[R-lang] "Zero" problem with lmer
Marie Coppola
marie.coppola@gmail.com
Sat Oct 9 23:04:00 PDT 2010
Dear R-users and -experts,
I am performing a rather simple analysis on a small data set (pasted below
this email) and am having detecting any effects because of invariant
responses in some conditions. I understand from a previous query from Laura
de Ruiter that this is because the model cannot estimate the standard error
when there are no responses for a given level of a factor. Roger suggested
adding an extra data point to make those cells non-zero. This fixed the
wildly high standard errors I was getting, and resulted in a significant
interaction.
But I would like to analyze the actual dataset ;) . I considered following
Roger's advice to Laura, in which he showed how to use a likelihood-ratio
test to compare the full model with a simpler one, in which one collapses
two levels of one of the factors). I do not see how I can do that here
because I only have two levels of the factor in question. I would appreciate
any suggestions. (I am facing this problem in several analyses.)
I am testing whether the factor "Agent" (which has two levels: "agent"
and "no_agent")
is a significant predictor for the binary variable "Handshape". The random
factor is "Subject". The distribution of the data is as follows, and the
real data are the same except for zeroes in two of the cells that currently
display ones (annotated):
Thanks in advance for your help!
Marie Coppola
--------------------------------------------------------------------------------------------------
Marie Coppola, Ph.D.
Assistant Professor
Departments of Psychology and Linguistics
University of Connecticut
Mailing address:
Department of Psychology
University of Connecticut
406 Babbidge Road
Unit 1020
Storrs CT 06269-1020
USA
Office: +1 860 486-4907 | Lab: +1 860 486-2185 | Fax: +1 860
486-2760
-----------------------------------------------------
> xtabs (~ Handshape + Agent + Construction, data = planes_olderPlusHand)
, , Construction = Classifier
Agent
Handshape agent no_agent
handling 36 1 (added)
object 27 65
, , Construction = Lexical_item
Agent
Handshape agent no_agent
handling 1 1 (added)
object 45 54
I get a significant interaction now, having substituted the ones, but is
there another solution? The model and results are below, along with the full
dataset:
-----------------------------------------------------
> planes_olderPlusHand.lmer
Generalized linear mixed model fit by the Laplace approximation
Formula: Handshape ~ Agent * Construction_sum + (1 | Subject)
Data: planes_olderPlusHand
AIC BIC logLik deviance
125.4 142.6 -57.68 115.4
Random effects:
Groups Name Variance Std.Dev.
Subject (Intercept) 0.15923 0.39904
Number of obs: 230, groups: Subject, 6
Fixed effects:
Estimate Std. Error z value
(Intercept) 1.8304 0.5611 3.262
Agentno_agent 2.3869 0.9051 2.637
Construction_sum1 -2.1184 0.5351 -3.959
Agentno_agent:Construction_sum1 2.2068 0.9062 2.435
Pr(>|z|)
(Intercept) 0.00111 **
Agentno_agent 0.00836 **
Construction_sum1 7.54e-05 ***
Agentno_agent:Construction_sum1 0.01488 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Correlation of Fixed Effects:
(Intr) Agntn_ Cnst_1
Agentno_gnt -0.557
Cnstrctn_s1 -0.845 0.516
Agntn_g:C_1 0.500 -0.306 -0.591
-----------------------------------------------------
Full dataset: planes_olderPlusHand (2 extra data points in the ZERO cells
are in bold)
Group Subject Agent Construction Handshape
older_child 1 agent Classifier object
older_child 1 agent Classifier object
older_child 1 agent Classifier object
older_child 1 agent Classifier object
older_child 1 agent Classifier object
older_child 1 agent Classifier handling
older_child 1 agent Classifier handling
older_child 1 agent Classifier handling
older_child 1 agent Classifier handling
older_child 1 agent Classifier handling
older_child 1 agent Lexical_item object
older_child 1 agent Lexical_item object
older_child 1 agent Lexical_item object
older_child 1 agent Lexical_item object
older_child 1 agent Lexical_item object
older_child 1 agent Lexical_item object
older_child 1 agent Lexical_item object
older_child 1 no_agent Classifier object
older_child 1 no_agent Classifier object
older_child 1 no_agent Classifier object
older_child 1 no_agent Classifier object
