NEWS

---

miceadds 2.3

NOTE * updated incorrect examples in miceadds::micombine.chisquare

• and miceadds::micombine.F (thanks to Nicholas Breitborde)

NOTE * restructured Rcpp functions

DATA * included/modified datasets:

EXAMP * included/modified examples: micombine.F (1),

• micombine.chisquare (2)

miceadds 2.2

FIXED * fixed bug in data processing 'mice.impute.pls' and

• 'mice.impute.plausible.values'. Additional arguments 'envir_pos' and 'extract_data' have been included (thanks to Peter Lenz).

FIXED * fixed problems in 'mice.impute.pls' due to derived predictor

• variables such as interactions due to standard deviations of zero (thanks to Peter Lenz)

NOTE * included some utility descriptiptive statistics functions

• 'stats0', 'mean0', 'sd0', ...

NOTE * included correct attributes in 'scale_datlist' function for

• objects of class datlist (thanks to Andrew Frank-Wilson)

NOTE * extended 'scale_datlist' function to handle multiple variables to

• be standardized

DATA * included/modified datasets:

EXAMP * included/modified examples: stats0 (1), scale_datlist (3

miceadds 2.1

NOTE * added utility function 'filename_split' for splitting file names

NOTE * added utility function 'files_move' for moving files from one

• directory into another directory

NOTE * included starting values in imputations in the function

• 'mice.impute.2l.latentgroupmean.MCMC' which are obtained from previous iterations in MCMC imputation chain

DATA * included/modified datasets:

EXAMP * included/modified examples: filename_split (1), files_move (1

miceadds 2.0

FIXED * fixed an incorrect calculation in D2 statistic which appeared

• differently in literature (thanks to David Tian)

NOTE * allow now vectors of strings to specify file names in 'load.data

• Also included the value NULL of the argument 'path' if a path should not be specified in this argument.

ADDED * included mice imputation method 'mice.impute.hotDeck' for

• probabilistic hot deck imputation

FIXED * fixed a bug included in 'mice.impute.plausible.values' using

• likelihood objects which was recently introduced in miceadds 1.9

FIXED * fixed a bug in predicted mean matching of two-level data in

• function 'mice.impute.2l.pmm'

DATA * included/modified datasets:

EXAMP * included/modified examples: mice.impute.hotDeck (1

miceadds 1.9

FIXED * fixed a bug in 'mice.impute.2l.binary'. Random slopes were

• not properly handled in the previuos package version (miceadds 1.8).

ADDED * included lme4-based and blme-based imputation of normally

• distributed two-level data in 'mice.impute.2l.continuous' function. Predictive mean matching for two-level data is also added as the 'mice.impute.2l.pmm' function.

ADDED * included imputation function '2lonly.function' for level 2

• imputation based on (arbitrary) level 1 imputation function

ADDED * added general group-wise imputation function 'mice.impute.bygroup

NOTE * included t values and p values in output of 'pool_mi' for

• inference of multiply imputed datasets (due to a request on R help list of Jennifer Lorenz)

NOTE * renamed PLS imputation method '2l.pls' into 'mice.impute.pls

NOTE * renamed plausible value imputation method into

• 'mice.impute.plausible.values'

NOTE * renamed 'mice.impute.2l.eap' into 'mice.impute.eap

NOTE * Defunct functions: 'mice.impute.2l.pls', 'mice.impute.2l.pls2

• 'fast.groupmean', 'fast.groupsum', 'mice.impute.2l.plausible.values', 'mice.impute.2l.eap', 'mice.impute.2lonly.norm2', 'mice.impute.2lonly.pmm2'

DATA * included/modified datasets:

EXAMP * included/modified examples: mice.impute.2l.lmer (1

• mice.impute.2lonly.function (1), mice.imputation.bygroup (1), lm.cluster(1), mice.impute.pls (1)

miceadds 1.8

NOTE * added argument 'subdir' in 'write.datlist' indicating whether

• output should be written in a subdirectory or directly into the working directory

NOTE * fixed a minor bug in creation of Mplus input files in

• 'write.mice.imputation' and 'write.datlist'

NOTE * deleted display of chi square approximation p value in

• 'micombine.F' and 'micombine.chisquare' (after a discussion with Joanna Kaye)

NOTE * extended 'subset' methods for integer input of argument

• 'subset' which allows easier selection of rows by specifying row indices

NOTE * changed dimnames handling in 'NMIwaldtest' which should have

• no practical side effects

ADDED * added utility functions 'ma.wtd.skewnessNA' and

• 'ma.wtd.curtosisNA' for calculating skewness and curtosis (due to a correspondence with Timo Ehmke)

