[R-lang] Re: trouble with random effects in factorial design

[Daniel Ezra Johnson]

Hi Roger,

I'm trying to check that out. Even though I had gotten "lme4.0" running a
month or so ago, subsequent updates are making it hard to install that
older version on a Mac system, at least, but I'm going to try.

This seems like a possible bug. There is no way that the deviance can be 24
units different but the fixed effect estimates are still identical to six
decimal places.

Dan


On Tue, Dec 3, 2013 at 12:17 PM, Levy, Roger <rlevy@ucsd.edu> wrote:

> Sorry — “other” should have read “related”.
>
> Roger
>
> On Dec 3, 2013, at 9:11 AM, Levy, Roger <rlevy@ucsd.edu> wrote:
>
> > Daniel — do you get the same problem with the pre-1.0 version of lme4?
>  We have had other issues with lme4_1.0*.
> >
> > Roger
> >
> > On Dec 3, 2013, at 1:35 AM, Daniel Ezra Johnson <
> danielezrajohnson@gmail.com> wrote:
> >
> >> Dear R-Lang,
> >>
> >> I have noticed a difference in the random effect results depending on
> the order of terms in the model, something that (to say the least) I don't
> think should be happening.
> >>
> >> The fixed effects results are identical. This is with lme4_1.0-5.
> >>
> >> I have some (simplified) data that you can load as follows:
> >>
> >> dat <- read.csv("http://www.danielezrajohnson.com/dej_test.csv")
> >>
> >> Briefly, the data has 32 subjects and 32 items. Each subject has four
> observations of "response" in each of four conditions (focus: "VP" vs.
> "object", order: "vpo" vs. "vop"), so there are 32 x 16 = 512 observations.
> >>
> >> The design is (not perfectly) counterbalanced by Latin Square so that
> each subject saw 16 items, but the combination of items and conditions was
> different from subject to subject. Put another way, each of the 32 items is
> supposed to occur equally in each of the four conditions. This is not
> exactly true in the example, but I don't think it should be affecting the
> results.
> >>
> >> mm.1 <- lmer(response ~ focus * order + (focus * order | subject) +
> (focus * order | item), dat, control = lmerControl(optCtrl = list(maxfun =
> 100000)))
> >>
> >> mm.2 <- lmer(response ~ order * focus + (order * focus | subject) +
> (order * focus | item), dat, control = lmerControl(optCtrl = list(maxfun =
> 100000)))
> >>
> >>> fixef(mm.1)
> >>     (Intercept)          focusVP         ordervpo focusVP:ordervpo
> >>       8.7265625        0.3359375        0.1171875       -0.7578125
> >>> fixef(mm.2)
> >>     (Intercept)         ordervpo          focusVP ordervpo:focusVP
> >>       8.7265625        0.1171875        0.3359375       -0.7578125
> >>
> >> You can see that the fixed effects estimates are EXACTLY the same.
> >>
> >> The random effects, however, are somewhat different:
> >>
> >>> VarCorr(mm.1)
> >> Groups   Name             Std.Dev. Corr
> >> subject  (Intercept)      1.36674
> >>          focusVP          1.02059  -0.808
> >>          ordervpo         1.75084  -0.898  0.820
> >>          focusVP:ordervpo 2.99477   0.862 -0.930 -0.886
> >> item     (Intercept)      0.65516
> >>          focusVP          0.78447  -0.749
> >>          ordervpo         1.20179  -0.205  0.256
> >>          focusVP:ordervpo 1.38629   0.253 -0.063 -0.719
> >> Residual                  1.61041
> >>> VarCorr(mm.2)
> >> Groups   Name             Std.Dev. Corr
> >> subject  (Intercept)      1.03365
> >>          ordervpo         0.77706  -0.675
> >>          focusVP          1.27217   0.542 -0.064
> >>          ordervpo:focusVP 1.73912   0.603 -0.124  0.609
> >> item     (Intercept)      0.10477
> >>          ordervpo         0.92461   1.000
> >>          focusVP          0.47122   0.682  0.686
> >>          ordervpo:focusVP 1.68445  -0.137 -0.134  0.469
> >> Residual                  1.60852
> >>
> >> The deviance estimates are also not quite the same.
> >>
> >>> deviance(mm.1)
> >>   REML
> >> 2151.61
> >>> deviance(mm.2)
> >>    REML
> >> 2175.503
> >>
> >> My real question is why the models are not identical. A secondary
> question is, given that they're not, why are the fixed effects identical,
> but really I think the fixed effects should be identical, and it's a
> mystery to me why the random effects are different.
> >>
> >> To reiterate, the only difference in the two models is the order in
> which the two random slopes are entered into the formula.
> >>
> >> I hope someone can shed some light onto this, if indeed it hasn't been
> asked before.
> >>
> >> Thanks very much,
> >> Dan
> >
>
>
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