-------------- MICE NEWS------------------------------------------- MICE: Multivariate Imputation by Chained Equations MICE is an R package implementing multiple imputation of incomplete multivariate data according the principle of Fully Conditional Specification (FCS). Question or suggestions about MICE can be send to stef.vanbuuren at tno.nl c.g.m.oudshoorn at utwente.nl CHANGELOG MICE ~~~~~~~~~~~~~~ V2.17 10-05-2013 SvB ADDED new form argument to mice() to specify imputation models using forms (contributed Ross Boylan) FIXED with.mids(), is.mids(), is.mira() and is.mipo() exported FIXED eliminated errors in the documentation of pool.scalar() FIXED error in mice.impute.ri() (thanks Shahab Jolani) V2.16 27-04-2013 SvB ADDED random indicator imputation by mice.impute.ri() for nonignorable models (thanks Shahab Jolani) ADDED workhorse functions .norm.draw() and .pmm.match() are exported FIXED bug in 2.14 and 2.15 in mice.impute.pmm() that produced an error on factors FIXED bug that crashed R when the class variable was incomplete (thanks Robert Long) FIXED bug in 2l.pan and 2l.norm by convert a class factor to integer (thanks Robert Long) FIXED warning eliminated caused by character variables (thanks Robert Long) V2.15 - 02-04-2013 SvB CHANGED complete reorganization of documentation and source files ADDED source published on GitHub.com ADDED new imputation method mice.impute.cart() (thanks Lisa Doove) FIXED calculation of degrees of freedom in pool.compare() (thanks Lorenz Uhlmann) FIXED error in DESCRIPTION file (thanks Kurt Hornik) V2.14 - 11-03-2013 / SvB ADDED mice.impute.2l.mean() for imputing class means at level 2 ADDED sampler(): new checks of degrees of freedom per variable at iteration 1 ADDED function check.df() to throw a warning about low degrees of freedom FIXED tolower() added in "2l" test in sampler() FIXED conversion of factors that have other roles (multilevel) in padModel() FIXED family argument in call to glm() in glm.mids() (thanks Nicholas Horton) FIXED .norm.draw(): evading NaN imputed values by setting df in rchisq() to a minimum of 1 FIXED bug in mice.df() that prevented the classic Rubin df calculation (thanks Jean-Batiste Pingaul) FIXED bug fixed in mice.impute.2l.norm() (thanks Robert Long) CHANGED faster .pmm.match2() from version 2.12 renamed to default .pmm.match() V2.13 - 03-07-2012 / SvB ADDED new multilevel functions 2l.pan(), 2lonly.norm(), 2lonly.pmm() (contributed by Alexander Robitzsch) ADDED new quadratic imputation function: quadratic() (contributed by Gerko Vink) ADDED pmm2(), five times faster than pmm() ADDED new argument data.init in mice() for initialization (suggested by Alexander Robitzsch) ADDED mice() now accepts pmm as method for (ordered) factors ADDED warning and a note to 2l.norm() that advises to use type=2 for the predictors FIXED bug that chrashed plot.mids() if there was only one incomplete variable (thanks Dennis Prangle) FIXED bug in sample() in .pmm.match() when donor=1 (thanks Alexander Robitzsch) FIXED bug in sample() in mice.impute.sample() FIXED fixed '?data' bug in check.method() REMOVED wp.twin(). Now available from the AGD package V2.12 - 25-03-2012 / SvB UPDATE version for launch of Flexible Imputation of Missing Data (FIMD) ADDED code fimd1.r-fim9.r to inst/doc for calculating solutions in FIMD FIXED more robust version of supports.transparent() (thanks Brian Ripley) ADDED auxiliary functions ifdo(), long2mids(), appendbreak(), extractBS(), wp.twin() ADDED getfit() function ADDED datasets: tbc, potthoffroy, selfreport, walking, fdd, fdgs, pattern1-pattern4, mammalsleep FIXED as.mira() added to namespace ADDED functions flux(), fluxplot() and fico() for missing data patterns ADDED function nelsonaalen() for imputing survival data CHANGED