ADDED * added the function 'ma.wtd.quantileNA' for weighted quantile

• calculation

NOTE * extended 'ma.wtd.statNA' functions to handle objects of

• class 'BIFIEdata' from the BIFIEsurvey package

NOTE * renamed 'fast.groupmean' and 'fast.groupsum' into 'GroupMean

• and 'GroupSum' and added function 'GroupSD' for calculation of group-wise standard deviations

NOTE * replace 'Hmisc::wtd.var' import by 'TAM::weighted_sd

NOTE * shift Hmisc, inline, MBESS and pls packages from Imports

• to Suggests and removed bayesm from Imports

NOTE * rewrite of 'scan.vec' which avoids temporary file savings

NOTE * extended 'micombine.cor' to nested multiply imputed datasets

• for objects of classes 'datlist' and 'nested.datlist' and single datasets (optionally non-imputed), i.e. the input of 'micombine.cor' must not be mids objects

NOTE * added function 'micombine.cov' which has same functionality

• as 'micombine.cor'

NOTE * added attributes in 'datlist' and 'nested.datlist' for cases

• of varying sample sizes in imputed datasets

FIXED * added functionality of handling single imputed datasets in

• 'pool_mi' function

ADDED * added inference for partial correlation in 'micombine.cor

• using the argument 'partial'

FIXED * fixed an unnecessary warning message in 'datalist2mids' for

• class checking (thanks to Janet Kwok)

ADDED * included imputation methode '2l.binary' of binary variable

• with two-level logistic regression models

DATA * included/modified datasets:

EXAMP * included/modified examples: subset.datlist (1),

• ma.wtd.statsNA (1,2,3,4), GroupMean (1), mi.combine.cor (1,2)

miceadds 1.7

NOTE * allowed alternative specification of weighting variable in

• 'scale_datlist' which now allows for group-wise standardizations

NOTE * included arguments 'index' and 'systime' in 'save.data' for

• automatic inclusion of indices and time stamps in saved datasets

NOTE * included argument 'se' in 'NMIcombine' function which can be

• used if only standard errors instead of covariance matrices are available

ADDED * added utility function 'pool_mi' for inference of multiply

• imputed datasets which has the same functionality as 'mice::pool' or 'mitools::MIcombine'. This function provides summary, coef and vcov S3 methods.

NOTE * function 'datalist2mids' is now also accessible via

• 'datlist2mids' (which is more coherent to class 'datlist')

NOTE * defined 'pool_nmi' synonymously to 'NMIcombine

NOTE * added S3 print method for 'datlist', 'nested.datlist

• 'NestedImputationList'

ADDED * added subsetting methods 'subset_datlist' (and the S3 method

• subset) for multiply imputed datasets and 'subset_nested.datlist' for nested multiply imputed datasets

NOTE * added further calculation of fraction of missing information for

• nested multiply imputed datasets according to Harel and Schafer (2002) in 'NMIcombine' which can be assessed by the argument 'method=2'.

NOTE * extended imputation of latent group means to lme4-based imputation

• in 'mice.impute.2l.latentgroupmean.ML' and MCMCglmm based imputation in 'mice.impute.2l.latentgroupmean.MCMC'

NOTE * added with and within methods for objects of class 'datlist

• and 'nested.datlist'

ADDED * added convenience functions 'withPool_MI' and 'withPool_NMI' for

• pooling (averaging) estimates for (nested) multiply imputed datasets

ADDED * added utility function 'scan0' which is 'scan' with default

• what='character'

ADDED * added utility functions 'nestedList2List' and 'List2nestedList

• for list conversions

ADDED * added functions 'nested.datlist2datlist' and 'datlist2nested.datlist

• for converting nested multiply and multiply imputed datasets

NOTE * extended argument 'type' in 'save.data' for saving a dataset in

• multiple file formats

NOTE * added example for plausible value imputation in Amelia package

• in draw.pv.ctt.Rd (Example 1)

NOTE * added 'print' methods for 'mids.1chain' and 'mids.nmi' objects

• (the method is equivalent to 'summary')

NOTE * exported 'write.fwf2' and 'read.fwf2' for writing and reading

• files in fixed width format

NOTE * added utility function 'VariableNames2String' for handling

• variable names which should be converted into strings

ADDED * added utility function 'write.datlist' for writing multiply

• imputed datasets

ADDED * included function 'mi_dstat' for relating missingness

• indicators to covariates

DATA * included/modified datasets:

