mice: Multivariate Imputation by Chained Equations

Multiple imputation using Fully Conditional Specification (FCS) implemented by the MICE algorithm as described in Van Buuren and Groothuis-Oudshoorn (2011) <doi:10.18637/jss.v045.i03>. Each variable has its own imputation model. Built-in imputation models are provided for continuous data (predictive mean matching, normal), binary data (logistic regression), unordered categorical data (polytomous logistic regression) and ordered categorical data (proportional odds). MICE can also impute continuous two-level data (normal model, pan, second-level variables). Passive imputation can be used to maintain consistency between variables. Various diagnostic plots are available to inspect the quality of the imputations.

Install the latest version of this package by entering the following in R:
install.packages("mice")
AuthorStef van Buuren [aut, cre], Karin Groothuis-Oudshoorn [aut], Alexander Robitzsch [ctb], Gerko Vink [ctb], Lisa Doove [ctb], Shahab Jolani [ctb], Rianne Schouten [ctb], Philipp Gaffert [ctb], Florian Meinfelder [ctb]
Date of publication2017-02-18 22:39:19
MaintainerStef van Buuren <stef.vanbuuren@tno.nl>
LicenseGPL-2 | GPL-3
Version2.30
http://www.stefvanbuuren.nl
http://www.multiple-imputation.com

View on CRAN

Man pages

ampute: Generate Missing Data for Simulation Purposes

ampute.continuous: Multivariate Amputation Based On Continuous Probability...

ampute.default.freq: Default 'freq' in 'ampute'

ampute.default.odds: Default 'odds' in 'ampute()'

ampute.default.patterns: Default 'patterns' in 'ampute'

ampute.default.type: Default 'type' in 'ampute()'

ampute.default.weights: Default 'weights' in 'ampute'

ampute.discrete: Multivariate Amputation Based On Discrete Probability...

ampute.mcar: Multivariate Amputation In A MCAR Manner

appendbreak: Appends specified break to the data

as.mids: Converts an multiply imputed dataset (long format) into a...

as.mira: Create a 'mira' object from repeated analyses

boys: Growth of Dutch boys

bwplot.mads: Box-and-whisker plot of amputed and non-amputed data

bwplot.mids: Box-and-whisker plot of observed and imputed data

cbind.mids: Columnwise combination of a 'mids' object.

cc: Select complete cases

cci: Complete case indicator

complete: Creates imputed data sets from a 'mids' object

densityplot.mids: Density plot of observed and imputed data

extractBS: Extract broken stick estimates from a 'lmer' object

fdd: SE Fireworks disaster data

fdgs: Fifth Dutch growth study 2009

fico: Fraction of incomplete cases among cases with observed

flux: Influx and outflux of multivariate missing data patterns

fluxplot: Fluxplot of the missing data pattern

getfit: Extracts fit objects from 'mira' object

glm.mids: Generalized linear model for 'mids' object

ibind: Combine imputations fitted to the same data

ic: Select incomplete cases

ici: Incomplete case indicator

ifdo: Conditional imputation helper

is.mads: Check for 'mads' object

is.mids: Check for 'mids' object

is.mipo: Check for 'mipo' object

is.mira: Check for 'mira' object

leiden85: Leiden 85+ study

lm.mids: Linear regression for 'mids' object

long2mids: Conversion of a imputed data set (long form) to a 'mids'...

mads-class: Multivariate Amputed Data Set ('mads')

mammalsleep: Mammal sleep data

mdc: Graphical parameter for missing data plots.

md.pairs: Missing data pattern by variable pairs

md.pattern: Missing data pattern

mice: Multivariate Imputation by Chained Equations (MICE)

mice.impute.2l.norm: Imputation by a two-level normal model

mice.impute.2lonly.mean: Imputation of the mean within the class

mice.impute.2lonly.norm: Imputation at level 2 by Bayesian linear regression

mice.impute.2lonly.pmm: Imputation at level 2 by predictive mean matching

mice.impute.2l.pan: Imputation by a two-level normal model using 'pan'

mice.impute.cart: Imputation by classification and regression trees

mice.impute.fastpmm: Imputation by fast predictive mean matching

mice.impute.lda: Imputation by linear discriminant analysis

mice.impute.logreg: Imputation by logistic regression

mice.impute.logreg.boot: Imputation by logistic regression using the bootstrap

mice.impute.mean: Imputation by the mean

mice.impute.midastouch: Predictive Mean Matching with distance aided selection of...

