MuMIn package news: Version: 1.8.0 (2012-11-21) This version introduces support for GEE models ('gee','geeglm' and 'yags') ranked by QIC (note that 'yags' seems to be still quite buggy). Also 'clmm' and 'clm' from package 'ordinal' are now handled properly. QIC, quasiLik: new functions for use with GEE models (p)dredge: argument 'subset' can be now a logical matrix representing allowed parameter combinations. Some improvements for speed have been made. (p)dredge, model.avg: new argument 'ct.args' for passing extra arguments to 'coefTable'. Version: 1.7.12 (2012-11-11) tests/classes.R: fixed compatibility spdep-0.5.53. (spdep::spautolm now uses method="eigen", was "full") Version: 1.7.11 (2012-07-13) coefTable.multinom: fixed an error when coefficients and standard errors were matrices get.models: now checks for the object class of the passed arguments Version: 1.7.10 (2012-06-07) (fixed) dredge: bug with an error message when number of predictor exceeded maximum (thanks to Corina Logan for spotting this). manual: added 'glmmADMB' to the list of supported classes (reported by Rocio Jana) 'coxme' moved from 'Suggested' to 'Enhances' (to avoid build error when the dependency is missing) Version: 1.7.9 (2012-04-03) Added 'predict' methods for 'lme' and 'lmer' (both can calculate 'se.fit'). 'predict.lme' is a wrapper for its namesake from 'nlme' package (it is not exported, so it's visibility depends on the order the packages were loaded - but is always visible from MuMIn namespace). Version: 1.7.8 (2012-04-01) (fixed) 'coef.model.selection' returns now proper coefficients Version: 1.7.7 (2012-04-01) fixed dependencies in tests Version: 1.7.6 (2012-04-01) dredge: with nested formula designs, 'marg.ex' is now found automatically predict.averaging: is now more flexible in how the predictions from generalized models are calculated (new attribute "backtransform"). Version: 1.7.5 (2012-03-27) Added methods for 'MCMCglmm' class, and function 'DIC': works with 'model.sel' and 'dredge' (but not 'model.avg'). 'unmarked' is removed from 'Suggested' packages (recently it is often unavailable on CRAN and causes errors during R CHECK). Added workarounds to pass (=cheat) the R CHECK. Version: 1.7.3 (2012-02-01) Added methods for 'glimML' class from package 'aod' Version: 1.7.2 (2012-01-30) (fixed) 'nobs.coxme' returned the number of events was returned rather than the number of observations. (fixed) 'coefTable' gave an error for 'coxph' null model. (fixed) 'r.squaredLR' was evaluating the null model for 'lme' in a wrong environment. (fixed) 'getAllTerms' method for 'zeroinfl' was not registered. dredge: checks each generated model for the correct number of observations. Version: 1.7.1 (2012-01-26) Added methods for 'hurdle' and 'zeroinfl' classes (package 'pscf'). coef, coefTable: new methods to extract coefficients from model selection tables. Documentation: list of supported models put into a separate page. Version: 1.7.0 (2012-01-25) This version adds possibility to model average and re-rank (with another IC) a model selection table without recreating the fitted models. Models from package 'coxme' are now supported. Model selection tables include now extra columns showing differences in attributes of the modelling function call. model.avg: use 'model.selection' without refitting the models. Fixed a problem with averaging different types of models together (happened when 'df's were available only for some of component models). dredge: coefficient tables added to the result (attribute "coefTables"). The code has been simplified. print.model.selection: now reports random terms also for objects generated by 'model.sel'. get.models: can handle 'model.selection' objects from 'model.sel' model.sel: re-ranking 'model.selection' without recreating original models (works only if the IC can be applied to logLik). Output has additional columns showing differences between models (based on call's arguments) Added generic methods for 'coxme' and 'lmekin' classes (package 'coxme'). Version: 1.6.6 (2012-01-07) model.avg: fixed error occurring when non-estimable coefficients existed in the component models (problem reported by Annabel Smith) Version: 1.6.5 (2011-11-28) pdredge example changed to use SOCK cluster type (portability issue). Version: 1.6.4 (2011-11-26) coefTable: replaces 'tTable' (which still exists, but is deprecated), it accepts an argument 'dispersion'. The dispersion parameter can be also passed from 'model.avg'. pdredge: collects all the warnings and errors which occur during fitting, and stores them. They are printed below the table. The function does more thorough checking of the cluster nodes' environment, for possible missing variables and functions. get.models: "subset" argument can be now a character vector giving model names. Added demos for model selection with models from 'unmarked' package using 'dredge' and 'pdredge'. Version: 1.6.3 (2011-11-15) pget.models: new function, parallel version of 'get.models'. (p)get.models: important change of the default behaviour: without the 'subset' argument, ALL models are returned. Also the '...' arguments were not used to update the returned models - this is corrected now. Version: 1.6.2 (2011-11-13) pdredge: new function, a parallel version of dredge (experimental). Version: 1.6.1 (2011-11-11) dredge: added generic support for all 'unmarked' models, and fixed some bugs with it. model.names: new function (previously was internal only) CAICF: adds to the collection of rarely used information criteria. Version: 1.6.0 (2011-11-07) dredge: most important change (although invisible to the user) is in the way the model objects are updated. The new function 'makeArgs' is used to generate the updated call. This results in a very flexible interface to the modelling functions. The default method updates the 'formula' argument, other methods can be used to deal with more problematic calls (the models from package 'unmarked' were a challenge). Apart from the model classes previously supported by 'dredge', support for 'unmarkedFitOccu', 'unmarkedFitColExt' and several other 'unmarkedFit' objects has been added. dredge: has new argument 'extra' to add additional statistics into the model selection table. r.squared: new function to calculate likelihood-ratio based pseudo-R-squared subset method for 'model.selection' accepts a shorthand notation "has(x)" to select rows where a variable is present. support for 'survreg' and 'rq' models (packages 'survival' and 'quantreg') Version: 1.5.2 (2011-10-21) dredge: fixed a bug with wrong ordering of column names in the returned data.frame (thanks to Staffan Roos for reporting this). Version: 1.5.1 (2011-10-20) compatibility with R prior to 2.13.0: added workarounds for missing generic function 'nobs'. Version: 1.5.0 (2011-10-18) model.avg: removed the argument "method", the standard errors and confidence intervals are calculated only for coefficients averaged within a subset of models where they are present (method = "NA"). The "full" coefficients are also returned, but without std. errors. plot.model.selection: new function to visualize the model selection table manuals expanded, examples revised getAllTerms: should work for most of the classes derived from 'unmarkedFit' a load of small improvements, polishings and fixes, generally invisible to the user. Version: 1.4.4 (2011-10-16) QAIC: no longer uses model deviance, as it gave biased values. ICOMP, Cp: new information criteria model.avg: now performs a smarter check for duplicate models, fixed calculation of importance values model.sel: new alias to 'mod.sel' (eventually will replace 'mod.sel'). Version: 1.4.3 (2011-10-13) Beetle: new data - beetle mortality, with examples from B&A's book dredge: new arguments 'varying', 'm.min' and 'evaluate' manuals modified and corrected tests/gamm.R: tests for 'gamm'/'gamm4' support. Version: 1.4.2 (2011-10-11) support for 'gamm' and 'gamm4' gamm: added a wrapper for gamm, that allows for updating the object (hopefully needed only temporarily) Version: 1.4.1 (2011-10-10) A few changes to vignette 'gamm' Version: 1.4.0 (2011-10-05) importance: new function mod.sel: added method for a 'model.selection' object Version: 1.3.10 (2011-09-23) Reverted changes made in previous version (package dependencies) to succesfully pass checks. Version: 1.3.9 (2011-09-17) removed *.lmer *.glmer methods, added dependency on lme4 >= 0.999375-16 tTable.mer: minor change Version: 1.3.8 (2011-09-17) Restored compatibility with R 2.12.2 getAllTerms: new attribute 'intercept' Version: 1.3.7 (2011-09-16) handling double intercept (phi(Int) and p(Int)) in 'unmarked' Version: 1.3.6 (2011-09-12) changes in the documentation and vignette Version: 1.3.5 (2011-08-05) mod.sel: new function added methods for 'unmarkedFit' objects (package 'unmarked'), to provide (limited) support in 'model.avg' Version: 1.3.4 (2011-08-03) Added vignette document on model selection with 'gamm' and 'gamm4' (thanks to Graham MacDonald for an incentive) Version: 1.3.3 (2011-08-01) dredge: small improvements, no longer dependent on 'bitops' Polished the documentation Version: 1.3.2 (2011-08-01) nobs: updated methods Version: 1.3.1 (2011-07-31) dredge: bugs fixed Version: 1.3.0 (2011-07-29) model.avg: now may be used directly with 'model.selection' object summary.averaging: gives now more information Version: 1.2.4 (2011-07-29) fixed handling of spatial parameters (lambda, rho) in models from package 'spdep' dredge: modified for better performance dredge, get.models: can deal with glms with starting values provided ('start' argument) QAIC: added a note in documentation stating that is uses deviance rather than logLik in the calculation Version: 1.2.3 (2011-04-07) fixed some REML/ML issues, AICc rewritten (based on the new AIC code in stats) Version: 1.2.2 (2011-04-06) nobs: corrected methods for mixed models, added documentation page Version: 1.2.1 (2011-04-05) .GetLogLik - hidden helper function (returns the proper logLik to use) Version: 1.2.0 (2011-04-04) AICc has new argument REML used with mixed models. Thanks to Benjamin Augustine for suggestion. Version: 1.1.2 (2011-03-19) removed arguments 'alpha' and 'level' from model.avg. 'confint' is used instead to obtain CI Version: 1.1.1 (2011-03-18) the printed output of 'averaging' has been made consistent with that of lm and glm: 'print' gives concise information and 'summary' gives more details. confint.averaging: new function. print.summary.averaging: new function. Version: 1.1.0 (2011-03-10) added z-statistic, p-values (with significance stars) to model.avg output Version: 1.0.0 (2011-02-10) get.models: fixed - arguments in ... were not passed to updated models predict.averaging: predictions on response scale can be calculated (type=response) new functions (not exported): nobs, coefDf model.avg: now makes use of correct DF from component models in calculation of adjusted SE par.avg: calculates ASE if df are provided, example(QAIC) now demonstrates predictions with confidence intervals Version: 0.14.2 (2011-02-05) dredge: small changes, slightly faster manual corrected Version: 0.14.1 (2011-02-04) vcov.averaging, logLik.averaging: new methods, revised formula for unconditional variance manual reworked Version: 0.14.0 (2011-01-19) TODO: model.avg: added npar to the selection table predict.averaging: now can return averaged SE par.avg: may use revised formula for calculating averaged SE Version: 0.13.21 (2011-01-16) dredge: handling of update'd lmer models improved QAICc: new function Version: 0.13.20 (2011-01-16) Namespace exports updated (coxph methods) dredge: uses now QAIC for glms with 'quasi*' family, and if no rank is specified Version: 0.13.19 (2011-01-15) model.avg: fixed wrong ordering of model names (thanks to Dennis Jonason for noticing this) Version: 0.13.18 (2010-10-16) Support for coxph (package survival) Version: 0.13.17 (2010-09-13) model.avg: fixed a bug with models with binary response; dredge: added checking for na.omit'ting in the global model. new tests: varia.R Version: 0.13.16 (2010-09-07) dredge, model.avg: broken support for several types of models was fixed Version: 0.13.15 (2010-09-06) support for MASS::multinom Version: 0.13.14 (2010-09-03) print.model.selection:empty columns are not printed now Version: 0.13.13 (2010-09-02) dredge: handling of models with no intercept, added "call" attribute update.model.selection: new Version: 0.13.12 (2010-08-29) dredge, getAllTerms, dredge.Rd: small modifications Version: 0.13.11 (2010-08-28) getAllTerms: improved handling of interactions, random terms (lmer) and "offset()" formulaAllowed: now allows for exceptions in margins presence checking (new argument: "except") dredge: now tries to call fitting function directly rather than through update (more effective in case when model not passed as a variable). New arguments: "trace", and "marg.ex" - marginality checking exceptions. Version: 0.13.10 (2010-08-26) getAllTerms: fixed a bug with with wrong ordering of interaction terms (resulted with a:b or b:a depending on the set of terms). Improved handling of random terms in lme. Version: 0.13.9 (2010-08-24) dredge: fixed bugs introduced in the previous version Version: 0.13.8 (2010-08-03) QAIC: examples expanded Version: 0.13.7 (2010-08-02) dredge: prints errors generated by models as warnings (previously these were skipped silently) Version: 0.13.6 (2010-08-01) print.model.selection: improved column abbreviation. Version: 0.13.5 (2010-07-31) dredge: fixed a bug causing interaction coefficients to be stripped from model.selection table, new function 'fixCoefNames' (not exported) handles proper ordering of interaction components in coefficient names. Version: 0.13.4 (2010-07-21) 'beta.weights' now uses 'tTable' (support for more model types), 'dredge' with beta=TRUE tries out if it can get beta.weights working. Manual: added gls and rlm to the list of supported models Version: 0.13.3 (2010-07-15) Bug fixed in print.averaging Version: 0.13.2 (2010-07-14) Attributes for custom rank function in "dredge" and "model.avg" are now evaluated model-wise, if provided as expressions. Version: 0.13.0-1 (2010-07-12) Fixed compatibility issues with models of class "lme" and "sarlm". "model.avg" does now some checking whether all models were fitted to the same data and have the same response. Version: 0.12.13 (2010-07-09) 'recalc.weights' argument added to "subset.model.selection". Small bug fixed in dredge. Version: 0.12.12 (2010-07-08) New in "dredge": Subsetting models a priori according to a formula Version: 0.12.11 (2010-07-07) Subset/extract methods for 'model.selection' object Version: 0.12.10 (2010-07-05) Fixed "predict.averaging" for missing 'newdata' handling; Table returned by "dredge" now has factors for terms with more than one level (they were previously shown as '1') Version: 0.12.9 (2010-07-03) Finally fixed problems with variable exporting and hidden methods Version: 0.12.7-8 (2010-07-02) Small changes in namespace and documentation Version: 0.12.6 (2010-06-26) Tidying up the code, small changes. Version: 0.12.4 (2010-06-21) added: "predict.averaging" and "coef.averaging", 'averaging' object contains additional elements, so that several default methods work with it. Version: 0.12.2 (2009-06-14) fixed: 'alpha' in "model.avg" was not passed to "par.avg" Version: 0.12.1 (2009-04-20) fixed: method="NA" in model.avg, par.avg now accepts NA's in 'weight' Version: 0.12.0 (2009-03-24) Change in version number only. Had to make this jump in numbering, as there was a typo in DESCRIPTION file of an early version, (0.11.2 instead of 0.1.0), and since then R-forge mechanism seemed to ignore actual newer versions, as they had lower number. Version 0.1.1 (2009-03-22) Modified: dredge: added "fixed" and "m.max" arguments. Version 0.1.1 (2009-03-17) Fixed: par.avg: Variance estimate corrected (previous estimate was square root of variance). Thanks to Mick Wu. Fixed: dredge: Apparently "expand.grid" cannot handle too many combinations, so now dredge stops with a more explanatory message Version 0.1.0 dRedging (0.11.2) moved to R-Forge. Since model averaging is now the main focus of the package, its name changed to MuMIn - MUltiModelINference.