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

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

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

miceadds:  Some additional multiple imputation functions, 
           especially for mice


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

Alexander Robitzsch, Simon Grund & Thorsten Henke

Questions or suggestions about miceadds should be sent to

Alexander Robitzsch
robitzsch@ipn.uni-kiel.de

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

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


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





--------------------------------------------------------------------------
VERSIONS miceadds 3.17  |  2024-01-08  |  Last: miceadds 3.17-44
--------------------------------------------------------------------------
 
ADDED * added argument 'derived_vars' in mice.impute.pls() for including
        derived variables in PLS dimension reduction
        (requested by Karoline Sachse)
FIXED * fixed specification issues in mice.1chain()
NOTE  * rechanged functionality of systime() due to changes of the 
        Sys.time() function since R 4.3.1
NOTE  * complete functions in miceadds are now declared as a method in
        the manual. Moreover, renamed argument 'x' into 'data'
        (requested by Kurt Hornik from the CRAN team)

DATA  * ---
EXAMP * mice.impute.pls (1), lm.cluster (3)

--------------------------------------------------------------------------
VERSIONS miceadds 3.16  |  2023-01-06  |  Last: miceadds 3.16-18
--------------------------------------------------------------------------
 
NOTE  * allow RDS objects in load.data() and save.data()
NOTE  * added argument 'RDS' in load.Rdata2()
NOTE  * automatically create missing directories in calls 
        of files_move()
ADDED * added function for generating synthetic data syn_da()
        based on the data augmentation method of Jiang et al. (2022)
FIXED * fixed an issue of not runnable models in 'ml.lmer' imputation 
        method when random slopes are used (thanks to Rushani Wijesuriya)
FIXED * tried to avoid numerical issue in 'mice.impute.pls' by including
        several numerical checks (thanks to Karoline Sachse)

DATA  * data.ma09
EXAMP * ---

--------------------------------------------------------------------------
VERSIONS miceadds 3.15  |  2022-09-22  |  Last: miceadds 3.15-21
--------------------------------------------------------------------------
 
ADDED * included utility function datlist2Amelia()
        (suggested by @atanasj, Github Issue #26)
ADDED * added imputation function mice.impute.catpmm() that performs
        multivariate predictive mean matching for categotical variables
NOTE  * included imputation method 'catpmm' in mice.impute.pls()

DATA  * ---
EXAMP * datlist2Amelia (1), mice.impute.catpmm (1)

--------------------------------------------------------------------------
VERSIONS miceadds 3.14  |  2022-08-24  |  Last: miceadds 3.14-3
--------------------------------------------------------------------------
 
NOTE  * fixed issues in CRAN checks due to the recent use 
        of KaTeX

DATA  * ---
EXAMP * ---

--------------------------------------------------------------------------
VERSIONS miceadds 3.13  |  2022-05-30  |  Last: miceadds 3.13-12
--------------------------------------------------------------------------
 
FIXED * fixed an issue with automatic removal of predictors in lme4::lmer()
        for imputation methods '2l.norm' and '2l.pmm'
        (thanks to Adam Kuczynski)

DATA  * ---
EXAMP * ---

---------------------------------------------------------------------
VERSIONS miceadds 3.12  |  2022-04-04  |  Last: miceadds 3.12-26
---------------------------------------------------------------------

FIXED * fixed a bug in syn.mice()
FIXED * fixed a bug in pool.mids.nmi()
        (thanks to Francis Huang @flh3, Github issue #21)
NOTE  * fixed memory issues in mice.impute.weighted.norm() and
        and mice.impute.weighted.pmm() 
        (thanks to Ryan Jarrett @jarretrt, Github issue #22)
FIXED * fixed incorrect matching in mice.impute.weighted.pmm()
        (thanks to Ryan Jarrett @jarretrt, Github issue #23)
FIXED * fixed a bug in imputation method 'ml.lmer' when no
        aggragated variables are used
ADDED * added argument 'iter_re' in mice.impute.ml.lmer()
ADDED * added argument 'elim' in gm() and GroupMean()
NOTE  * fixed issues in Rcpp code: warning: use of bitwise '&' 
        with boolean operands [-Wbitwise-instead-of-logical]
        (https://cran.r-project.org/web/checks/check_results_miceadds.html;
        communicated by Kurt Hornik)
NOTE  * no longer export mice.impute.grouped() because
        dependent grouped package is no longer available on CRAN

DATA  * included/modified datasets: ---
EXAMP * included/modified examples: syn.mice (1)