rm.whitespace() shortened FIXED bug in pool() that crashed on nonstandard behavior of survreg() (thanks Erich Studerus) CHANGED pool() streamlined, warnings about incompatibility in lengths of coef() and vcov() FIXED mdc() bug that ignored transparent=FALSE argument, now made visible FIXED bug in md.pattern() for >32 variables (thanks Sascha Vieweg, Joshua Wiley) V2.11 - 21-11-2011 / SvB UPDATED definite reference to JSS paper ADDED rm.whitespace() to do string manipulation (thanks Gerko Vink) ADDED function mids2mplus() to export data to Mplus (thanks Gerko Vink) CHANGED plot.mids() changed into trellis version ADDED code used in JSS-paper FIXED bug in check.method() (thanks Gerko Vink) V2.10 - 14-09-2011 / SvB FIXED: arguments dec and sep in mids2spss (thanks Nicole Haag) FIXED: bug in keyword "monotone" in mice() (thanks Alain D) V2.9 - 31-08-2011 / SvB FIXED: appropriate trimming of ynames and xnames in Trellis plots FIXED: exported: spss2mids(), mice.impute.2L.norm() ADDED: mice.impute.norm.predict(), mice.impute.norm.boot(), mice.impute.logreg.boot() ADDED: supports.transparent() to detect whether .Device can do semi-transparent colors FIXED: stringr package is now properly loaded ADDED: trellis version of plot.mids() ADDED: automatic semi-transparancy detection in mdc() FIXED: documentation of mira class (thanks Sandro Tsang) V2.8 - 24-03-2011 / SvB FIXED: bug fixed in find.collinear() that bombed when only one variable was left V2.7 - 16-03-2011 / SvB CHANGED: check.data(), remove.lindep(): fully missing variables are imputed if allow.na=TRUE (Alexander Robitzsch) FIXED: bug in check.data(). Now checks collinearity in predictors only (Alexander Robitzsch) CHANGED: abbreviations of arguments eliminated to evade linux warnings V2.6 - 03-03-2011 / SvB ADDED: bwplot(), stripplot(), densityplot() and xyplot() for creating Trellis graphs ADDED: function mdc() and mice.theme() for graphical parameters ADDED: argument passing from mice() to lower-level functions (requested by Juned Siddique) FIXED: erroneous rgamma() replaced by rchisq() in .norm.draw, lowers variance a bit for small n ADDED: with.mids() extended to handle expression objects FIXED: reporting bug in summary.mipo() CHANGED: df calculation in pool(), intervals may become slightly wider ADDED: internal functions mice.df() and df.residual() FIXED: error in rm calculation for "likelihood" in pool.compare() CHANGED: default ridge parameter changed V2.5 - 06-01-2011 / SvB ADDED: various stability enhancements and code clean-up ADDED: find.collinear() function CHANGED: automatic removal of constant and collinear variables ADDED: ridge parameter in .norm.draw() and .norm.fix() ADDED: mice.impute.polr() for ordered factors FIXED: chainMean and chainVar in mice.mids() FIXED: iteration counter for mice.mids and sampler() ADDED: component 'loggedEvents' to mids-object for logging actions REMOVED: annoying warnings about removed predictors ADDED: updateLog() function CHANGED: smarter handling of model setup in mice() CHANGED: .pmm.match() now draws from the three closest donors ADDED: mids2spss() for shipping a mids-object to SPSS FIXED: change in summary.mipo() to work with as.mira() ADDED: function mice.impute.2L.norm.noint() ADDED: function as.mira() FIXED: global assign() removed from mice.impute.polyreg() FIXED: improved handling of factors by complete() FIXED: improved labeling of nhanes2 data V2.4 - 17-10-2010 / SvB ADDED: pool() now supports class 'polr' (Jean-Baptiste Pingault) FIXED: solved problem in mice.impute.polyreg when one of the variables was named y or x FIXED: remove.lindep: intercept prediction bug ADDED: version() function ADDED: cc(), cci() and ccn() convenience functions V2.3 - 14-02-2010 / SvB FIXED: check.method: logicals