older_child 1 no_agent Classifier object
older_child 1 no_agent Classifier object
older_child 1 no_agent Classifier object
older_child 1 no_agent Classifier object
older_child 1 no_agent Classifier object
older_child 1 no_agent Lexical_item object
older_child 1 no_agent Lexical_item object
older_child 1 no_agent Lexical_item object
older_child 1 no_agent Lexical_item object
older_child 1 no_agent Lexical_item object
older_child 1 no_agent Lexical_item object
older_child 1 no_agent Lexical_item object
older_child 1 no_agent Lexical_item object
older_child 1 no_agent Lexical_item object
older_child 2 agent Classifier object
older_child 2 agent Classifier object
older_child 2 agent Classifier object
older_child 2 agent Classifier object
older_child 2 agent Classifier object
older_child 2 agent Classifier object
older_child 2 agent Classifier object
older_child 2 agent Classifier handling
older_child 2 agent Classifier handling
older_child 2 agent Classifier handling
older_child 2 agent Classifier handling
older_child 2 agent Classifier handling
older_child 2 agent Classifier handling
older_child 2 agent Classifier handling
older_child 2 agent Lexical_item object
older_child 2 agent Lexical_item object
older_child 2 agent Lexical_item object
older_child 2 agent Lexical_item object
older_child 2 agent Lexical_item object
older_child 2 agent Lexical_item object
older_child 2 agent Lexical_item object
older_child 2 agent Lexical_item handling
older_child 2 no_agent Classifier object
older_child 2 no_agent Classifier object
older_child 2 no_agent Classifier object
older_child 2 no_agent Classifier object
older_child 2 no_agent Classifier object
older_child 2 no_agent Classifier object
older_child 2 no_agent Classifier object
older_child 2 no_agent Classifier object
older_child 2 no_agent Classifier object
older_child 2 no_agent Classifier object
older_child 2 no_agent Classifier object
older_child 2 no_agent Classifier object
older_child 2 no_agent Classifier object
older_child 2 no_agent Lexical_item object
older_child 2 no_agent Lexical_item object
older_child 2 no_agent Lexical_item object
older_child 2 no_agent Lexical_item object
older_child 2 no_agent Lexical_item object
older_child 2 no_agent Lexical_item object
older_child 2 no_agent Lexical_item object
older_child 2 no_agent Lexical_item object
older_child 2 no_agent Lexical_item object
older_child 3 agent Classifier object
older_child 3 agent Classifier object
older_child 3 agent Classifier handling
older_child 3 agent Classifier handling
older_child 3 agent Classifier handling
older_child 3 agent Lexical_item object
older_child 3 agent Lexical_item object
older_child 3 agent Lexical_item object
older_child 3 no_agent Classifier object
older_child 3 no_agent Classifier object
older_child 3 no_agent Classifier object
older_child 3 no_agent Classifier object
older_child 3 no_agent Lexical_item object
older_child 3 no_agent Lexical_item object
older_child 3 no_agent Lexical_item object
older_child 3 no_agent Lexical_item object
older_child 4 agent Classifier object
older_child 4 agent Classifier object
older_child 4 agent Classifier object
older_child 4 agent Classifier object
older_child 4 agent Classifier object
older_child 4 agent Classifier object
older_child 4 agent Classifier object
older_child 4 agent Classifier handling
older_child 4 agent Classifier handling
older_child 4 agent Classifier handling
older_child 4 agent Classifier handling
older_child 4 agent Classifier handling
older_child 4 agent Lexical_item object
older_child 4 agent Lexical_item object
older_child 4 agent Lexical_item object
older_child 4 agent Lexical_item object
older_child 4 agent Lexical_item object
older_child 4 agent Lexical_item object
older_child 4 agent Lexical_item object
older_child 4 agent Lexical_item object
older_child 4 agent Lexical_item object
older_child 4 agent Lexical_item object
older_child 4 agent Lexical_item object
older_child 4 no_agent Classifier object
older_child 4 no_agent Classifier object
older_child 4 no_agent Classifier object
older_child 4 no_agent Classifier object
older_child 4 no_agent Classifier object
older_child 4 no_agent Classifier object
older_child 4 no_agent Classifier object
older_child 4 no_agent Classifier object
older_child 4 no_agent Classifier object
