[R-sig-ME] Collinearity diagnostics for (mixed) multinomial models

Juho Kristian Ruohonen juho@kr|@t|@n@ruohonen @end|ng |rom gm@||@com
Sat Feb 26 17:39:50 CET 2022


Dear John,


> In my experience, collinearity
> problems are relatively rare -- do you have a reason to believe that you
> have a collinearity problem?


This is observational linguistic data, where it is thought to be very
common. True or not, the research community expects to see the risk
acknowledged somehow.

Also, as an approximation, you'd likely do
> well just to look at the VIFs or GVIFs based only on the model matrix,
> as would be appropriate for a linear model.
>

Great, thanks a lot!

Best,

Juho


la 26. helmik. 2022 klo 17.37 John Fox (jfox using mcmaster.ca) kirjoitti:

> Dear Juho,
>
> On 2022-02-26 2:15 a.m., Juho Kristian Ruohonen wrote:
> > Many thanks, John. This is rather unfortunate news as it leaves me with
> > no way to present statistics on the degree to which my multinomial
> > models are affected by collinearity. But it's good to hear it directly
> > from a consummate expert.
>
> First, thank you for the compliment.
>
> Your conclusion is probably pessimistic. In my experience, collinearity
> problems are relatively rare -- do you have a reason to believe that you
> have a collinearity problem? Also, as an approximation, you'd likely do
> well just to look at the VIFs or GVIFs based only on the model matrix,
> as would be appropriate for a linear model.
>
> Best,
>   John
>
> >
> > Best,
> >
> > Juho
> >
> >
> > la 26. helmik. 2022 klo 1.16 John Fox (jfox using mcmaster.ca
> > <mailto:jfox using mcmaster.ca>) kirjoitti:
> >
> >     Dear Juho,
> >
> >     For some reason, my previous response to you (shown below your most
> >     recent message) doesn't seem to have made it to the list. Let's hope
> >     that this reply does:
> >
> >     On 2022-02-25 2:52 p.m., Juho Kristian Ruohonen wrote:
> >      > Dear John (Fox, and other list members),
> >      >
> >      > Could we achieve the invariance Professor Fox refers to by
> >     altering my
> >      > initial approach in the following ways:
> >      >
> >      >  1. Instead of fitting a _linear_ model with a mock continuous
> >     response
> >      >     to each subdataset and applying *vif() *to that, we fit to
> each
> >      >     subdataset an actual binary GLM with a real pairing of two
> >     response
> >      >     categories as LHS.
> >      >  2. Instead of fitting only C-1 binary sub-GLMs for which to
> >     calculate
> >      >     GVIF diagnostics, we fit *choose(C, 2) *such submodels, i.e.
> _one
> >      >     for every possible pairing of response categories_.
> >      >  3. Finally, for each coefficient, we average the GVIF statistic
> over
> >      >     the *choose(C, 2)* submodels in order to obtain a summary
> >     statistic.
> >      >
> >      > What do you gentlemen think?
> >
> >     This ad-hoc solution doesn't seem to me a good idea. The starting
> point
> >     should be a criterion for what should be invariant with respect to
> >     reparametrizations of the LHS of the model that leave the fitted
> >     probabilities unchanged. I think that it would be natural to require
> >     that the relative sizes of the joint confidence regions for all of
> the
> >     coefficients of a term in the data and the utopian data be invariant.
> >
> >     I don't know the answer to the question posed in this manner, but I
> >     suspect that it is the application of the formula for the GVIF to the
> >     subset of coefficients representing the term in question for all of
> the
> >     levels of the response in an arbitrary parametrization.
> >
> >     I may think about this a bit more when I have some time.
> >
> >     Best,
> >        John
> >
> >      >
> >      > Best,
> >      >
> >      > Juho
> >      >
> >      >
> >      >
> >      > pe 25. helmik. 2022 klo 19.40 John Fox (jfox using mcmaster.ca
> >     <mailto:jfox using mcmaster.ca>
> >      > <mailto:jfox using mcmaster.ca <mailto:jfox using mcmaster.ca>>) kirjoitti:
> >      >
> >      >     Dear Juhu,
> >      >
> >      >     Apologies for my slow response -- I had a busy morning.
