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| ************************* | |
| ** afex VERSION 0.19-x ** | |
| ************************* | |
| Changes in afex Version 0.19-0 | |
| Released xxx 2017 | |
| Bugfixes | |
| o lsmeans did not work with mixed objects if type=2 and method used nested | |
| model comparions (e.g., LRT or PB). | |
| ************************* | |
| ** afex VERSION 0.18-x ** | |
| ************************* | |
| Changes in afex Version 0.18-0 | |
| Released May 2017 | |
| Bugfixes | |
| o aov_ez did not work with more than one covariate | |
| (https://github.com/singmann/afex/issues/29). | |
| ************************* | |
| ** afex VERSION 0.17-x ** | |
| ************************* | |
| Changes in afex Version 0.17-x | |
| Released April 2017 | |
| Significant User Visible Changes and New Features | |
| o Added Satterthwaite approximation (method="S") to mixed(), which is | |
| implemented via lmerTest. Satterthwaite approximates the degrees-of- | |
| freedom of an F-test, similar to the default Kenward-Roger method, but | |
| requires less RAM. | |
| o mixed() methods "KR" and "S" are now obtained via tests on the full | |
| model directly. No restricted models are calculated for these methods. | |
| The former KR method is still available: method="nested-KR" | |
| o mixed() now per default exports and uses lmerTest::lmer and not | |
| lme4::lmer(). This can be changed via calling | |
| afex_options(lmer_function = "lme4") | |
| o afex does not depend on reshape2 any more. It is only imported. | |
| o All arguments with "." in the name have been renamed to use "_". The old | |
| names have been deprecated (i.e., still work, but should not be used). | |
| check.contrasts = check_contrasts, test.intercept = test_intercept, | |
| args.test = args_test, ... | |
| o Names of slots of mixed model objects with "." have been renamed to have | |
| a "_" instead: full.model = full_model and restricted.models = | |
| restricted_models | |
| o afex_options() now uses the global R options accessible via options() | |
| (with prefix afex.) and allows to reset all options via list (i.e.,: | |
| aop <- afex_options(); ...; afex_options(aov); works). | |
| o renamed allFit() to all_fit() and argument meth.tab to meth_tab. | |
| Added method dfoptim::nmkb() to all_fit(). To use nmkb, dfoptim needs to | |
| be loaded explicitly via library (see examples). | |
| o Added argument all_fit to mixed(). If TRUE, each model is fitted with | |
| all available optimizers and the best fit in each case selected. | |
| o mixed objects have an additional slot, "data", that contains the data | |
| used for fitting. | |
| o Added vignette with extensive mixed model example. | |
| o Created forum for providing afex support: http://afex.singmann.science/ | |
| Bugfixes | |
| o Sphericity correction now correctly displayed as none if all within- | |
| factors have only two levels (bug removed by Frederik Aust). | |
| o removed bug when calling nice() on afex_aov objects created with | |
| explicit effect size. | |
| o aov_...(): anova_table = list(intercept = TRUE) now correctly suppresses | |
| the intercept (bug removed by Frederik Aust). | |
| o aov_...(): return = "nice" did not work (bug removed by Frederik Aust). | |
| o aov_...() now supports column names with spaces (using backticks), see: | |
| https://github.com/singmann/afex/issues/22 Thx to Jonathan Love for fix. | |
| o changed license to GPL >=2 (as it call some function from GPL >=2 | |
| packages). | |
| o removed bug that mixed() object with type=2 could not be printed. | |
| o removed bug that model names for anova.mixed with multiple models were | |
| incorrect. | |
| o all_fit() now uses a data argument correctly and passes it update(). | |
| This again allows to use it for data with suppressed correlations. | |
| all_fit(... verbose = TRUE) now correctly signals if a fit failed. | |
| ************************* | |
| ** afex VERSION 0.16-x ** | |
| ************************* | |
| Changes in afex Version 0.16-x | |
| Released April 2016 | |
| Significant User Visible Changes and New Features | |
| o added "correction" and "observed" attributes to the anova_table slot of | |
| afex_aov objects, which is used per default by nice(). This ensures | |