---------------------------------------------------------------------
VERSIONS miceadds 3.11  |  2021-01-21  |  Last: miceadds 3.11-6
---------------------------------------------------------------------

FIXED * fixed a bug in ml_mcmc() when using the argument
        'inits_lme4=FALSE' (thanks to a discussion with
        Rushani Wijesuriya regarding the mdmb::frm_fb() function)

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

---------------------------------------------------------------------
VERSIONS miceadds 3.10  |  2020-07-29  |  Last: miceadds 3.10-28
---------------------------------------------------------------------

ADDED * added wrapper function syn.mice() for including mice imputation
        methods for use in synthpop package for synthesizing data
ADDED * added synthesizing method syn.constant() for using fixed
        values of a variable.
ADDED * included imputation method mice.impute.constant() for
        imputation of a known vector of values
ADDED * added wrapper function mice.impute.synthpop() for using a
        synthpop synthesizing method in the mice package
ADDED * function syn_mice() allows generation of synthesized data
        using mice imputation methods

DATA  * included/modified datasets: ---
EXAMP * included/modified examples: syn.mice (1), syn.constant (1),
        mice.impute.synthpop (1), syn_mice (1), 
        mice.impute.constant(1)

---------------------------------------------------------------------
VERSIONS miceadds 3.9  |  2020-05-09  |  Last: miceadds 3.9-14
---------------------------------------------------------------------

FIXED * fixed a bug in mice.impute.smcfcs() (thanks to Bryor Snefjella)
NOTE  * included example of substantive model with quadratic effects in
        mice.impute.smcfcs() (provided by Bryor Snefjella)
ADDED * included wrapper imputation functions to imputeR package in
        mice.impute.imputeR.lmFun() and mice.impute.imputeR.cFun()
ADDED * included wrapper imputation methods to simputation package
        in mice.impute.simputation() function
        
DATA  * included/modified datasets: ---
EXAMP * included/modified examples: mice.impute.smcfcs (2),
        mice.impute.imputeR.lmFun (1), mice.impute.simputation (1)

---------------------------------------------------------------------
VERSIONS miceadds 3.8  |  2020-02-17  |  Last: miceadds 3.8-9
---------------------------------------------------------------------

NOTE  * included '\dontrun{}' in ?jomo2datlist (due to changes in
        mice package; requested by Stef van Buuren)
FIXED * fixed handling of factor levels in subset_datlist()
        (thanks to @jwilliman; Github issue #20)

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

---------------------------------------------------------------------
VERSIONS miceadds 3.7  |  2019-12-15  |  Last: miceadds 3.7-6
---------------------------------------------------------------------

FIXED * changes in ma.wtd.stats() functions because since R 4.0
        matrices are also of class "array" which causes ambiguity
        in code evaluation (requested by CRAN checks)

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

---------------------------------------------------------------------
VERSIONS miceadds 3.6  |  2019-11-04  |  Last: miceadds 3.6-21
---------------------------------------------------------------------

FIXED * fixed a bug in ma.wtd.covNA() and ma.wtd.corNA() functions
        (thanks to Thomas Kiefer)
NOTE  * subset_datlist() now also works for list of datasets with
        unequal number of cases (thanks to Michael Grosche)
NOTE  * added an example involving partial correlations in
        micombine.cor() (thanks to Carolin Just)
NOTE  * allow vector argument of variables of 'partial' in 
        micombine.cor()
FIXED * fixed a bug with handling factor variables in 
        mice.impute.2lonly.function()
        (thanks to @markseeto, Github issue #19)

DATA  * included/modified datasets: ---
EXAMP * included/modified examples: micombine.cor (1)

---------------------------------------------------------------------
VERSIONS miceadds 3.5  |  2019-08-23  |  Last: miceadds 3.5-14
---------------------------------------------------------------------

FIXED * fixed issue with missing type argument in user-defined
        imputation models in mice.impute.pls() function
FIXED * fixed a bug in pool.mids.nmi() due to changes in 
        arguments in mice::pool() function
        (thanks to Christian Schwahn)
NOTE  * corrected an error in manual for subset_datlist() for
        argument 'expr_subset' (thanks to Michael Grosche)

DATA  * included/modified datasets: ---
EXAMP * included/modified examples: subset_datlist (1,2)

---------------------------------------------------------------------
VERSIONS miceadds 3.4  |  2019-06-19  |  Last: miceadds 3.4-17
---------------------------------------------------------------------