> >      >
> >      >     I hadn't thought about generalizing VIFs to multinomial
> >     regression
> >      >     models, and I haven't thought the question through now, but I
> >     don't
> >      >     think that what you propose makes sense.
> >      >
> >      >     For a linear model, the vif() function in the car packages
> >     computes
> >      >     generalized VIFs, as proposed by Fox and Monette in the paper
> >      >     referenced
> >      >     in ?vif. That is, for the linear model y ~ 1 + X, where X is a
> >      >     matrix of
> >      >     regressors, the generalized VIF associated with the regression
> >      >     coefficients for a column subset of X, say X_j, is GVIF_j =
> >     det R_{jj}
> >      >     det R_{-j, -j}/det R, which is interpretable as the size
> >     (hypervolume)
> >      >     of a confidence ellipsoid for the coefficients of X_j
> >     relative to the
> >      >     size of the confidence ellipsoid for similar "utopian" data
> >     in which
> >      >     X_j
> >      >     and X_{-j} are uncorrelated. Here, det R_{jj} is the
> >     determinant of the
> >      >     correlation matrix among the columns of X_j, det R_{-j, -j}
> >     is the
> >      >     determinant of the correlation matrix among the remaining
> >     columns of X,
> >      >     and det R is the correlation matrix among all of the columns
> >     of X.
> >      >
> >      >     This has the nice property that the bases for the subspaces
> >     spanned by
> >      >     the columns of X_j and X_{-j} are irrelevant, and thus, e.g.,
> it
> >      >     doesn't
> >      >     matter what kind of contrasts one uses for a factor. Also
> >     when X_j is
> >      >     just one column of X, the GVIF specializes to the usual VIF.
> >      >
> >      >     Actually, vif() uses the correlation matrix of the
> >     coefficients R_{bb}
> >      >     rather than the correlations of the variables R, but that
> >     turns out to
> >      >     be equivalent, and also suggests a generalization to other
> >     regression
> >      >     models, such as GLMs. More generally, however (that is,
> >     beyond linear
> >      >     models), the correlations of the coefficients involve y as
> >     well as X,
> >      >     and so there's some slippage in interpretation -- now the
> >     utopian data
> >      >     are no longer necessarily for uncorrelated Xs. This is true
> >     as well for
> >      >     some other diagnostics generalized beyond linear models, such
> as
> >      >     hatvalues, which, e.g., for GLMs, depend on the ys as well as
> >     the Xs.
> >      >
> >      >     Analogously, in generalizing GVIFs further to a model such as
> a
> >      >     multinomial regression one would want a result that doesn't
> >     depend on
> >      >     the arbitrary parametrization of the LHS of the model -- for
> >     example,
> >      >     which level of the response is taken as the reference level.
> >     As I said,
> >      >     I haven't tried to think that through, but your solution isn't
> >      >     invariant
> >      >     in this way.
> >      >
> >      >     I hope this helps,
> >      >        John
> >      >
> >      >     On 2022-02-25 3:23 a.m., Juho Kristian Ruohonen wrote:
> >      >      > Dear John (and anyone else qualified to comment),
> >      >      >
> >      >      > I fit lots of mixed-effects multinomial models in my
> >     research, and I
> >      >      > would like to see some (multi)collinearity diagnostics on
> >     the fixed
> >      >      > effects, of which there are over 30. My models are fit
> >     using the
> >      >      > Bayesian *brms* package because I know of no frequentist
> >     packages
> >      >     with
> >      >      > multinomial GLMM compatibility.
> >      >      >
> >      >      > With continuous or dichotomous outcomes, my go-to function
> for
> >      >      > calculating multicollinearity diagnostics is of course
> *vif()*
> >      >     from the
> >      >      > /car/ package. As expected, however, this function does
> >     not report
> >      >      > sensible diagnostics for multinomial models -- not even
> >     for standard
> >      >      > ones fit by the /nnet/ package's *multinom()* function. The
> >      >     reason, I
> >      >      > presume, is because a multinomial model is not really one
> >     but C-1
> >      >      > regression models  (where C is the number of response
> >     categories)
> >      >     and
> >      >      > the *vif()* function is not designed to deal with this
> >     scenario.