| that nice(object) and object always return the same data.frame. | |
| Also added "nice_table" class to data.frame returned by nice which | |
| print the value of the slots for information. | |
| Both contributed by Frederik Aust (who was also promoted to author). | |
| o added return="data" for mixed. This allows to obtain the data set used | |
| for fitting a model. Can be useful in combination with expand.re=TRUE | |
| and allFit() or for obtaining predictions. See ?allFit for a simple | |
| example. | |
| Bugfixes | |
| o increased required version of R (>= 3.1.0) and the following packages | |
| to ensure afex runs with older versions of R: lme4 (>= 1.1-8), | |
| pbkrtest (>= 0.4-1), and Matrix (>= 1.1.1). | |
| ************************* | |
| ** afex VERSION 0.15-x ** | |
| ************************* | |
| Changes in afex Version 0.15-x | |
| Released October 2015 | |
| Significant User Visible Changes and New Features | |
| o added p.adjust.method argument for ANOVA functions (anova and nice | |
| methods). Can be used to control for multiple comparisons in | |
| exploratory ANOVAs (see Cramer, et al., 2015; PB&R). Functionality | |
| contributed by Frederik Aust (https://github.com/singmann/afex/pull/3). | |
| Bugfixes | |
| o ANOVA functions work with dplyr data.frames now (data is transformed | |
| via as.data.frame). See: https://github.com/singmann/afex/issues/6 | |
| o formulas for mixed can now be of a maximum length of 500 characters | |
| (was 60 chars previously): https://github.com/singmann/afex/issues/5 | |
| o aov_car et al. did not work with within-subject factors that were also | |
| included outside the Error term. This was caused by the use of regular | |
| expressions not appropriate for the new stringi backend of stringr. | |
| Thanks to Tom Wenseleers for reporting this bug. | |
| ************************* | |
| ** afex VERSION 0.14-x ** | |
| ************************* | |
| Changes in afex Version 0.14-x | |
| Released August 2015 | |
| Significant User Visible Changes and New Features | |
| o new default return argument for ANOVA functions, afex_aov, | |
| an S3 object containing the following: | |
| (1) ANOVA table of class "anova" | |
| (2) ANOVA fitted with base R's aov (can be passed to lsmeans | |
| for post-hoc tests) | |
| (3) output from car::Anova (for tests of effects), | |
| ANOVA table (1) is based on this model | |
| (4) lm object passed to car::Anova | |
| (5) data used for estimating (2) and (4) | |
| o added support for lsmeans: objects of class afex_aov can be | |
| passed to lsmeans directly. afex now depends on lsmeans. | |
| o added afex_options() functionality for setting options globally. | |
| o added expand_re argument to mixed which, if TRUE, correctly interprets | |
| the || notation in random effects with factors (i.e., suppresses | |
| estimation of correlation among random effects). lmer_alt is a wrapper | |
| for mixed which uses expand_re = TRUE, returns an object of class | |
| merMod (i.e., does not calculate p-values), and otherwise behaves | |
| like g/lmer (i.e., does not enforce certain contrasts) | |
| o added three new data sets (Singmann & Klauer, 2011; Klauer & | |
| Singmann, 2013) and a vignette showing how to calculate | |
| contrasts after ANOVA. | |
| o ANOVA functions renamed to aov_car, aov_ez, and aov_4. Old | |
| functions are now deprecated. | |
| o first element in mixed object renamed to anova_table. | |
| o nice.anova renamed to nice. nice() can be called for afex_aov | |
| and mixed objects and returns a nicely formatted (numbers | |
| converted to characters) results table (which is also the | |
| default print method for both objects). | |
| o anova() can be called for afex_aov and mixed objects and returns | |
| the numeric anova table (i.e., the first element of each object). | |
| There also exists print methods for those data.frames. | |
| o summary method for mixed objects now calls summary.merMod on | |
| full model. | |
| o afex does not depend on car package anymore, it is only imported. | |
| o afex is now hosted on github: https://github.com/singmann/afex | |
| Bugfixes | |
| o ANOVA: for "aov"-objects, contrasts are only set for factors. | |
| o compare.2.vector failed when the two means were exactly equal | |