FIXED * fixed a bug with missing parameter names in MIwaldtest()
        (thanks to Joost van Ginkel)
FIXED * fixed issues in cases with one or no predictors in
        mice.impute.ml.lmer()
FIXED * fixed bug in mice.impute.ml.lmer() with more than one random
        effect if lme4 automatically changes the order of random
        effects in model output
NOTE  * handle cases of removed predictors in mice.impute.ml.lmer()
        by lme4::lmer() function (thanks to Rushani Wijesuriya)

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

---------------------------------------------------------------------
VERSIONS miceadds 3.3  |  2019-05-11  |  Last: miceadds 3.3-33
---------------------------------------------------------------------

ADDED * added imputation methods "rlm", "lqs", "lm" and "lm_fun"
        based on robust and non-robust linear models and 
        transformations of dependent variable
NOTE  * included argument 'col1_numeric' in split_to_matrix()
NOTE  * corrected a mistake in ?mice.impute.ml.lmer manual
        (thanks to Rima Izem)
ADDED * included argument 'remove_lindep' in mice.impute.pls()
        which allows to enable the procedure for removing predictors
NOTE  * replaced multiwaycov package by sandwich package in
        lm.cluster() and glm.cluster (thanks to @jaySf, Github issue #16).
        Included arguments 'weights' and 'subset' in these functions.
NOTE  * included argument 'donors' in mice.impute.pls()

DATA  * included/modified datasets: ---
EXAMP * included/modified examples: mice.impute.rlm (1),
        filename_split (5), mice.impute.ml.lmer (1)

---------------------------------------------------------------------
VERSIONS miceadds 3.2  |  2019-04-15  |  Last: miceadds 3.2-48
---------------------------------------------------------------------

NOTE  * changed default 'inits_lme4=TRUE' to 'inits_lme4=FALSE' (do not
        use lme4::lmer() for starting values) in ml_mcmc()
NOTE  * use optimizer 'bobyqa' by default in multilevel imputations which 
        rely on lme4 package (mice.impute.2l.foo() for foo="pmm","binary"
        and "continuous" and mice.impute.ml.lmer()) if a 'control' argument 
        is not provided to lme4::lmer() or lme4::glmer()
FIXED * fixed a bug in handling arguments in mice.impute.ml.lmer()
FIXED * fixed a bug in ma.wtd.statsNA() functions for objects of class
        BIFIEdata if a statistic for a single variable is requested
        (thanks to Peter Lenz)
NOTE  * included argument 'ridge' in ml_mcmc() and ml_mcmc_fit() for
        stabilizing MCMC sampling in case of convergence issues
NOTE  * change in computing matches for weighted predictive mean matching
        (function mice.impute.weighted.pmm())
FIXED * fixed a bug in NMIcombine() with inference of a single parameter
NOTE  * included example of using mice.impute.pls() at the level of
        a variable
FIXED * fixed a bug in formula handling of ml_mcmc()
ADDED * included option for Bayesian bootstrap in mice.impute.pls()
        by requesting 'use_boot=TRUE'
NOTE  * included argument 'wt' in pca.covridge()
NOTE  * exported utility function mice_imputation_get_states()
NOTE  * included argument 'wy' in mice.impute.weighted.norm(),
        mice.impute.weighted.pmm(), mice.impute.bygroup() and
        mice.impute.2lonly.function()
NOTE  * changed internal handling of grouping variable in
        mice.impute.bygroup() (due to an example provided by 
        Sandro Tsang; Github issue #15)
ADDED * included substantive model compatible imputation in
        mice.impute.smcfcs() method
NOTE  * removed mice.impute.2l.eap() function

DATA  * included/modified datasets: ---
EXAMP * included/modified examples: mice.impute.ml.lmer (1.2),
        mice.impute.pls (1), mice.impute.smcfcs (1)

---------------------------------------------------------------------
VERSIONS miceadds 3.1  |  2019-03-18  |  Last: miceadds 3.1-37
---------------------------------------------------------------------

