Hello R-help subscribers,

I am analyzing a data set using a mixed logit model, and I have recently
discovered some curious behavior. I am hoping you all can help.

I first ran the following model in December 2012.

lmer(Response.binary ~ ItemType.c * Block + (1  | Subject) + (1 | Word),
data=lexdec, family="binomial")

I then took a break from the data for the holidays. I returned to the data
yesterday and discovered that running the exact same model on the exact
same data set yields different output. The overall patterns are the same,
but the coefficients, variance estimates, and model fits (AIC, BIC) differ.
The model outputs from the old and current attempt are appended below.

I have triple checked the code and the data set to ensure that what I'm
working with now is the same as in December. Having found no differences, I
can only suspect that some function has changed. During my hiatus from
these data, I updated plyr and its dependencies (and maybe some other
packages). But to my understanding, these updates mostly concerned
documentation, not algorithms. Any ideas then about why the model outputs
differ?

Thank you for your help!
Kodi
*

OLD MODEL OUTPUT*:
Generalized linear mixed model fit by the Laplace approximation
Formula: Response.binary ~ ItemType.c * Block + (1 + ItemType.c + Block |
Subject) + (1 | Word)
   Data: lexdec
  AIC  BIC logLik deviance
 4788 4957  -2370     4740
Random effects:
 Groups  Name                 Variance Std.Dev. Corr
 Word    (Intercept)          1.66447  1.29014
 Subject (Intercept)          0.50865  0.71320
         ItemType.cFV-L       0.89270  0.94483   0.261
         ItemType.cFV-R       1.26385  1.12421   0.210  0.978
         ItemType.cFV-B       1.33556  1.15566   0.143  0.916  0.979
         Blockpost            0.93878  0.96891  -0.349 -0.093  0.037  0.163
Number of obs: 8500, groups: Word, 298; Subject, 17

Fixed effects:
                                  Estimate Std. Error z value Pr(>|z|)
(Intercept)                         3.8233     0.2688  14.225  < 2e-16 ***
ItemType.cFV-L                     -6.0547     0.3749 -16.149  < 2e-16 ***
ItemType.cFV-R                     -6.8649     0.4130 -16.621  < 2e-16 ***
ItemType.cFV-B                     -7.3542     0.4285 -17.164  < 2e-16 ***
Blockpost                           0.9754     0.3238   3.013  0.00259 **
ItemType.cFV-L:Blockpost            0.5921     0.2725   2.173  0.02980 *
ItemType.cFV-R:Blockpost            0.5835     0.2926   1.994  0.04612 *
ItemType.cFV-B:Blockpost           -0.2718     0.3083  -0.882  0.37793
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1



*NEW MODEL OUTPUT:
*Generalized linear mixed model fit by the Laplace approximation
Formula: Response.binary ~ ItemType.c * Block + (1 + ItemType.c + Block |
Subject) + (1 | Word)
   Data: lexdec
  AIC  BIC logLik deviance
 4791 4961  -2372     4743
Random effects:
 Groups  Name            Variance Std.Dev. Corr
 Word    (Intercept)     1.57837  1.25633
 Subject (Intercept)     0.58476  0.76470
         ItemType.cFV-L  0.92922  0.96396  -0.105
         ItemType.cFV-R  1.36398  1.16790  -0.241  0.990
         ItemType.cFV-B  1.59667  1.26360  -0.323  0.956  0.978
         Blockpost       1.03413  1.01692  -0.511  0.198  0.264  0.406
Number of obs: 8500, groups: Word, 298; Subject, 17

Fixed effects:
                                  Estimate Std. Error z value Pr(>|z|)
(Intercept)                         3.3659     0.2704  12.448  < 2e-16 ***
ItemType.cFV-L                     -5.6366     0.3710 -15.193  < 2e-16 ***
ItemType.cFV-R                     -6.3466     0.4128 -15.376  < 2e-16 ***
ItemType.cFV-B                     -6.6767     0.4372 -15.271  < 2e-16 ***
Blockpost                           1.1657     0.3288   3.546 0.000391 ***
ItemType.cFV-L:Blockpost            0.5119     0.2681   1.909 0.056243 .
ItemType.cFV-R:Blockpost            0.4834     0.2859   1.691 0.090886 .
ItemType.cFV-B:Blockpost           -0.4394     0.3002  -1.463 0.143336
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 *
*

-- 
Kodi Weatherholtz
Ph.D. Student
Department of Linguistics
The Ohio State University

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