> >      >      >
> >      >      > Therefore, in order to obtain meaningful collinearity
> >     metrics, my
> >      >      > present plan is to write a simple helper function that uses
> >      >     *vif() *to
> >      >      > calculate and present (generalized) variance inflation
> metrics
> >      >     for the
> >      >      > C-1 sub-datasets to which the C-1 component binomial
> >     models of the
> >      >      > overall multinomial model are fit. In other words, it will
> >      >     partition the
> >      >      > data into those C-1 subsets, and then apply *vif()* to as
> many
> >      >     linear
> >      >      > regressions using a made-up continuous response and the
> fixed
> >      >     effects of
> >      >      > interest.
> >      >      >
> >      >      > Does this seem like a sensible approach?
> >      >      >
> >      >      > Best,
> >      >      >
> >      >      > Juho
> >      >      >
> >      >      >
> >      >      >
> >      >      >
> >      >      > ma 27. syysk. 2021 klo 19.26 John Fox (jfox using mcmaster.ca
> >     <mailto:jfox using mcmaster.ca>
> >      >     <mailto:jfox using mcmaster.ca <mailto:jfox using mcmaster.ca>>
> >      >      > <mailto:jfox using mcmaster.ca <mailto:jfox using mcmaster.ca>
> >     <mailto:jfox using mcmaster.ca <mailto:jfox using mcmaster.ca>>>) kirjoitti:
> >      >      >
> >      >      >     Dear Simon,
> >      >      >
> >      >      >     I believe that Russ's point is that the fact that the
> >      >     additive model
> >      >      >     allows you to estimate nonsensical quantities like a
> >     mean for
> >      >     girls in
> >      >      >     all-boys' schools implies a problem with the model.
> >     Why not
> >      >     do as I
> >      >      >     suggested and define two dichotomous factors: sex of
> >     student
> >      >      >     (male/female) and type of school (coed, same-sex)? The
> >     four
> >      >      >     combinations
> >      >      >     of levels then make sense.
> >      >      >
> >      >      >     Best,
> >      >      >        John
> >      >      >
> >      >      >     On 2021-09-27 12:09 p.m., Simon Harmel wrote:
> >      >      >      > Thanks, Russ! There is one thing that I still don't
> >      >     understand. We
> >      >      >      > have two completely empty cells (boys in girl-only
> >     & girls in
> >      >      >     boy-only
> >      >      >      > schools). Then, how are the means of those empty
> cells
> >      >     computed (what
> >      >      >      > data is used in their place in the additive model)?
> >      >      >      >
> >      >      >      > Let's' simplify the model for clarity:
> >      >      >      >
> >      >      >      > library(R2MLwiN)
> >      >      >      > library(emmeans)
> >      >      >      >
> >      >      >      > Form3 <- normexam ~ schgend + sex ## + standlrt +
> >      >     (standlrt | school)
> >      >      >      > model3 <- lm(Form3, data = tutorial)
> >      >      >      >
> >      >      >      > emmeans(model3, pairwise~sex+schgend)$emmeans
> >      >      >      >
> >      >      >      >   sex  schgend   emmean     SE   df lower.CL
> upper.CL
> >      >      >      >   boy  mixedsch -0.2160 0.0297 4055  -0.2742
> -0.15780
> >      >      >      >   girl mixedsch  0.0248 0.0304 4055  -0.0348
> 0.08437
> >      >      >      >   boy  boysch    0.0234 0.0437 4055  -0.0623
> 0.10897
> >      >      >      >   girl boysch    0.2641 0.0609 4055   0.1447
> >     0.38360<-how
> >      >     computed?
> >      >      >      >   boy  girlsch  -0.0948 0.0502 4055  -0.1931
> >     0.00358<-how
> >      >     computed?
