Thank you, Henrik! This is very useful! Best
Roger > On Aug 25, 2015, at 5:32 AM, Henrik Singmann <singm...@psychologie.uzh.ch> > wrote: > > Dear list, (I apologize for crossposting with R-SIG-MIXED) > > I have released a new version of afex (0.14-2) to CRAN with several new > features which may be of interest. > > The most important feature for this audience is perhaps that afex can now > correctly suppress the estimation of correlations among factor random slopes > using the "||" notation. This is achieved by first creating the model matrix > for the random factors and then passing the so created numerical variables > instead of the original factors. For convenience, I have created a wrapper > function, lmer_alt(), which expands the random effects in such a way but > otherwise behaves like lmer (or glmer if a family argument is passed). That > also means it does not enforce a specific factor coding (in contrast to the > other afex functions that per default use sum-to-zero contrasts). > The following example (from Reinhold Kliegl, > https://rpubs.com/Reinhold/22193) shows this: > > require(afex) > data("Machines", package = "MEMSS") > contrasts(Machines$Machine) <- contr.treatment(3) > m1a <- lmer(score ~ Machine + (Machine|Worker), Machines, REML=FALSE) > summary(m1a)$varcor > ## Groups Name Std.Dev. Corr > ## Worker (Intercept) 3.71695 > ## Machine2 5.35595 0.488 > ## Machine3 3.35308 -0.363 0.296 > ## Residual 0.96158 > m1b <- lmer(score ~ Machine + (Machine||Worker), Machines, REML=FALSE) > summary(m1b)$varcor > ## Groups Name Std.Dev. Corr > ## Worker (Intercept) 0.49674 > ## Worker.1 MachineA 3.68361 > ## MachineB 7.85482 0.805 > ## MachineC 3.96965 0.618 0.772 > ## Residual 0.96158 > m1c <- lmer_alt(score~Machine+(Machine||Worker), Machines, REML=FALSE) > summary(m1c)$varcor > ## Groups Name Std.Dev. > ## Worker (Intercept) 3.71176 > ## Worker.1 re1.Machine2 5.36912 > ## Worker.2 re1.Machine3 3.30637 > ## Residual 0.96257 > > As can be seen, lmer_alt behaves like one would be expect and not like lmer. > This behavior can also be activated for the afex mixed() function by setting > expand_re = TRUE. > > Furthermore, afex is now fully integrated with lsmeans for all types of > follow-up tests and contrasts. This is particularly noteworthy for the ANOVA > functions (which have been renamed to aov_ez, aov_car, and aov_4) which now > return per default an object of class "afex_aov". This object contains the > ANOVA estimated with both car::Anova (for correct Type II/II tests) and > stats::aov (for follow-up tests) and can be directly passed to lsmeans. This > means one can directly run any type of post-hoc tests/contrasts on ANOVA > independent of whether or not these tests relate to between- or > within-factors or a mix thereof. The new vignette shows this in detail: > https://cran.rstudio.com/web/packages/afex/vignettes/anova_posthoc.html > > The full list of changes is available here: > https://cran.rstudio.com/web/packages/afex/NEWS > > afex has also moved to github now (where all the cool kids are) so I am happy > for any comments there (https://github.com/singmann/afex), here, or per mail. > > Cheers, > Henrik > > PS: Due to a bug in the current CRAN version of stringi the following warning > message appears regularly in afex, but can be safely ignored: > In stri_c(..., sep = sep, collapse = collapse, ignore_null = TRUE) : > longer object length is not a multiple of shorter object length > > Updating stringi from github (https://github.com/Rexamine/stringi/) removes > this warning. >