EXAMP * included/modified examples: scale_datlist (1), save.data (1

• pool.mids.nmi (1,2), pool_mi (1), subset_datlist (1,2), datlist2mids (1), with.miceadds (1,2), scan.vec (1), nestedList2List (1), datlist_create (4), save.data (1), draw.pv.ctt (1), write.fwf2 (1), data.graham (1,2), VariableNames2String (1), write.datlist (1), mi_dstat (1)

miceadds 1.6

NOTE * included argument 'X' in 'mids2datlist' and 'mids2mlwin'

• which allows the inclusion of further variables in list of multiply imputed datasets

NOTE * output of function 'mids2datlist' is now of class 'datlist'

• or 'nested.datlist'

ADDED * extended weighted statistics 'ma.wtd.statNA' to (nested

• multiply imputed datasets

NOTE * included 'datlist_create' and 'nested.datlist_create' utility

• function

NOTE * changed estimation method in imputation of latent group means

• in 'mice.impute.2l.latentgroupmean' to MCMC estimation using the MCMCglmm package

ADDED * added 'scale_datlist' for adding a standardized variable to a

• list of multiply imputed datasets

NOTE * cleaned namespace file and defined imported functions

• in a more explicit way

DATA * included/modified datasets:

EXAMP * included/modified examples: mids2datlist (3),

• ma.wtd.statNA (1,2,3), datlist_create (1,2), scale_datlist (1,2), cxxfunction.copy (1)

miceadds 1.5

NOTE * changed function 'save.data' due to changes in a recent sjmisc

• package update on CRAN

DATA * included/modified datasets:

EXAMP * included/modified examples:

miceadds 1.4

NOTE * included argument 'suffix' in 'save.data' for easier

• inclusion of parts of file names when saving data

FIXED * fixed a bug in imputation method '2l.latentgroupmean

• (reported by Simon Grund)

ADDED * added Spearman rank correlation for 'micombine.cor' and

• an example for statistical inference for Kendalls tau (see 'micombine.cor', Example 2) (suggested by Kathleen Gali)

DATA * included/modified datasets:

EXAMP * included/modified examples: micombine.cor (2

miceadds 1.3

ADDED * added imputation method 'grouped' for grouped (coarsed) data

ADDED * included 'NMIcombine' function as an extension to

• 'MIcombine' (mitools package) to nested multiply imputed datasets

ADDED * included function 'NMIwaldtest' which performs a multi

• parameter Wald test for nested multiply imputed datasets

NOTE * added argument 'extend' in 'fast.groupmean' which is useful

• for the inclusion of group means in original datasets

ADDED * added D1 statistic (Wald test) 'MIwaldtest' as a

• multiparameter test for multiply imputed datasets

FIXED * fixed a bug in 'lm.cluster' and 'glm.cluster'.

NOTE * The 'cluster' argument in 'lm.cluster' now allows vector input

NOTE * included datasets from missing data book of Graham (data.graham)

NOTE * included some examples of the jomo package

NOTE * added argument 'NMI' in 'NMIcombine' function which now also

• allows input for non-nested multiple imputation

ADDED * added 'NMIextract' function as an extension of 'MIextract

• (mitools package) to nested multiply imputed datasets

NOTE * added utility function 'library_install' which loads packages

• and conducts installations if required

DATA * included/modified datasets: data.ma06, data.graham

EXAMP * included/modified examples: mice.impute.grouped (1

• pool.mids.nmi (1.4,1.5), NMIwaldtest (1,2), fast.groupmean (1), lm.cluster (1,2), jomo2datlist (1), pool.mids.nmi (1), library_install (1)

miceadds 1.2

NOTE * fixed a bug in 'load.data' for loading datasets of type 'table

ADDED * included utility function 'mids2mlwin' for writing MLwiN files

• (contributed by Thorsten Luka)

NOTE * added suggestions to sav file writing functions in haven and

• sjmisc packages

NOTE * removed dependency on PSPP for writing sav files in 'save.data

• Now, the function 'write_spss' from the sjmisc package is used.