> >      >      >      >   girl girlsch   0.1460 0.0267 4055   0.0938
> 0.19829
> >      >      >      >
> >      >      >      >
> >      >      >      >
> >      >      >      >
> >      >      >      >
> >      >      >      > On Sun, Sep 26, 2021 at 8:22 PM Lenth, Russell V
> >      >      >      > <russell-lenth using uiowa.edu
> >     <mailto:russell-lenth using uiowa.edu> <mailto:russell-lenth using uiowa.edu
> >     <mailto:russell-lenth using uiowa.edu>>
> >      >     <mailto:russell-lenth using uiowa.edu
> >     <mailto:russell-lenth using uiowa.edu> <mailto:russell-lenth using uiowa.edu
> >     <mailto:russell-lenth using uiowa.edu>>>>
> >      >     wrote:
> >      >      >      >>
> >      >      >      >> By the way, returning to the topic of interpreting
> >      >     coefficients,
> >      >      >     you ought to have fun with the ones from the model I
> >     just fitted:
> >      >      >      >>
> >      >      >      >> Fixed effects:
> >      >      >      >>                 Estimate Std. Error t value
> >      >      >      >> (Intercept)    -0.18882    0.05135  -3.677
> >      >      >      >> standlrt        0.55442    0.01994  27.807
> >      >      >      >> schgendboysch   0.17986    0.09915   1.814
> >      >      >      >> schgendgirlsch  0.17482    0.07877   2.219
> >      >      >      >> sexgirl         0.16826    0.03382   4.975
> >      >      >      >>
> >      >      >      >> One curious thing you'll notice is that there are
> no
> >      >      >     coefficients for the interaction terms. Why? Because
> >     those terms
> >      >      >     were "thrown out" of the model, and so they are not
> >     shown. I
> >      >     think
> >      >      >     it is unwise to not show what was thrown out (e.g., lm
> >     would have
> >      >      >     shown them as NAs), because in fact what we see is but
> >     one of
> >      >      >     infinitely many possible solutions to the regression
> >      >     equations. This
> >      >      >     is the solution where the last two coefficients are
> >      >     constrained to
> >      >      >     zero. There is another equally reasonable one where the
> >      >     coefficients
> >      >      >     for schgendboysch and schgendgirlsch  are constrained
> to
> >      >     zero, and
> >      >      >     the two interaction effects would then be non-zero. And
> >      >     infinitely
> >      >      >     more where all 7 coefficients are non-zero, and there
> >     are two
> >      >     linear
> >      >      >     constraints among them.
> >      >      >      >>
> >      >      >      >> Of course, since the particular estimate shown
> >     consists
> >      >     of all
> >      >      >     the main effects and interactions are constrained to
> >     zero, it
> >      >     does
> >      >      >     demonstrate that the additive model *could* have been
> >     used to
> >      >     obtain
> >      >      >     the same estimates and standard errors, and you can
> >     see that by
> >      >      >     comparing the results (and ignoring the invalid ones
> >     from the
> >      >      >     additive model). But it is just a lucky coincidence
> >     that it
> >      >     worked
> >      >      >     out this way, and the additive model did lead us down
> >     a primrose
> >      >      >     path containing silly results among the correct ones.
> >      >      >      >>
> >      >      >      >> Russ
> >      >      >      >>
> >      >      >      >> -----Original Message-----
> >      >      >      >> From: Lenth, Russell V
> >      >      >      >> Sent: Sunday, September 26, 2021 7:43 PM
> >      >      >      >> To: Simon Harmel <sim.harmel using gmail.com
> >     <mailto:sim.harmel using gmail.com>
> >      >     <mailto:sim.harmel using gmail.com <mailto:sim.harmel using gmail.com>>
> >      >      >     <mailto:sim.harmel using gmail.com
> >     <mailto:sim.harmel using gmail.com> <mailto:sim.harmel using gmail.com
> >     <mailto:sim.harmel using gmail.com>>>>
> >      >      >      >> Cc: r-sig-mixed-models using r-project.org
> >     <mailto:r-sig-mixed-models using r-project.org>
> >      >     <mailto:r-sig-mixed-models using r-project.org
> >     <mailto:r-sig-mixed-models using r-project.org>>
> >      >      >     <mailto:r-sig-mixed-models using r-project.org
> >     <mailto:r-sig-mixed-models using r-project.org>
> >      >     <mailto:r-sig-mixed-models using r-project.org
> >     <mailto:r-sig-mixed-models using r-project.org>>>
> >      >      >      >> Subject: RE: [External] Re: [R-sig-ME] Help with
> >     interpreting
> >      >      >     one fixed-effect coefficient
> >      >      >      >>
> >      >      >      >> I guess correctness is in the eyes of the
> >     beholder. But I
> >      >     think
> >      >      >     this illustrates the folly of the additive model.
