[R-lang] Weird outcome logit mixed-effect model

Mon Dec 22 12:59:04 PST 2008

Dear Laura,

this model is most certainly overfit. for a binomial model the rule of thumb
for the absolute upper limit for the number of paramters in the model is
min(outcome A, outcome B) / 10, which in your case is 12/ 10 ~ 1. you're
using 2 parameters for fixed effects (and 1 for a random intercept).

Most of your subjects will have 0 deaccented syllables, making it hard to
impossible for the model to estimate the effects of info. I am still a bit
puzzled by the output though. did the fitting process not through a warning
(I am leaving town tomorrow, so i did not have time to load your data and
see for myself).

Florian

On Mon, Dec 22, 2008 at 4:57 AM, Laura de Ruiter <Laura.deRuiter at mpi.nl>wrote:

> Dear R-users and -experts,
>
> I am performing a rather simple analysis on a small data set (pasted below
> this email) and keep getting a to me inexplicable result. Perhaps I am
> missing something here - it would be great if someone could point out to me
> what I am doing wrong.
>
> I want to test whether the factor "Info" (which has three levels: "new",
> "given", "accessible") is a significant predictor for the binary variable
> "DeaccYN". The random factor is "Subject". The distribution of the data
> looks as follows:
>
>
> -----------------------------------------------------------------------------
> xtabs (~ DeaccYN + Info, data = dat)
> Info
> DeaccYN given new accessible
> no 25 42 21
> yes 11 0 1
>
> ------------------------------------------------------------------------------
>
> This is the model:
>
>
> ----------------------------------------------------------------------------------------------------------
> deacc.lmer = lmer (DeaccYN ~ Info + (1|Subject), data = dat, family =
> "binomial")
>
> -----------------------------------------------------------------------------------------------------------------
>
> However, given the distribution above, this outcome seems rather weird to
> me:
>
>
> ---------------------------------------------------------------------------------------------------------
> summary (deacc.lmer)
> Generalized linear mixed model fit using Laplace
> Formula: DeaccYN ~ Info + (1 | Subject)
> Data: dat
> Family: binomial(logit link)
> AIC BIC logLik deviance
> 60.4 70.82 -26.2 52.4
> Random effects:
> Groups Name Variance Std.Dev.
> Subject (Intercept) 0.18797 0.43356
> number of obs: 100, groups: Subject, 21
>
> Estimated scale (compare to 1 ) 0.7316067
>
> Fixed effects:
> Estimate Std. Error z value Pr(>|z|)
> (Intercept) -0.8635 0.3795 -2.2754 0.0229 *
> Infonew -18.7451 2764.2445 -0.0068 0.9946
> Infoaccessible -2.2496 1.1186 -2.0110 0.0443 *
> ---
> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
>
> Correlation of Fixed Effects:
> (Intr) Infonw
> Infonew 0.000
> Infoaccssbl -0.315 0.000
>
> ----------------------------------------------------------------------------------------------------
>
> Why should the difference between 25/11 and 21/1 be significant, but the
> difference between 25/11 and 42/0 not? Very odd to me seems the standard
> error of 2764!
> First I was wondering whether the problem had sth. to do with the fact that
> I had read in an SPSS file, but I keep getting this result even when I first
> save the SPSS file as a tabdelim. text and read it into R then. I couldn't
> find anything strange going on with the Subject factor either (and I have
> also tried the model with "Item" as random factor, which didn't change
> anything).
>
> I was wondering: Is it perhaps a problem for the model that there are no
> cases in the DeaccYN == "yes" category for Info == "given"? And if this is
> the case, why?
> Am I overlooking something here?
>
> Any help with this would be very much appreciated!
>
> Thanks a lot in advance for your answers & happy holidays,
>
> Laura de Ruiter
>
> ---------------------------------------
> The data set:
>
> dat
> Subject Info Deacc
> 1 93 new no
> 2 93 new no
> 3 93 given yes
> 4 93 new no
> 5 93 given no
> 6 94 new no
> 7 94 new no
> 8 94 given no
> 9 94 new no
> 10 94 given no
> 11 94 given no
> 12 94 accessible no
> 13 95 given no
> 14 95 new no
> 15 95 accessible no
> 16 95 new no
> 17 95 accessible no
> 18 95 new no
> 19 97 new no
> 20 98 new no
> 21 98 new no
> 22 98 given yes
> 23 98 given no
> 24 101 new no
> 25 101 new no
> 26 101 given yes
> 27 101 accessible no
> 28 101 new no
> 29 101 given yes
> 30 101 given no
> 31 101 accessible no
> 32 102 new no
> 33 102 new no
> 34 102 given no
> 35 102 given no
> 36 102 accessible no
> 37 104 new no
> 38 104 accessible no
> 39 104 new no
> 40 104 given yes
> 41 104 new no
> 42 104 given no
> 43 104 accessible no
> 44 107 new no
> 45 107 given no
> 46 107 accessible no
> 47 107 new no
> 48 109 new no
> 49 109 given yes
> 50 109 new no
> 51 110 accessible no
> 52 110 new no
> 53 110 new no
> 54 110 given no
> 55 113 new no
> 56 113 given yes
> 57 113 new no
> 58 113 given yes
> 59 114 new no
> 60 114 accessible no
> 61 114 new no
> 62 114 given no
> 63 114 accessible no
> 64 114 new no
> 65 114 given yes
> 66 114 accessible yes
> 67 115 accessible no
> 68 115 given no
> 69 115 given no
> 70 116 accessible no
> 71 116 new no
> 72 116 given no
> 73 116 new no
> 74 116 new no
> 75 116 accessible no
> 76 117 accessible no
> 77 117 given no
> 78 117 new no
> 79 117 new no
> 80 117 given no
> 81 117 accessible no
> 82 118 new no
> 83 118 accessible no
> 84 118 given no
> 85 118 new no
> 86 118 given no
> 87 118 accessible no
> 88 119 given no
> 89 119 given yes
> 90 119 given no
> 91 119 accessible no
> 92 121 given no
> 93 121 given no
> 94 131 new no
> 95 131 new no
> 96 131 new no
> 97 131 new no
> 98 132 given yes
> 99 132 given no
> 100 132 accessible no
> ------------------------------------------------
>
> --
> //////////////////////////////////////////////////////
>
> Laura de Ruiter
> PhD student
> Language Acquisition Group
> Max Planck Institute for Psycholinguistics
> P.O. Box 310
> 6500 AH Nijmegen
> Netherlands
>
> Phone: 0031-24-3521 456
> Homepage: http://www.mpi.nl/Members/LauradeRuiter
>
> ///////////////////////////////////////////////////
>
>
> _______________________________________________
> R-lang mailing list
> R-lang at ling.ucsd.edu
> http://pidgin.ucsd.edu/mailman/listinfo/r-lang
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://pidgin.ucsd.edu/pipermail/r-lang/attachments/20081222/017d2907/attachment.html>