| (due to an issue with median_test). This only throws a warning | |
| now. | |
| o compare.2.vector documentation updated for coin 1-1.0. | |
| ************************* | |
| ** afex VERSION 0.13-x ** | |
| ************************* | |
| Changes in afex Version 0.13-x | |
| Released January 2015 | |
| Significant User Visible Changes and New Features | |
| o added ems() function for deriving the expected values of the | |
| mean squares for factorial designs (contributed by Jake | |
| Westfall). | |
| Bugfixes | |
| o aov.car et al. stop with error message if a factor has only one | |
| level. | |
| o aov.car transforms id variable to factor which ensures that | |
| return = "aov" provides equivalent results. | |
| o changed regex for detecting "observed" variables to work with | |
| the new version of stringr which uses stringi. | |
| ************************* | |
| ** afex VERSION 0.12-x ** | |
| ************************* | |
| Changes in afex Version 0.12-x | |
| Released November 2014 | |
| Significant User Visible Changes and New Features | |
| o ANOVA functions give informative error if some parameters are | |
| not estimable (most likely due to structural missings, i.e. | |
| empty cells). | |
| Bugfixes | |
| o mixed(..., method = "PB") does not fail anymore when only | |
| having a single fixed effect (thanks to Kiyoshi Sasaki for | |
| reporting it). | |
| o aov.car() failed when a within-subject factor had empty levels. | |
| Unused factor levels are now dropped. This bug was probably | |
| introduced in Rev 126 as part of an attempt to solve a bug. | |
| (thanks to Will Bowditch for reporting it). | |
| ************************* | |
| ** afex VERSION 0.11-x ** | |
| ************************* | |
| Changes in afex Version 0.11-x | |
| Released October 2014 | |
| Significant User Visible Changes and New Features | |
| o added allFit() function (written by Ben Bolker). | |
| o mixed() gives warning if nested model provides worse fit | |
| (logLik) than full model (when fitted with ML). | |
| o print, summary, and anova method for mixed objects are now | |
| identical. | |
| o description of returned object from mixed() extended (Thanks | |
| to Ben Bolker, see http://stackoverflow.com/a/25612960/289572) | |
| o added return = "aov" to aov.car which returns the ANOVA | |
| fitted with aov (with correct Error strata) so that it can be | |
| passed to lsmeans for post-hoc tests or plotting (lsmip). | |
| Bugfixes | |
| o all required functions are now correctly imported avoiding | |
| CRAN warnings and better functioning. | |
| o data argument to lmer calls in mixed set correctly. Note that | |
| still contrasts added to the data in mixed may prohibit use of | |
| predict.merMod() or similar functions. It is recommended to | |
| set the contrasts globally to "contr.sum", e.g., | |
| via set_sum_contrasts(), for correct functioning | |
| (disable via set.data.arg argument for mixed). | |
| ************************ | |
| ** afex VERSION 0.10-x ** | |
| ************************ | |
| Changes in afex Version 0.10-x | |
| Released August 2014 | |
| Significant User Visible Changes and New Features | |
| o afex does not change the global contrasts anymore when loading | |
| the package (due to popular demand). | |
| o new functions to globally set contrasts: set_sum_contrasts & | |
| set_treatment_contrasts (and some more wrappers). | |
| o Added more mixed model examples from Maxwell & Delaney, Chapter | |
| 15 ("Multilevel Models for within subjects designs"), see ?mixed | |
| and ?md_15.1. Thanks to Ulf Mertens. | |
| Bugfixes | |
| o removed bug when factor levels of within-subject factors | |
| contained "+" or "-" and were not converted correctly. Added | |
| tests for known bugs in aov.car. | |
| ************************ | |
| ** afex VERSION 0.9-x ** | |
| ************************ | |
| Changes in afex Version 0.9-x | |
| Released April 2014 | |
| Significant User Visible Changes and New Features | |
| o added function aov4: another wrapper of car::Anova for ANOVA | |
| models specified via lme4::lmer syntax. | |
| o added return="marginal" to aov.car which returns the marginal | |
| means of all effects (i.e., grand mean and mean of main | |
| effects and interactions). Is also returned if return="full". | |