> >     Having additive
> >      >      >     effects suggests a belief that you can vary one factor
> >     more
> >      >     or less
> >      >      >     independently of the other. In his comments, John Fox
> >     makes a
> >      >     good
> >      >      >     point that escaped my earlier cursory view of the
> original
> >      >     question,
> >      >      >     that you don't have data on girls attending all-boys'
> >      >     schools, nor
> >      >      >     boys attending all-girls' schools; yet the model that
> >     was fitted
> >      >      >     estimates a mean response for both those situations.
> >     That's a
> >      >     pretty
> >      >      >     clear testament to the failure of that model – and
> >     also why the
> >      >      >     coefficients don't make sense. And finally why we have
> >      >     estimates of
> >      >      >     15 comparisons (some of which are aliased with one
> >     another), when
> >      >      >     only 6 of them make sense.
> >      >      >      >>
> >      >      >      >> If instead, a model with interaction were fitted,
> it
> >      >     would be a
> >      >      >     rank-deficient model because two cells are empty.
> Perhaps
> >      >     there is
> >      >      >     some sort of nesting structure that could be used to
> >     work around
> >      >      >     that. However, it doesn't matter much because emmeans
> >     assesses
> >      >      >     estimability, and the two combinations I mentioned
> >     above would be
> >      >      >     flagged as non-estimable. One could then more
> >     judiciously use the
> >      >      >     contrast function to test meaningful contrasts across
> this
> >      >     irregular
> >      >      >     array of cell means. Or even injudiciously asking for
> all
> >      >     pairwise
> >      >      >     comparisons, you will see 6 estimable ones and 9
> >      >     non-estimable ones.
> >      >      >     See output below.
> >      >      >      >>
> >      >      >      >> Russ
> >      >      >      >>
> >      >      >      >> ----- Interactive model -----
> >      >      >      >>
> >      >      >      >>> Form <- normexam ~ 1 + standlrt + schgend * sex +
> >      >     (standlrt |
> >      >      >     school)
> >      >      >      >>> model <- lmer(Form, data = tutorial, REML = FALSE)
> >      >      >      >> fixed-effect model matrix is rank deficient so
> >     dropping 2
> >      >      >     columns / coefficients
> >      >      >      >>>
> >      >      >      >>> emmeans(model, pairwise~schgend+sex)
> >      >      >      >>
> >      >      >      >> ... messages deleted ...