are now treated as binary variables (Emmanuel Charpentier) FIXED: complete: the NULL imputation case is now properly handled FIXED: mice.impute.pmm: now creates between imputation variability for univariate predictor FIXED: remove.lindep: returns 'keep' vector instead of data V2.2 - 13-01-2010 / SvB ADDED: pool() now supports class 'multinom' (Jean-Baptiste Pingault) FIXED: bug fixed in check.data for data consisting of two columns (Rogier Donders, Thomas Koepsell) ADDED: new function remove.lindep() that removes predictors that are (almost) linearly dependent FIXED: bug fixed in pool() that produced an (innocent) warning message (Qi Zheng) V2.1 - 14-09-2009 / SvB ADDED: pool() now also supports class 'mer' CHANGED: nlme and lme4 are now only loaded if needed (by pool()) FIXED: bug fixed in mice.impute.polyreg() when there was one missing entry (Emmanuel Charpentier) FIXED: bug fixed in plot.mids() when there was one missing entry (Emmanuel Charpentier) CHANGED: NAMESPACE expanded to allow easy access to function code FIXED: mice() can now find mice.impute.xxx() functions in the .GlobalEnv v2.0 - 26-08-2009 / SvB, KO Major upgrade for JSS manuscript ADDED: new functions cbind.mids(), rbind.mids(), ibind() ADDED: new argument in mice(): 'post' in post-processing imputations ADDED: new functions: pool.scaler(), pool.compare(), pool.r.squared() ADDED: new data: boys, popmis, windspeed FIXED: function summary.mipo all(object$df) command fixed DELETED: data.frame.to.matrix replaced by the internal data.matrix function ADDED: new imputation method mice.impute.2l.norm() for multilevel data CHANGED: pool now works for any class having a vcov() method ADDED: with.mids() provides a general complete-data analysis ADDED: type checking in mice() to ensure appropriate imputation methods ADDED: warning added in mice() for constant predictors ADDED: prevention of perfect prediction in mice.impute.logreg() and mice.impute.polyreg() CHANGED: mice.impute.norm.improper() changed into mice.impute.norm.nob() DELETED: mice.impute.polyreg2() deleted ADDED: new 'include' argument in complete() ADDED: support for the empty imputation method in mice() ADDED: new function md.pairs() ADDED: support for intercept imputation ADDED: new function quickpred() FIXED: plot.mids() bug fix when number of variables > 5 v1.21 - 15/3/2009 SvB Maintainance release FIXED: Stricter type checking on logicals in mice() to evade warnings. CHANGED: Modernization of all help files. FIXED: padModel: treatment changed to contr.treatment CHANGED: Functions check.visitSequence, check.predictorMatrix, check.imputationMethod are now coded as local to mice() FIXED: existsFunction in check.imputationMethod now works both under S-Plus and R v1.16 - 6/25/2007 FIXED: The impution function impute.logreg used convergence criteria that were too optimistic when fitting a GLM with glm.fit. Thanks to Ulrike Gromping. v1.15 - 01/09/2006 FIXED: In the lm.mids and glm.mids functions, parameters were not passed through to glm and lm. v1.14R - 9/26/2005 11:44AM FIXED: Passive imputation works again. (Roel de Jong) CHANGED: Random seed is now left alone, UNLESS the argument "seed" is specified. This means that unless you specify identical seed values, imputations of the same dataset will be different for multiple calls to mice. (Roel de Jong) FIXED (docs): Documentation for "impute.mean" (Roel de Jong) FIXED: Function 'summary.mids' now works (Roel de Jong) FIXED: Imputation function 'impute.polyreg' and 'impute.lda' should now work under R v1.13 Changed function checkImputationMethod, Feb 6, 2004 v1.12 Maintainance, S-Plus 6.1 and R 1.8 unicode, January 2004 v1.1 R version (with help of Peter Malewski and Frank Harrell), Feb 2001 v1.0 Original S-PLUS release, June 14 2000