NOTE  * included argument '...' in grep.vec() for passing arguments to
        base::grep() (thanks to Boris Girnat)
NOTE  * handle now strings of length one in string_to_matrix()
FIXED * fixed labeling issue in ma.wtd.corNA() functions when applied
        to BIFIEdata objects (thanks to Peter Lenz)
NOTE  * fixed a bug in Example 2 of ?NMIWaldtest caused by changes in
        mice::pool() output (thanks to Joost van Ginkel)
NOTE  * included argument 'path2_name' in files_move()
ADDED * included arguments 'psi_nu0_list' and 'psi_S0_list' in ml_mcmc()
        for specification of inverse Wishart prior distribution for
        covariance matrix of random effects
FIXED * fixed a bug in ml_mcmc() when formula arguments was used
NOTE  * changed default to noninformative prior distributions in
        ml_mcmc(), i.e. nu0=-3 scale degrees of freedom and zero
        diagonal scale matrix
NOTE  * changed default argument values of 'type' in load.data() and
        load.files() to 'NULL'
NOTE  * fixed warning message of incorrect argument use of 
        'imputationMethod' in datalist2mids() (thanks to Valentin Fuchs) 
NOTE  * Replaced all remaining 'imputationMethod' arguments in 
        mice::mice() by 'method' in the manual
NOTE  * allowed factor variables for PMM imputation methods 'pmm3',
        'pmm4', 'pmm5', 'pmm6', '2l.contextual.pmm', '2l.pmm',
        'bygroup', '2lonly.function', 'ml.lmer', 'pls',
        'tricube.pmm', 'tricube.pmm2'
NOTE  * imputation method 'tricube.pmm2' is renamed as 'tricube.pmm'.
        The imputation method 'tricube.pmm2' is now defunct.
ADDED * added import format 'xlsx' (or 'xls') in load.data() function
        using the readxl::read_excel function (package readxl is now 
        included in list of 'Suggests' packages)
ADDED * added user-defined data input function in load.data() by
        including the argument 'load_fun'

DATA  * included/modified datasets: ---
EXAMP * included/modified examples: filename_split (4),
        NMIWaldtest (2), mi.anova (1), load.data (1)

---------------------------------------------------------------------
VERSIONS miceadds 3.0  |  2018-12-11  |  Last: miceadds 3.0-16
---------------------------------------------------------------------

NOTE  * included separator "\t" in scan.vec() (thanks Thomas Kiefer)
FIXED * fixed bug in 'summary' method of glm.cluster() 
        (thanks to tra6sdc; Github issue #14)
NOTE  * included utility function load.files() for reading multiple
        files in a data frame
NOTE  * corrected a bug in mice.impute.2l.pls2() and in Example 1 of
        ?mice.impute.pls (thanks to a discussion with Peter Lenz)

DATA  * included/modified datasets: ---
EXAMP * included/modified examples: scan.vec (1)

---------------------------------------------------------------------
VERSIONS miceadds 2.15  |  2018-10-19  |  Last: miceadds 2.15-22
---------------------------------------------------------------------

NOTE  * internal changes in mice.imputation.ml.lmer() caused
        by application within mice.impute.bygroup() imputation method
        (thanks to Sophie Stallasch; Github issue #12)
NOTE  * renamed ma.wtd.curtosisNA() into ma.wtd.kurtosisNA()
ADDED * included simulation function fleishman_sim() for generating
        non-normal data based on Fleishman polynomial
ADDED * included simulation functions  nnig_sim() and nnig_coef()
        for simulating multivariate linearly related non-normally
        distributed variables (Foldnes & Olsson, 2016)

DATA  * included/modified datasets: ---
EXAMP * included/modified examples: ma.wtd.statNA (1), fleishman_sim (1),
        nnig_sim (1)

---------------------------------------------------------------------
VERSIONS miceadds 2.14  |  2018-09-18  |  Last: miceadds 2.14-26
---------------------------------------------------------------------

NOTE  * corrected Example 2 in ?micombine.cor (thanks to jamesrrae; #9)
FIXED * fixed a bug in mice.impute.bygroup() with two-level imputation
        models if factor variables are used (see Example 2 in
        ?mice.impute.bygroup)
FIXED * fixed numerical problems when principal component analysis
        is used for dimension reduction
NOTE  * included some examples of using mice::make.predictorMatrix()
        and mice::make.method() functions in the miceadds manual
NOTE  * included argument 'pls.facs' for PLS dimension reduction in
        mice.impute.2l.contextual.pmm() and mice.impute.2l.contextual.norm()
        (communicated by Laura Helbling)

DATA  * included/modified datasets: ---
EXAMP * included/modified examples: micombine.cor (2),
        mice.impute.bygroup (2), mice.impute.2l.contextual.pmm (1)

---------------------------------------------------------------------
VERSIONS miceadds 2.13  |  2018-07-05  |  Last: miceadds 2.13-63
---------------------------------------------------------------------