| o testing the intercept in mixed models in now only optional. | |
| The default is that the new argument test.intercept = FALSE. | |
| o removed return="lme4" from aov.car. | |
| o added argument intercept to nice.anova (default FALSE) which | |
| allows to selective display the intercept in an ANOVA table. | |
| o added method = "F" to mixed() which only returns the F-value | |
| but no ddf (and hence no p-value). Experimental, not documented. | |
| o renamed colname "stat" to "F" when method = "KR" (mixed). | |
| o added tests (currently mainly for mixed()) via pkg testthat, | |
| see tests/testthat. | |
| Bugfixes | |
| o increased requirement of R version and lme4 version. | |
| o print.mixed should now propagate all warnings from lme4 (i.e., | |
| also the new convergence warnings). | |
| o lme4 is now loaded at worker nodes for mixed (default, | |
| turn of via check.contrasts) | |
| ************************ | |
| ** afex VERSION 0.8-x ** | |
| ************************ | |
| Changes in afex Version 0.8-x | |
| Released February 2014 | |
| Significant User Visible Changes and New Features | |
| o removed renaming of within subject factor levels to names | |
| with length 1 (which was introduced in 0.6). | |
| o helper function round_ps which nicely rounds p-values | |
| is now exported. | |
| o warning about numerical non-centered variables in mixed | |
| is now a message only. | |
| o added examples data sets from Maxwell & Delaney (2004) for | |
| within-subjects ANOVA and mixed models. | |
| o reshape2 is now again in depends but coin only imported. | |
| Bugfixes | |
| o the default effect size (ges: generalized eta-squared) was | |
| calculated wrong (the error term for the intercept was not | |
| included). Sorry. This is now corrected (with new examples). | |
| o removed bug that aov.car didn't work when running some ANCOVAs | |
| (thanks to Gang Chen for reporting this). | |
| ************************ | |
| ** afex VERSION 0.7-x ** | |
| ************************ | |
| Changes in afex Version 0.7-x | |
| Released December 2013 | |
| Significant User Visible Changes and New Features | |
| o nicer output of print.mixed | |
| Bugfixes | |
| o mixed() correctly converts all non-formula arguments to | |
| formula correctly to a formula (gave error if formula | |
| was a different object and not-available on cluster nodes). | |
| Prints message if formula is converted to a formula. | |
| o Using multicore for fitting the models prodcued erroneous | |
| results (did not use correct contrasts at nodes). Now the | |
| current contrasts are also set at the nodes. | |
| o mixed() sets REML = FALSE if method = "LRT" and no | |
| family argument is present (i.e., for LMMs) as LRTs | |
| for models fitted with REML are not recommended. | |
| o on the cluster nodes now only the lme4 namespace is | |
| loaded (instead of using library) to avoid a CRAN note. | |
| ************************ | |
| ** afex VERSION 0.6-x ** | |
| ************************ | |
| Changes in afex Version 0.6-x | |
| Released September 2013 | |
| Significant User Visible Changes and New Features | |
| o added LRT tests to mixed() which should replicate | |
| the recommended test by Barr et al. (2013, JML). | |
| o multicore estimation of (g)lmer models now available | |
| through package parallel (argument cl) for mixed(). | |
| o added experimental "lme4" return method for | |
| aov.car and ez.glm (which fits the data using lmer). | |
| o reshape2 and stringr are not any more loaded when | |
| loading afex (are now only imported via Imports) | |
| Bugfixes | |
| o Type 2 tests of mixed() were implemented incorrectly (i.e., | |
| they did not give what they should have given according | |
| to the description in the help file). | |
| o aov.car() and ez.glm() now convert factor levels of within | |
| subjects factors to be of length one so that long levels | |
| do not lead to problems when constructing the call to lm. | |
| Thanks to Isaac Schwabacher for noticing this, see also: | |
| https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15377 | |
| o mixed should now work with missing values as it construes | |
| a new data object if the model.matrix from which the | |
| different versions are fitted has nrow different to | |