> >      >      >      >>
> >      >      >      >> $emmeans
> >      >      >      >>   schgend  sex    emmean     SE  df asymp.LCL
> >     asymp.UCL
> >      >      >      >>   mixedsch boy  -0.18781 0.0514 Inf   -0.2885
> >       -0.0871
> >      >      >      >>   boysch   boy  -0.00795 0.0880 Inf   -0.1805
> >     0.1646
> >      >      >      >>   girlsch  boy    nonEst     NA  NA        NA
> >        NA
> >      >      >      >>   mixedsch girl -0.01955 0.0521 Inf   -0.1216
> >     0.0825
> >      >      >      >>   boysch   girl   nonEst     NA  NA        NA
> >        NA
> >      >      >      >>   girlsch  girl  0.15527 0.0632 Inf    0.0313
> >     0.2792
> >      >      >      >>
> >      >      >      >> Degrees-of-freedom method: asymptotic
> >      >      >      >> Confidence level used: 0.95
> >      >      >      >>
> >      >      >      >> $contrasts
> >      >      >      >>   contrast                     estimate     SE  df
> >      >     z.ratio p.value
> >      >      >      >>   mixedsch boy - boysch boy     -0.1799 0.0991 Inf
> >      >     -1.814  0.4565
> >      >      >      >>   mixedsch boy - girlsch boy     nonEst     NA  NA
> >      >     NA      NA
> >      >      >      >>   mixedsch boy - mixedsch girl  -0.1683 0.0338 Inf
> >      >     -4.975  <.0001
> >      >      >      >>   mixedsch boy - boysch girl     nonEst     NA  NA
> >      >     NA      NA
> >      >      >      >>   mixedsch boy - girlsch girl   -0.3431 0.0780 Inf
> >      >     -4.396  0.0002
> >      >      >      >>   boysch boy - girlsch boy       nonEst     NA  NA
> >      >     NA      NA
> >      >      >      >>   boysch boy - mixedsch girl     0.0116 0.0997 Inf
> >      >       0.116  1.0000
> >      >      >      >>   boysch boy - boysch girl       nonEst     NA  NA
> >      >     NA      NA
> >      >      >      >>   boysch boy - girlsch girl     -0.1632 0.1058 Inf
> >      >     -1.543  0.6361
> >      >      >      >>   girlsch boy - mixedsch girl    nonEst     NA  NA
> >      >     NA      NA
> >      >      >      >>   girlsch boy - boysch girl      nonEst     NA  NA
> >      >     NA      NA
> >      >      >      >>   girlsch boy - girlsch girl     nonEst     NA  NA
> >      >     NA      NA
> >      >      >      >>   mixedsch girl - boysch girl    nonEst     NA  NA
> >      >     NA      NA
> >      >      >      >>   mixedsch girl - girlsch girl  -0.1748 0.0788 Inf
> >      >     -2.219  0.2287
> >      >      >      >>   boysch girl - girlsch girl     nonEst     NA  NA
> >      >     NA      NA
> >      >      >      >>
> >      >      >      >> Degrees-of-freedom method: asymptotic
> >      >      >      >> P value adjustment: tukey method for comparing a
> >     family of 6
> >      >      >     estimates
> >      >      >      >>
> >      >      >      >>
> >      >      >      >>
> >     ---------------------------------------------------------
> >      >      >      >> From: Simon Harmel <sim.harmel using gmail.com
> >     <mailto:sim.harmel using gmail.com>
> >      >     <mailto:sim.harmel using gmail.com <mailto:sim.harmel using gmail.com>>
> >      >      >     <mailto:sim.harmel using gmail.com
> >     <mailto:sim.harmel using gmail.com> <mailto:sim.harmel using gmail.com
> >     <mailto:sim.harmel using gmail.com>>>>
> >      >      >      >> Sent: Sunday, September 26, 2021 3:08 PM
> >      >      >      >> To: Lenth, Russell V <russell-lenth using uiowa.edu
> >     <mailto:russell-lenth using uiowa.edu>
> >      >     <mailto:russell-lenth using uiowa.edu <mailto:
> russell-lenth using uiowa.edu>>
> >      >      >     <mailto:russell-lenth using uiowa.edu
> >     <mailto:russell-lenth using uiowa.edu>
> >      >     <mailto:russell-lenth using uiowa.edu
> >     <mailto:russell-lenth using uiowa.edu>>>>
> >      >      >      >> Cc: r-sig-mixed-models using r-project.org
> >     <mailto:r-sig-mixed-models using r-project.org>
> >      >     <mailto:r-sig-mixed-models using r-project.org
> >     <mailto:r-sig-mixed-models using r-project.org>>
> >      >      >     <mailto:r-sig-mixed-models using r-project.org
> >     <mailto:r-sig-mixed-models using r-project.org>