ADDED * included group mean function gm() and centering around
        group mean function cwc()
NOTE  * included utility functions ma_lme4_formula_terms() and 
        ma_lme4_formula_design_matrices() for handling lme4 formulas 
        and generating design matrices for mixed effects models
FIXED * fixed a bug in mice.impute.weighted.norm() and ...pmm()
        due to recent changes in mice 3.0
ADDED * added MCMC function ml_mcmc() and ml_mcmc_fit() for 
        estimating mixed effects models. Exported several 
        sub-functions of ml_mcmc().
NOTE  * included utility function string_to_matrix() for
        converting string vectors into matrices
NOTE  * added utility functions filename_split_vec() and
        Rcppfunction_remove_classes()
ADDED * added functions lmer_vcov() and lmer_pool() for inference
        of lme4 models for multiply imputed datasets

DATA  * included/modified datasets: data.ma08
EXAMP * included/modified examples: GroupMean (2),
        ma_lme4_formula_terms (1,2), ml_mcmc (1), filename_split(3), 
        Rfunction_include_argument_values (1), lmer_vcov (1,2)

---------------------------------------------------------------------
VERSIONS miceadds 2.12  |  2018-06-06  |  Last: miceadds 2.12-24
---------------------------------------------------------------------

NOTE  * internal restructure of functions NMIwaldtest() and
        MIwaldtest()
FIXED * fixed broken functions due to changes in recent CRAN
        version mice 3.0.0 (communicated by Stef van Buuren):
        mice.impute.plausible.values(), mice.1chain(), 
        mice.impute.ml.lmer(), mice.impute.2l.pls2()
ADDED * added utility function mice_inits(), ma_exists_get(),
        ma_exists()
NOTE  * included argument 'remove_empty' in string_extract_part()
NOTE  * included argument 'cluster_var' for specifying cluster-level
        variable in mice.impute.2lonly.function()

DATA  * included/modified datasets: ---
EXAMP * included/modified examples: mice.impute.plausible.values (1),
        mice_inits (1)

---------------------------------------------------------------------
VERSIONS miceadds 2.11  |  2018-05-21  |  Last: miceadds 2.11-87
---------------------------------------------------------------------

ADDED * included utility Rcpp sourcing function source.Rcpp.all()
NOTE  * included utility functions Revalpr_maxabs() and 
        Revalpr_round()
FIXED * fixed bug in Rfunction_include_argument_values() when some
        arguments contain parentheses
FIXED * fixed a bug in mice.1chain() with implausible input arguments
        (communicated by Linying Ji)
FIXED * corrected a bug in ANSI_create_table() if only one empty row
        or column should be included
NOTE  * included utility functions grep_leading(), grepvec_leading()
        and grepvec()
NOTE  * included utility function rcpp_create_header_file() for
        writing cpp header files
FIXED * fixed a bug in mice.impute.pmm6() which caused installation
        problems (thanks to Stef van Buuren)
NOTE  * changed output in datalist2mids() due to changes of data type
        of 'visitSequence' in mice (>= 3.0) (requested by Stef 
        van Buuren; Github miceadds ...\6#issuecomment-390218252)
NOTE  * handle also character input of visit sequence in 
        visitSequence.determine() for coming changes in mice (>= 3.0)

DATA  * included/modified datasets: ---
EXAMP * included/modified examples: grep.vec (1)

---------------------------------------------------------------------
VERSIONS miceadds 2.10  |  2018-03-29  |  Last: miceadds 2.10-14
---------------------------------------------------------------------

FIXED * fixed a bug in mice.impute.bygroup() if only one predictor
        variable is used
FIXED * fixed a bug in mice.impute.bygroup() whoch was caused by using
        the recently included "wy" argument in the mice package
NOTE  * modified mice.impute.bygroup() function for groupwise 
        imputation with multilevel imputation methods ("2l" functions)
NOTE  * fixed numerical instabilities in plausible values imputation
        method
NOTE  * included argument 'control_latreg' in imputation method
        'plausible.values' for providing control arguments for 
        function TAM::tam.latreg()
NOTE  * excluded some packages from list of package 'Suggests'

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

---------------------------------------------------------------------
VERSIONS miceadds 2.9  |  2017-12-18  |  Last: miceadds 2.9-15
---------------------------------------------------------------------