| nrow(data) (with warning). Thanks to Daniel Bunker | |
| for reporting this. | |
| o mixed should work with the newest version of lme4 (>= 1.0.4) | |
| and the newst version of pbkrtest (>= 0.3-5.1), but not | |
| with older versions (due to CRAN policy to disallow :::). | |
| ************************ | |
| ** afex VERSION 0.5-x ** | |
| ************************ | |
| Changes in afex Version 0.5-x | |
| Released May 2013 | |
| Significant User Visible Changes and New Features | |
| o added argument factorize (default: TRUE) to aov.car and ez.glm: | |
| all variables are now factorized per default. (now it is | |
| necessary to set factorize=FALSE for ANCOVAs!) | |
| o added argument per.parameter to mixed() which allows to specify | |
| variables for which each parameter is tested (not only the | |
| overall effect). Can be useful to test for ordered factors. | |
| (only implemented for "Type 3" tests) | |
| o added more informative startup message (thanks to Robert Volcic | |
| and Lars Konieczny) | |
| o mixed, ez.glm and aov.car now check for correct contrasts and set | |
| factors to contr.sum if other contrasts are found (can be tunred | |
| off via check.contrasts argument). Resetting the default contrast | |
| to contr.treatment should therefore not interfere with afex. | |
| (this is not intensly tested, so please report anything) | |
| o mixed checks numeric variables if they are centered on 0 (and | |
| gives warning if not). | |
| Bugfixes | |
| o checks if observed variable is in the data and throws | |
| an error if not (nice.anova) | |
| ************************ | |
| ** afex VERSION 0.4-x ** | |
| ************************ | |
| Changes in afex Version 0.4-x | |
| Released February 2013 | |
| Significant User Visible Changes and New Features | |
| o added generalized and partial eta-squared effect | |
| sizes to nice.anova (this also included adding | |
| observed arguments to aov.car, ez.glm, nice.anova) | |
| o added new return arguments to aov.car and ez.glm | |
| (nice, lm, data). | |
| o changed default return value of aov.car and ez.glm | |
| to "nice" which now returns a nice ANOVA table | |
| (nice.anova) | |
| o mixed has method = "PB" for obtaining parametric | |
| bootstrapped p-values (e.g., for GLMMs) | |
| o added alternative argument to compare.2.vectors. | |
| o aov.car (and ez.glm) now give a warning if | |
| observations are missing on within-subject factors. | |
| (As before, cases with missing values are simply | |
| excluded from the analysis) | |
| o had to disable saving of the previous contrasts and | |
| resetting those after detaching afex due to | |
| CRAN policies (no assignment in global environment). | |
| Bugfixes | |
| o Bug when running mixed() inside a function and | |
| handing the data.frame over as an argument fixed | |
| (thanks, again, to Florent Duyme). See | |
| bugs/eval.scoping.bug.R | |
| o nice.anova did not work with a model with only one | |
| within-subjects factor. | |
| ************************ | |
| ** afex VERSION 0.3-x ** | |
| ************************ | |
| Changes in afex Version 0.3-x | |
| Released August/September 2012 | |
| Significant User Visible Changes and New Features | |
| o added function compare.2.vectors(). | |
| o Name of function univariate() changed to univ(), as | |
| a function with this name is part of package multcomp. | |
| This may leed to problems. Thanks to Florent Duyme for | |
| spotting this. | |
| o added return argument to aov.car() and ez.glm(). | |
| o added rather dubious Type 2 tests to mixed(). | |
| o aov.car checks if each id is only present in one | |
| cell of the between subjects design. | |
| Bugfixes | |
| o aov.car now uses do.call when calling lm() to avoid local | |
| variables in the call to lm() which could led to problems when | |
| working with the lm model. | |
| o mixed() now passes ... (further arguments to lmer) correctly. | |
| (Now mixed uses match.call and eval on the call instead of | |
| invoking lmer directly.) | |
| o corrected bug that was introduced by pbkrtest v3.2 when | |
| invoking the print method to an object of class mixed | |
| (again thanks to Florent Duyme for spotting this). | |
| o removed bug when factor levels of within-subject factors | |
| were non-legal names (solution uses make.names). | |