mice.impute.norm: Imputation by Bayesian linear regression

mice.impute.norm.boot: Imputation by linear regression, bootstrap method

mice.impute.norm.nob: Imputation by linear regression (non Bayesian)

mice.impute.norm.predict: Imputation by linear regression, prediction method

mice.impute.passive: Passive imputation

mice.impute.pmm: Imputation by predictive mean matching

mice.impute.polr: Imputation by polytomous regression - ordered

mice.impute.polyreg: Imputation by polytomous regression - unordered

mice.impute.quadratic: Imputation of quadratric terms

mice.impute.rf: Imputation by random forests

mice.impute.ri: Imputation by the random indicator method for nonignorable...

mice.impute.sample: Imputation by simple random sampling

mice.mids: Multivariate Imputation by Chained Equations (Iteration Step)

mice.theme: Set the theme for the plotting Trellis functions

mids2mplus: Export 'mids' object to Mplus

mids2spss: Export 'mids' object to SPSS

mids-class: Multiply imputed data set ('mids')

mipo-class: Multiply imputed pooled analysis ('mipo')

mira-class: Multiply imputed repeated analyses ('mira')

ncc: Number of complete cases

nelsonaalen: Cumulative hazard rate or Nelson-Aalen estimator

nhanes: NHANES example - all variables numerical

nhanes2: NHANES example - mixed numerical and discrete variables

nic: Number of incomplete cases

norm.draw: Draws values of beta and sigma by Bayesian linear regression

pattern: Datasets with various missing data patterns

plot.mids: Plot the trace lines of the MICE algorithm

pmm.match: Finds an imputed value from matches in the predictive metric

pool: Multiple imputation pooling

pool.compare: Compare two nested models fitted to imputed data

pool.r.squared: Pooling: R squared

pool.scalar: Multiple imputation pooling: univariate version

popmis: Hox pupil popularity data with missing popularity scores

pops: Project on preterm and small for gestational age infants...

potthoffroy: Potthoff-Roy data

print: Print a 'mids' object

print.mads: Print a 'mads' object

quickpred: Quick selection of predictors from the data

rbind.mids: Rowwise combination of a 'mids' object.

selfreport: Self-reported and measured BMI

squeeze: Squeeze the imputed values to be within specified boundaries.

stripplot.mids: Stripplot of observed and imputed data

summary: Summary of a 'mira' object

supports.transparent: Supports semi-transparent foreground colors?

tbc: Terneuzen birth cohort

version: Echoes the package version number

walking: Walking disability data

windspeed: Subset of Irish wind speed data

with.mids: Evaluate an expression in multiple imputed datasets

xyplot.mads: Scatterplot of amputed and non-amputed data against weighted...