> >      >     <mailto:r-sig-mixed-models using r-project.org
> >     <mailto:r-sig-mixed-models using r-project.org>>>
> >      >      >      >> Subject: [External] Re: [R-sig-ME] Help with
> >     interpreting one
> >      >      >     fixed-effect coefficient
> >      >      >      >>
> >      >      >      >> Dear Russ and the List Members,
> >      >      >      >>
> >      >      >      >> If we use Russ' great package (emmeans), we see
> >     that although
> >      >      >     meaningless, but "schgendgirl-only" can be interpreted
> >     using the
> >      >      >     logic I mentioned here:
> >      >      >
> >      >
> >     https://stat.ethz.ch/pipermail/r-sig-mixed-models/2021q3/029723.html
> >     <
> https://stat.ethz.ch/pipermail/r-sig-mixed-models/2021q3/029723.html>
> >      >
> >       <
> https://stat.ethz.ch/pipermail/r-sig-mixed-models/2021q3/029723.html <
> https://stat.ethz.ch/pipermail/r-sig-mixed-models/2021q3/029723.html>>
> >      >      >
> >      >
> >       <
> https://stat.ethz.ch/pipermail/r-sig-mixed-models/2021q3/029723.html <
> https://stat.ethz.ch/pipermail/r-sig-mixed-models/2021q3/029723.html> <
> https://stat.ethz.ch/pipermail/r-sig-mixed-models/2021q3/029723.html <
> https://stat.ethz.ch/pipermail/r-sig-mixed-models/2021q3/029723.html>>> .
> >      >      >      >>
> >      >      >      >> That is, "schgendgirl-only" can meaninglessly
> >     mean: ***diff.
> >      >      >     bet. boys in girl-only vs. mixed schools*** just like
> >     it can
> >      >      >     meaningfully mean:  ***diff. bet. girls in girl-only
> >     vs. mixed
> >      >      >     schools***
> >      >      >      >>
> >      >      >      >> Russ, have I used emmeans correctly?
> >      >      >      >>
> >      >      >      >> Simon
> >      >      >      >>
> >      >      >      >> Here is a reproducible code:
> >      >      >      >>
> >      >      >      >> library(R2MLwiN) # For the dataset
> >      >      >      >> library(lme4)
> >      >      >      >> library(emmeans)
> >      >      >      >>
> >      >      >      >> data("tutorial")
> >      >      >      >>
> >      >      >      >> Form <- normexam ~ 1 + standlrt + schgend + sex +
> >     (standlrt |
> >      >      >     school)
> >      >      >      >> model <- lmer(Form, data = tutorial, REML = FALSE)
> >      >      >      >>
> >      >      >      >> emmeans(model, pairwise~schgend+sex)$contrast
> >      >      >      >>
> >      >      >      >> contrast                     estimate     SE  df
> >     z.ratio
> >      >     p.value
> >      >      >      >> mixedsch boy - boysch boy    -0.17986 0.0991 Inf
> >     -1.814
> >      >     0.4565
> >      >      >      >> mixedsch boy - girlsch boy   -0.17482 0.0788 Inf
> >     -2.219
> >      >     0.2287
> >      >      >       <--This coef. equals
> >      >      >      >> mixedsch boy - mixedsch girl -0.16826 0.0338 Inf
> >     -4.975
> >      >     <.0001
> >      >      >      >> mixedsch boy - boysch girl   -0.34813 0.1096 Inf
> >     -3.178
> >      >     0.0186
> >      >      >      >> mixedsch boy - girlsch girl  -0.34308 0.0780 Inf
> >     -4.396
> >      >     0.0002
> >      >      >      >> boysch boy - girlsch boy      0.00505 0.1110 Inf
> >     0.045
> >      >     1.0000
> >      >      >      >> boysch boy - mixedsch girl    0.01160 0.0997 Inf
> >     0.116
> >      >     1.0000
> >      >      >      >> boysch boy - boysch girl     -0.16826 0.0338 Inf
> >     -4.975
> >      >     <.0001
> >      >      >      >> boysch boy - girlsch girl    -0.16322 0.1058 Inf
> >     -1.543
> >      >     0.6361
> >      >      >      >> girlsch boy - mixedsch girl   0.00656 0.0928 Inf
> >     0.071
> >      >     1.0000
> >      >      >      >> girlsch boy - boysch girl    -0.17331 0.1255 Inf
> >     -1.381
> >      >     0.7388
> >      >      >      >> girlsch boy - girlsch girl   -0.16826 0.0338 Inf
> >     -4.975
> >      >     <.0001
> >      >      >      >> mixedsch girl - boysch girl  -0.17986 0.0991 Inf
> >     -1.814
> >      >     0.4565
> >      >      >      >> mixedsch girl - girlsch girl -0.17482 0.0788 Inf
> >     -2.219
> >      >     0.2287
> >      >      >       <--This coef.