FIXED * replaced the modified pmm6() imputation method causing a bug
        by a previous one (thanks to Peter Lenz)
NOTE  * included ridge operator for covariance matrix of predictors
        in mice.impute.plausible.values()
FIXED * fixed a bug in case of perfectly correlated regression
        coefficients in mice.impute.plausible.values()

DATA  * included/modified datasets: ---
EXAMP * included/modified examples: mice.impute.plausible.values (3)

---------------------------------------------------------------------
VERSIONS miceadds 2.8  |  2017-11-20  |  Last: miceadds 2.8-24
---------------------------------------------------------------------

NOTE  * changed default value of argument 'progress' in 
        datalist2mids() to FALSE
NOTE  * included utility functions in_CI() and string_extract_part()
NOTE  * changed names of imputation methods mice.impute.2l.latentgroupmean.ML()
        and mice.impute.2l.latentgroupmean.MCMC() to
        mice.impute.2l.latentgroupmean.ml() and 
        mice.impute.2l.latentgroupmean.mcmc()
NOTE  * changed function name of internal function mice.impute.2l.lmer()
        to mice_impute_2l_lmer() to avoid confusion because a function 
        mice::mice.impute.2l.lmer() has been recently included in the 
        mice package
NOTE  * added example for computing global F-test in lm.cluster()
        (suggested by Thiemo Knaust)        

DATA  * included/modified datasets: ---
EXAMP * included/modified examples: in_CI (1), filenames_split (2),
        lm.cluster (2)

---------------------------------------------------------------------
VERSIONS miceadds 2.7  |  2017-08-24  |  Last: miceadds 2.7-19
---------------------------------------------------------------------

ADDED * added function jomo2mids() which converts imputation output 
        of the jomo package into an object of class mids
FIXED * fixed a bug in mice.impute.2l.pls2() which did not find 
        a C routine in .Call()
ADDED * added imputation function mice.impute.ml.lmer() for imputation
        models based on the linear mixed effects specification in
        lme4. Hierarchical and non-hierarchical levels are allowed and
        imputation at higher levels is accomodated.
NOTE  * added utility functions ma_rmvnorm(), 
        Rfunction_include_argument_values() and
        Rfunction_output_list_result_function()

DATA  * included/modified datasets: data.ma07
EXAMP * included/modified examples: jomo2datlist (1), 
        mice.impute.ml.lmer (1), ma_rmvnorm (1),
        Rfunction_include_argument_values (1)

---------------------------------------------------------------------
VERSIONS miceadds 2.6  |  2017-08-09  |  Last: miceadds 2.6-21
---------------------------------------------------------------------

NOTE  * removed MASS package from 'Imports'. 
        Moved blme, car, foreign, grouped, MCMCglmm, multiwayvcov 
        and sjlabelled packages from 'Imports' to 'Suggests'. 
        Included hmi and micemd packages in 'Suggests'.
NOTE  * added comments about hmi and micemd packages in the manual
        of mice.impute.2l.lmer.Rd.
ADDED * added functionality for string variables in 'write.fwf2'
        (suggested by Tung Nguyen) 

DATA  * included/modified datasets: ---
EXAMP * included/modified examples: write.fwf2 (2)

---------------------------------------------------------------------
VERSIONS miceadds 2.5  |  2017-06-17  |  Last: miceadds 2.5-9
---------------------------------------------------------------------

NOTE  * fixed an incorrect description in the manual of 'micombine.F'
        and 'micombine.chisquare' (thanks to Tobias Rolfes)
NOTE  * dependency for writing SPSS data to the sjmisc packahe in 
        save.data function has been changed to the sjlabelled package
        because imported functions were moved from sjmisc to sjlabelled
        (requested by the maintainer Daniel Luedecke)

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

---------------------------------------------------------------------
VERSIONS miceadds 2.4  |  2017-04-19  |  Last: miceadds 2.4-12
---------------------------------------------------------------------

NOTE  * included argument 'draw.fixed' in 'mice.impute.2l.latentgroupmean.MCMC'
        which allows to specify whether fixed effects parameters
        should be sampled or not in imputation
NOTE  * included 'mice.impute.2l.pls2' from previous miceadds versions
        to ensure backward compatability 

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

---------------------------------------------------------------------
Versions 2.3  -- 2017-02-21  --  CRAN miceadds 2.3-0
---------------------------------------------------------------------

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)

---------------------------------------------------------------------
Versions 2.2  -- 2017-01-11  --  CRAN miceadds 2.2-0
---------------------------------------------------------------------

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)

---------------------------------------------------------------------
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