xyplot.mids: Scatterplot of observed and imputed data

Functions

2l.norm Man page
2lonly.mean Man page
2lonly.norm Man page
2lonly.pmm Man page
2l.pan Man page
ampute Man page
ampute.continuous Man page
ampute.default.freq Man page
ampute.default.odds Man page
ampute.default.patterns Man page
ampute.default.type Man page
ampute.default.weights Man page
ampute.discrete Man page
ampute.mcar Man page
appendbreak Man page
as.mids Man page
as.mira Man page
boys Man page
bwplot Man page
bwplot.mads Man page
bwplot.mids Man page
cart Man page
cbind.mids Man page
cc Man page
cci Man page
complete Man page
densityplot Man page
densityplot.mids Man page
extractBS Man page
fastpmm Man page
fdd Man page
fdd.pred Man page
fdgs Man page
fico Man page
flux Man page
fluxplot Man page
getfit Man page
glm.mids Man page
hazard Man page
ibind Man page
ic Man page
ici Man page
ici,data.frame-method Man page
ici,matrix-method Man page
ici,mids-method Man page
ifdo Man page
is.mads Man page
is.mids Man page
is.mipo Man page
is.mira Man page
leiden85 Man page
lm.mids Man page
long2mids Man page
mads-class Man page
mammalsleep Man page
mdc Man page
md.pairs Man page
md.pattern Man page
mgg Man page
mice Man page
mice.impute.2l.norm Man page
mice.impute.2lonly.mean Man page
mice.impute.2lonly.norm Man page
mice.impute.2lonly.pmm Man page
mice.impute.2l.pan Man page
mice.impute.cart Man page
mice.impute.fastpmm Man page
mice.impute.lda Man page
mice.impute.logreg Man page
mice.impute.logreg.boot Man page
mice.impute.mean Man page
mice.impute.midastouch Man page
mice.impute.norm Man page
mice.impute.norm.boot Man page
mice.impute.norm.nob Man page
mice.impute.norm.predict Man page
mice.impute.passive Man page
mice.impute.pmm Man page
mice.impute.polr Man page
mice.impute.polyreg Man page
mice.impute.quadratic Man page
mice.impute.rf Man page
mice.impute.ri Man page
mice.impute.sample Man page
mice.mids Man page
mice.theme Man page
mids Man page
mids2mplus Man page
mids2spss Man page
mids-class Man page
mipo Man page
mipo-class Man page
mira Man page
mira-class Man page
ncc Man page
nelsonaalen Man page
nhanes Man page
nhanes2 Man page
nic Man page
norm Man page
norm.boot Man page
.norm.draw Man page
norm.draw Man page
norm.nob Man page
norm.predict Man page
pattern Man page
pattern1 Man page
pattern2 Man page
pattern3 Man page
pattern4 Man page
plot.mids Man page
pmm Man page
.pmm.match Man page
pool Man page
pool.compare Man page
pool.r.squared Man page
pool.scalar Man page
popmis Man page
pops Man page
pops.pred Man page
potthoffroy Man page
print.mads Man page
print.mids Man page
print.mipo Man page
print.mira Man page
quadratic Man page
quickpred Man page
rbind.mids Man page
ri Man page
selfreport Man page
sleep Man page
squeeze Man page
stripplot Man page
stripplot.mids Man page
summary.mads Man page
summary.mids Man page
summary.mipo Man page
summary.mira Man page
supports.transparent Man page
tbc Man page
tbc.target Man page
terneuzen Man page
transparent Man page
version Man page
walking Man page
windspeed Man page
with.mids Man page
xyplot Man page
xyplot.mads Man page
xyplot.mids Man page