> >      >      >      >> boysch girl - girlsch girl    0.00505 0.1110 Inf
> >     0.045
> >      >     1.0000
> >      >      >      >>
> >      >      >      >>
> >      >      >      >
> >      >      >      > _______________________________________________
> >      >      >      > R-sig-mixed-models using r-project.org
> >     <mailto:R-sig-mixed-models using r-project.org>
> >      >     <mailto:R-sig-mixed-models using r-project.org
> >     <mailto:R-sig-mixed-models using r-project.org>>
> >      >      >     <mailto:R-sig-mixed-models using r-project.org
> >     <mailto:R-sig-mixed-models using r-project.org>
> >      >     <mailto:R-sig-mixed-models using r-project.org
> >     <mailto:R-sig-mixed-models using r-project.org>>> mailing list
> >      >      >      >
> >     https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> >     <https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models>
> >      >     <https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> >     <https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models>>
> >      >      >
> >       <https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> >     <https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models>
> >      >     <https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> >     <https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models>>>
> >      >      >      >
> >      >      >     --
> >      >      >     John Fox, Professor Emeritus
> >      >      >     McMaster University
> >      >      >     Hamilton, Ontario, Canada
> >      >      >     web: https://socialsciences.mcmaster.ca/jfox/
> >     <https://socialsciences.mcmaster.ca/jfox/>
> >      >     <https://socialsciences.mcmaster.ca/jfox/
> >     <https://socialsciences.mcmaster.ca/jfox/>>
> >      >      >     <https://socialsciences.mcmaster.ca/jfox/
> >     <https://socialsciences.mcmaster.ca/jfox/>
> >      >     <https://socialsciences.mcmaster.ca/jfox/
> >     <https://socialsciences.mcmaster.ca/jfox/>>>
> >      >      >
> >      >      >     _______________________________________________
> >      >      > R-sig-mixed-models using r-project.org
> >     <mailto:R-sig-mixed-models using r-project.org>
> >      >     <mailto:R-sig-mixed-models using r-project.org
> >     <mailto:R-sig-mixed-models using r-project.org>>
> >      >      >     <mailto:R-sig-mixed-models using r-project.org
> >     <mailto:R-sig-mixed-models using r-project.org>
> >      >     <mailto:R-sig-mixed-models using r-project.org
> >     <mailto:R-sig-mixed-models using r-project.org>>> mailing list
> >      >      > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> >     <https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models>
> >      >     <https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> >     <https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models>>
> >      >      >
> >       <https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> >     <https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models>
> >      >     <https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> >     <https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models>>>
> >      >      >
> >      >     --
> >      >     John Fox, Professor Emeritus
> >      >     McMaster University
> >      >     Hamilton, Ontario, Canada
> >      >     web: https://socialsciences.mcmaster.ca/jfox/
> >     <https://socialsciences.mcmaster.ca/jfox/>
> >      >     <https://socialsciences.mcmaster.ca/jfox/
> >     <https://socialsciences.mcmaster.ca/jfox/>>
> >      >
> >     --
> >     John Fox, Professor Emeritus
> >     McMaster University
> >     Hamilton, Ontario, Canada
> >     web: https://socialsciences.mcmaster.ca/jfox/
> >     <https://socialsciences.mcmaster.ca/jfox/>
> >
> --
> John Fox, Professor Emeritus
> McMaster University
> Hamilton, Ontario, Canada
> web: https://socialsciences.mcmaster.ca/jfox/
>
>

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