NOTE * added further values in 'systime' function

ADDED * added a utility function 'visitSequence.determine' for

• determining visit sequence for an imputation model when passive variables are involved

ADDED * added function 'mice.nmi' for conducting nested multiple

• imputation generating objects of class 'mids.nmi'

ADDED * extended 'complete' function from mice package for objects of

• classes 'mids.1chain' (function 'complete.mids.1chain') and 'mids.nmi' (function 'complete.mids.nmi')

ADDED * extended 'mids2datlist' for objects of class 'mids.nmi

ADDED * added 'with' S3 method for objects of class 'mids.1chain' and

• 'mids.nmi' producing objects of class 'mira' (defined in mice) and 'mira.nmi'. For 'mira.nmi', a summary method is defined.

ADDED * added 'within' S3 methods for objects of class 'imputationList

• (which are defined in the mitools package)

ADDED * added statistical inference for nested multiply imputed datasets

• in 'pool.mids.nmi' function

ADDED * added functions 'lm.cluster' and 'glm.cluster' for cluster robust

• standard errors for 'lm' and 'glm' functions using the multiwaycov package (and the function 'cluster.vcov' therein)

ADDED * added function 'NestedImputationList' function for creating objects

• of class 'NestedImputationList'. S3 Methods 'with' and 'within' are defined for operating on this list of lists of datasets. The S3 method 'MIcombine' (from mitools package) is extended to objects of class 'Nested ImputationResultList'.

DATA * included/modified datasets:

EXAMP * included/modified examples: write.pspp (1), save.data (1

• systime (1), visitSequence.determine (1), datalist2mids (1), mice.nmi (1), complete.miceadds (1,2), mids2datlist (2), with.miceadds (1,2), pool.mids.nmi (1), lm.cluster (1), NestedImputationList (1)

miceadds 1.1

NOTE * extended 'datalist2mids' function to handle a single dataset

ADDED * included plausible value imputation via a provided

• individual likelihood

NOTE * included row.names argument and missing value argumant

• in 'save.data'

DATA * included/modified datasets:

EXAMP * included/modified examples: mice.impute.2l.plausible.values (2

miceadds 1.0 (2014-11-08)

NOTE * fixed a minor bug in write.pspp when a variable only

• contains values of zero

NOTE * allow specification of a part of the file name in 'load.data

• the most recent file is loaded

DATA * included/modified datasets:

EXAMP * included/modified examples:

miceadds 0.14

ADDED * included Type 3 sum of squares in ANOVA in 'mi.anova

• (thanks to Florian Buchwald)

ADDED * included a function 'load.Rdata2' which prevents from

• the definition of the output in the global environment as in 'load.Rdata'

ADDED * included utility function 'load.data' and 'save.data

• for loading and saving data files from and to several formats

DATA * included/modified datasets:

EXAMP * included/modified examples: mi.anova (1), load.Rdata

• load.data, save.data

miceadds 0.13

ADDED * included several R utility functions

DATA * included/modified datasets:

EXAMP * included/modified examples:

miceadds 0.12

FIXED * included bug fixes for 'mice.impute.2lonly.pmm' (mice version

• 2.21) as 'mice.impute.2lonly.pmm2' in miceadds -> the same for 'mice.impute.2lonly.norm'

DATA * included/modified datasets:

EXAMP * included/modified examples:

miceadds 0.11

FIXED * fixed a bug in tw.mcmc.imputation for rows with only missings

ADDED * included function write.pspp for writing SPSS files using PSPP

ADDED * included predict method for kernelpls.fit2 function

NOTE * export and extended fast.groupmean function to include weights

NOTE * export mice.impute.2l.pls and mice.impute.2l.pls2

FIXED * fixed a bug in the creation of interactions in

• mice.impute.2l.pls (thanks to Takuya Yanagida)

NOTE * included calculation of weighted covariance matrix with missing

• entries in datasets

ADDED * included mice.impute.pmm3, mice.impute.pmm4, mice.impute.pmm5 and

• mice.impute.pmm6

NOTE * included scale2 as a faster substitute for the scale function in R

ADDED * included mice.1chain as an alternative to the mice function

• which multiply imputes data from a long chain

ADDED * included imputation function 'mice.impute.2l.eap' for imputation

• from a known (normal) posterior distribution

ADDED * included function mids2datlist for conversion of a mids object

• into a list of datasets

NOTE * included datasets: all datasets contained in the package

NOTE * included examples: for all functions

• #### older miceadds versions (formerly micetrun)

miceadds 0.10

miceadds 0.8

miceadds 0.7

miceadds 0.6

miceadds 0.5

miceadds 0.4

miceadds 0.3

miceadds 0.2

miceadds 0.1