Files

inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/ampute.Rmd
inst/doc/fimd4.r inst/doc/fimd9.r inst/doc/fimd5.r inst/doc/ampute.R
inst/doc/ampute.html
inst/doc/fimd7.r inst/doc/JSScode.R inst/doc/fimd1.r inst/doc/fimd6.r inst/doc/fimd8.r inst/doc/fimd2.r inst/doc/fimd3.r
src
src/Makevars
src/match.cpp
src/Makevars.win
src/RcppExports.cpp
NAMESPACE
data
data/selfreport.rda
data/mammalsleep.rda
data/nhanes2.rda
data/nhanes.rda
data/fdd.rda
data/potthoffroy.rda
data/walking.rda
data/tbc.target.rda
data/windspeed.rda
data/leiden85.rda
data/boys.rda
data/pattern2.rda
data/fdd.pred.rda
data/pattern4.rda
data/fdgs.rda
data/popmis.rda
data/pattern3.rda
data/tbc.rda
data/pops.rda
data/pops.pred.rda
data/pattern1.rda
R
R/mids.r R/pool.compare.r R/df.residual.r R/supports.transparent.r R/mice.impute.polr.r R/ampute.mcar.R R/ampute.discrete.R R/mdc.r R/lm.r R/ncc.R R/complete.r R/mice.impute.mean.r R/stripplot.r R/mids2mplus.r R/cci.r R/ampute.default.R R/mice.impute.passive.r R/plot.r R/mice.impute.cart.r R/windspeed.r R/md.pairs.r R/flux.r R/long2mids.r R/tbc.r R/print.r R/mice.impute.2lonly.norm.r R/mice.impute.quadratic.r R/potthoffroy.r R/xyplot.mads.R R/mice.impute.polyreg.r R/boys.r R/mice.theme.r R/ampute.continuous.R R/squeeze.r R/mice.impute.fastpmm.r R/mice.impute.logreg.r R/walking.r R/mice.impute.rf.r R/ibind.r R/RcppExports.r R/nhanes.r R/fdgs.r R/densityplot.r R/nelsonaalen.r R/nhanes2.r R/mice.impute.norm.predict.r R/as.r R/Mads.R R/mice.impute.norm.r R/cbind.r R/pool.r R/mice.impute.norm.boot.r R/mice.impute.2l.norm.r R/xyplot.r R/quickpred.r R/mice.impute.2l.pan.r R/mice.impute.norm.nob.r R/bwplot.r R/mice.impute.midastouch.R R/rbind.r R/summary.r R/expandcov.r R/pops.r R/rm.whitespace.r R/auxiliary.r R/mice.impute.ri.r R/internal.r R/mids2spss.r R/bwplot.mads.R R/zzz.r R/pattern1.r R/fdd.r R/popmis.r R/Ampute.R R/mice.mids.r R/leiden85.r R/mice.impute.lda.r R/mira.r R/mice.impute.2lonly.mean.r R/selfreport.r R/mice.impute.sample.r R/md.pattern.r R/with.r R/mice.impute.2lony.pmm.r R/pool.r.squared.r R/mipo.r R/is.r R/cc.r R/getfit.r R/mice.df.r R/imports.R R/mice.impute.pmm.r R/mice.r R/mammalsleep.r R/pool.scalar.r
vignettes
vignettes/ampute.Rmd
vignettes/Figures
vignettes/Figures/Flowchart.pdf
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/pattern.Rd man/md.pattern.Rd man/mice.impute.sample.Rd man/ampute.mcar.Rd man/cci.Rd man/mice.impute.lda.Rd man/pool.Rd man/mice.theme.Rd man/mice.impute.norm.boot.Rd man/walking.Rd man/popmis.Rd man/mice.impute.fastpmm.Rd man/mids-class.Rd man/complete.Rd man/lm.mids.Rd man/mice.impute.2lonly.mean.Rd man/ampute.default.weights.Rd man/ibind.Rd man/mice.impute.logreg.Rd man/ampute.Rd man/bwplot.mads.Rd man/with.mids.Rd man/bwplot.mids.Rd man/mammalsleep.Rd man/mice.mids.Rd man/boys.Rd man/mice.impute.ri.Rd man/appendbreak.Rd man/selfreport.Rd man/extractBS.Rd man/mice.impute.quadratic.Rd man/mice.impute.mean.Rd man/version.Rd man/squeeze.Rd man/nic.Rd man/mice.impute.rf.Rd man/mira-class.Rd man/mice.Rd man/ic.Rd man/pool.scalar.Rd man/is.mipo.Rd man/rbind.mids.Rd man/leiden85.Rd man/potthoffroy.Rd man/xyplot.mids.Rd man/nelsonaalen.Rd man/windspeed.Rd man/pops.Rd man/mice.impute.norm.predict.Rd man/supports.transparent.Rd man/ampute.default.type.Rd man/nhanes2.Rd man/long2mids.Rd man/mice.impute.polr.Rd man/ampute.discrete.Rd man/mice.impute.norm.Rd man/quickpred.Rd man/mice.impute.polyreg.Rd man/nhanes.Rd man/xyplot.mads.Rd man/mids2spss.Rd man/mice.impute.norm.nob.Rd man/ncc.Rd man/ifdo.Rd man/is.mids.Rd man/ici.Rd man/pmm.match.Rd man/is.mads.Rd man/densityplot.mids.Rd man/plot.mids.Rd man/mdc.Rd man/fdgs.Rd man/mice.impute.2l.pan.Rd man/as.mira.Rd man/ampute.continuous.Rd man/norm.draw.Rd man/mice.impute.2l.norm.Rd man/print.mads.Rd man/mice.impute.passive.Rd man/mice.impute.2lonly.norm.Rd man/stripplot.mids.Rd man/is.mira.Rd man/fdd.Rd man/fico.Rd man/ampute.default.freq.Rd man/fluxplot.Rd man/mads-class.Rd man/mice.impute.cart.Rd man/cc.Rd man/getfit.Rd man/tbc.Rd man/ampute.default.odds.Rd man/pool.r.squared.Rd man/as.mids.Rd man/print.Rd man/md.pairs.Rd man/mipo-class.Rd man/flux.Rd man/ampute.default.patterns.Rd man/mice.impute.2lonly.pmm.Rd man/mice.impute.midastouch.Rd man/glm.mids.Rd man/mice.impute.logreg.boot.Rd man/mids2mplus.Rd man/summary.Rd man/pool.compare.Rd man/mice.impute.pmm.Rd man/cbind.mids.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.