+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

----------------------- miceadds NEWS -------------------------

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

miceadds:  Some additional multiple imputation functions, 
           especially for mice


                         (\-.
                         / _`> .---------.
                 _)     / _)=  |'-------'|
                (      / _/    |O   O   o|
                 `-.__(___)_   | o O . o |
                               `---------'
   
                                          oo__
                                         <;___)------
                                    oo__   " "
                                   <;___)------     oo__
                                     " "           <;___)------
                                                     " "

Alexander Robitzsch

Questions or suggestions about miceadds can be sent to
robitzsch@ipn.uni-kiel.de

In case of bug reporting, please always provide a
reproducible script.

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CHANGELOG miceadds
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

---------------------------------------------------------------------
Versions 2.1  -- 2016-11-25  --  CRAN miceadds 2.1-0
---------------------------------------------------------------------

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)

---------------------------------------------------------------------
Versions 2.0  -- 2016-08-29  --  CRAN miceadds 2.0-0
---------------------------------------------------------------------

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)

---------------------------------------------------------------------
Versions 1.9  -- 2016-07-13  --  CRAN miceadds 1.9-0
---------------------------------------------------------------------

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)

---------------------------------------------------------------------
Versions 1.8  -- 2016-05-31  --  CRAN miceadds 1.8-0
---------------------------------------------------------------------

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)

---------------------------------------------------------------------
Versions 1.7  -- 2016-02-18  --  CRAN miceadds 1.7-8
---------------------------------------------------------------------

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)

---------------------------------------------------------------------
Versions 1.6  -- 2016-01-30  --  CRAN miceadds 1.6-0
---------------------------------------------------------------------

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) 

---------------------------------------------------------------------
Versions 1.5  -- 2015-11-21  --  CRAN miceadds 1.5-0
---------------------------------------------------------------------

NOTE  * changed function 'save.data' due to changes in a recent sjmisc
        package update on CRAN

DATA  * included/modified datasets: ---
EXAMP * included/modified examples: ---

---------------------------------------------------------------------
Versions 1.4  -- 2015-11-04  --  CRAN miceadds 1.4-0
---------------------------------------------------------------------

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)

---------------------------------------------------------------------
Versions 1.3  -- 2015-07-10  --  CRAN miceadds 1.3-0
---------------------------------------------------------------------

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)

---------------------------------------------------------------------
Versions 1.2  -- 2015-05-20  --  CRAN miceadds 1.2-0
---------------------------------------------------------------------

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)        

---------------------------------------------------------------------
Versions 1.1  -- 2015-02-23  --  CRAN miceadds 1.1-1
---------------------------------------------------------------------

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)

---------------------------------------------------------------------
Versions 1.0  -- 2014-11-07  --  CRAN miceadds 1.0
---------------------------------------------------------------------

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: ---

---------------------------------------------------------------------
Versions 0.14 -- 2014-07-30  --  CRAN miceadds 0.14-9
---------------------------------------------------------------------

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

---------------------------------------------------------------------
Versions 0.13 -- 2014-06-27  --  CRAN miceadds 0.13-7
---------------------------------------------------------------------

ADDED * included several R utility functions

DATA  * included/modified datasets: ---
EXAMP * included/modified examples: ---

---------------------------------------------------------------------
Versions 0.12 -- 2014-05-08  --  CRAN miceadds 0.12-9
---------------------------------------------------------------------

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: ---

---------------------------------------------------------------------
Versions 0.11 -- 2014-02-19  --  CRAN miceadds 0.11-121
              [**** FIRST CRAN RELEASE ****]
---------------------------------------------------------------------

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)

Versions 0.10 -- 2013-08-18
Versions 0.8  -- 2012-10-18
Versions 0.7  -- 2012-06-18
Versions 0.6  -- 2011-11-29
Versions 0.5  -- 2011-06-02
Versions 0.4  -- 2008-05-31
Versions 0.3  -- 2008-04-07
Versions 0.2  -- 2008-03-27
Versions 0.1  -- 2007-10-21