older_child 4 no_agent Classifier object
older_child 4 no_agent Classifier object
older_child 4 no_agent Classifier object
older_child 4 no_agent Classifier object
older_child 4 no_agent Classifier object
older_child 4 no_agent Classifier object
older_child 4 no_agent Classifier object
older_child 4 no_agent Classifier object
older_child 4 no_agent Lexical_item object
older_child 4 no_agent Lexical_item object
older_child 4 no_agent Lexical_item object
older_child 4 no_agent Lexical_item object
older_child 4 no_agent Lexical_item object
older_child 4 no_agent Lexical_item object
older_child 4 no_agent Lexical_item object
older_child 4 no_agent Lexical_item object
older_child 5 agent Classifier object
older_child 5 agent Classifier object
older_child 5 agent Classifier object
older_child 5 agent Classifier object
older_child 5 agent Classifier handling
older_child 5 agent Classifier handling
older_child 5 agent Classifier handling
older_child 5 agent Classifier handling
older_child 5 agent Classifier handling
older_child 5 agent Lexical_item object
older_child 5 agent Lexical_item object
older_child 5 agent Lexical_item object
older_child 5 no_agent Classifier object
older_child 5 no_agent Classifier object
older_child 5 no_agent Classifier object
older_child 5 no_agent Classifier object
older_child 5 no_agent Lexical_item object
older_child 5 no_agent Lexical_item object
older_child 5 no_agent Lexical_item object
older_child 5 no_agent Lexical_item object
older_child 5 no_agent Lexical_item object
older_child 5 no_agent Lexical_item object
older_child 5 no_agent Lexical_item object
older_child 5 no_agent Lexical_item object
older_child 5 no_agent Lexical_item object
older_child 5 no_agent Lexical_item object
older_child 6 agent Classifier object
older_child 6 agent Classifier object
older_child 6 agent Classifier handling
older_child 6 agent Classifier handling
older_child 6 agent Classifier handling
older_child 6 agent Classifier handling
older_child 6 agent Classifier handling
older_child 6 agent Classifier handling
older_child 6 agent Classifier handling
older_child 6 agent Classifier handling
older_child 6 agent Classifier handling
older_child 6 agent Classifier handling
older_child 6 agent Classifier handling
older_child 6 agent Lexical_item object
older_child 6 agent Lexical_item object
older_child 6 agent Lexical_item object
older_child 6 agent Lexical_item object
older_child 6 agent Lexical_item object
older_child 6 agent Lexical_item object
older_child 6 agent Lexical_item object
older_child 6 agent Lexical_item object
older_child 6 agent Lexical_item object
older_child 6 agent Lexical_item object
older_child 6 agent Lexical_item object
older_child 6 agent Lexical_item object
older_child 6 agent Lexical_item object
older_child 6 agent Lexical_item object
older_child 6 no_agent Classifier object
older_child 6 no_agent Classifier object
older_child 6 no_agent Classifier object
older_child 6 no_agent Classifier object
older_child 6 no_agent Classifier object
older_child 6 no_agent Classifier object
older_child 6 no_agent Classifier object
older_child 6 no_agent Classifier object
older_child 6 no_agent Classifier object
older_child 6 no_agent Classifier object
older_child 6 no_agent Classifier object
older_child 6 no_agent Classifier object
older_child 6 no_agent Classifier object
older_child 6 no_agent Classifier object
older_child 6 no_agent Classifier object
older_child 6 no_agent Classifier object
older_child 6 no_agent Classifier object
older_child 6 no_agent Classifier object
*older_child 6 no_agent Classifier handling
*older_child 6 no_agent Lexical_item object
older_child 6 no_agent Lexical_item object
older_child 6 no_agent Lexical_item object
older_child 6 no_agent Lexical_item object
older_child 6 no_agent Lexical_item object
older_child 6 no_agent Lexical_item object
older_child 6 no_agent Lexical_item object
older_child 6 no_agent Lexical_item object
older_child 6 no_agent Lexical_item object
older_child 6 no_agent Lexical_item object
older_child 6 no_agent Lexical_item object
older_child 6 no_agent Lexical_item object
older_child 6 no_agent Lexical_item object
older_child 6 no_agent Lexical_item object
*older_child 6 no_agent Lexical_item handling
*
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