional specification in multivariate imputation. Journal ofStatistical Computation and Simulation, 76, 12, 1049--1064.

Van Buuren, S. (2007) Multiple imputation of discrete and continuous data byfully conditional specification. Statistical Methods in MedicalResearch, 16, 3, 219--242.

Van Buuren, S., Boshuizen, H.C., Knook, D.L. (1999) Multiple imputation ofmissing blood pressure covariates in survival analysis. Statistics inMedicine, 18, 681--694.

Brand, J.P.L. (1999) Development, implementation and evaluation ofmultiple imputation strategies for the statistical analysis of incompletedata sets. Dissertation. Rotterdam: Erasmus University.

See Also

mice, with.mids,pool, complete, ampute

mids, with.mids,set.seed, complete

Examples

Run this code

# do default multiple imputation on a numeric matriximp <- mice(nhanes)imp# list the actual imputations for BMIimp$imp$bmi# first completed data matrixcomplete(imp)# imputation on mixed data with a different method per columnmice(nhanes2, meth = c("sample", "pmm", "logreg", "norm"))if (FALSE) {# example where we fit the imputation model on the train data# and apply the model to impute the test dataset.seed(123)ignore <- sample(c(TRUE, FALSE), size = 25, replace = TRUE, prob = c(0.3, 0.7))# scenario 1: train and test in the same datasetimp <- mice(nhanes2, m = 2, ignore = ignore, print = FALSE, seed = 22112)imp.test1 <- filter(imp, ignore)imp.test1$datacomplete(imp.test1, 1)complete(imp.test1, 2)# scenario 2: train and test in separate datasetstraindata <- nhanes2[!ignore, ]testdata <- nhanes2[ignore, ]imp.train <- mice(traindata, m = 2, print = FALSE, seed = 22112)imp.test2 <- mice.mids(imp.train, newdata = testdata)complete(imp.test2, 1)complete(imp.test2, 2)}

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