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I ran a mixed effects model a few weeks ago, it all went fine, no errors. Here is the model:

logRT ~ condition * NumSpk * Group + (condition * NumSpk | Participant)

I tried to run now the exact same model - and I get a singular fit message. I didn't change anything, simply ran it again. I tried several times - I get this singular fit message every time.

When I observe the correlation matrix of the random effects - nothing changed between last time and this time. To my understanding, a singular fit would also reflect in correlations near +1 or -1. This is not the case, not then and not now. Here is the correlation matrix:

Random effects:
 Groups      Name                               Variance  Std.Dev. Corr                         
 Participant (Intercept)                        0.0066121 0.08131                               
             conditiondivided_vs_mean           0.0004034 0.02008  -0.48                        
             NumSpk2-1                          0.0004550 0.02133  -0.16  0.15                  
             NumSpk3-2                          0.0001917 0.01385  -0.68 -0.13  0.47            
             conditiondivided_vs_mean:NumSpk2-1 0.0001640 0.01281  -0.49  0.32  0.41  0.60      
             conditiondivided_vs_mean:NumSpk3-2 0.0004466 0.02113   0.11  0.02  0.41 -0.02  0.45
 Residual                                       0.0156130 0.12495                               
Number of obs: 11088, groups:  Participant, 69

Anyone has any idea what went wrong? Why did I get now this singular fit message?

EDITS:

  1. A picture of the message: enter image description here
  2. A link to the R data frame on which I run the model: https://drive.google.com/open?id=1qBOPjEk6oHv33OUyfObzOuJHmGNhvU8a
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  • $\begingroup$ Exactly what does the message state? $\endgroup$ – whuber Feb 13 '19 at 14:36
  • $\begingroup$ Just a red message that says "singular fit". In the summary of the model it also appears in the bottom (convergence code: 0, singular fit). $\endgroup$ – Galit Feb 13 '19 at 14:46
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    $\begingroup$ The estimated variances are quite low, so it is perhaps questionable whether the data supports those random effects. What is the scale of the numeric variables ? Rescaling might help. $\endgroup$ – Robert Long Feb 13 '19 at 16:45
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    $\begingroup$ Please post a link to your data. Anonymise it first if you need to. You should get some decent answers then. Otherwise people can only guess. $\endgroup$ – Robert Long Feb 14 '19 at 8:08
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    $\begingroup$ @RobertLong, Thank you. You are absolutely right, I'd be happy if anyone could take a look. This is the link to an R data frame, the input to the model stated in the question: drive.google.com/file/d/1qBOPjEk6oHv33OUyfObzOuJHmGNhvU8a/… $\endgroup$ – Galit Feb 15 '19 at 12:14
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I suspect that this may be due to the version of lme4 that you are using. I do not get the the warning. The random effects are estimated slightly differently so it hard to say if your warning is a false positive or not - I suspect that it is, and that the difference in the estimates is due to a different version, since they are very close.

As mentioned in my comment in the question, the variances of the random effects are very small, and I see very little advantage in fitting random slopes. I fitted the model without random slopes and found the fixed effects estimates almost unchanged. Also, a likelihood ratio test shows that the reduced model is indeed preferred.

Here is my relevantsessionInfo():

R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.1 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8    LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  splines   stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] emmeans_1.3.2      bindrcpp_0.2.2     dplyr_0.7.6        lme4_1.1-18-1      Matrix_1.2-15      deming_1.3        
 [7] rugarch_1.4-1      tfestimators_1.9.1 htmltools_0.3.6    DT_0.4             ggthemes_4.0.1     ggplot2_3.1.0     
[13] shiny_1.1.0        magrittr_1.5       rvest_0.3.2        xml2_1.2.0         gbm_2.1.3          lattice_0.20-38   
[19] survival_2.43-3    RPostgreSQL_0.6-2  DBI_1.0.0          jsonlite_1.5      

And here is the output from fitting the full model and running summary():

> lmm1 <- lmer(logRT ~ condition * NumSpk * Group + (condition * NumSpk | Participant), data = Bar_data_RT)
> summary(lmm1)
Linear mixed model fit by REML ['lmerMod']
Formula: logRT ~ condition * NumSpk * Group + (condition * NumSpk | Participant)
   Data: Bar_data_RT

REML criterion at convergence: -13991

Scaled residuals: 
   Min     1Q Median     3Q    Max 
-5.797 -0.670 -0.104  0.560  3.939 

Random effects:
 Groups      Name                               Variance Std.Dev. Corr                         
 Participant (Intercept)                        0.006919 0.0832                                
             conditiondivided_vs_mean           0.000426 0.0206   -0.48                        
             NumSpk2-1                          0.000495 0.0223   -0.16  0.15                  
             NumSpk3-2                          0.000208 0.0144   -0.67 -0.13  0.46            
             conditiondivided_vs_mean:NumSpk2-1 0.000193 0.0139   -0.47  0.30  0.37  0.61      
             conditiondivided_vs_mean:NumSpk3-2 0.000491 0.0222    0.11  0.02  0.40 -0.04  0.39
 Residual                                       0.015617 0.1250                                
Number of obs: 11088, groups:  Participant, 69

Fixed effects:
                                           Estimate Std. Error t value
(Intercept)                                7.112816   0.016751  424.61
conditiondivided_vs_mean                   0.019425   0.004574    4.25
NumSpk2-1                                  0.023218   0.006492    3.58
NumSpk3-2                                  0.016247   0.005673    2.86
Groupp                                    -0.014598   0.023935   -0.61
Groups                                     0.043286   0.025137    1.72
conditiondivided_vs_mean:NumSpk2-1         0.004727   0.005482    0.86
conditiondivided_vs_mean:NumSpk3-2         0.030852   0.006599    4.68
conditiondivided_vs_mean:Groupp            0.013792   0.006533    2.11
conditiondivided_vs_mean:Groups           -0.014269   0.006896   -2.07
NumSpk2-1:Groupp                          -0.002179   0.009259   -0.24
NumSpk3-2:Groupp                           0.000964   0.008088    0.12
NumSpk2-1:Groups                          -0.007775   0.009849   -0.79
NumSpk3-2:Groups                          -0.021268   0.008657   -2.46
conditiondivided_vs_mean:NumSpk2-1:Groupp -0.003391   0.007813   -0.43
conditiondivided_vs_mean:NumSpk3-2:Groupp -0.001763   0.009410   -0.19
conditiondivided_vs_mean:NumSpk2-1:Groups -0.009818   0.008354   -1.18
conditiondivided_vs_mean:NumSpk3-2:Groups -0.009678   0.010024   -0.97

Correlation matrix not shown by default, as p = 18 > 12.
Use print(x, correlation=TRUE)  or
    vcov(x)        if you need it

And finally, the likelihood ratio test:

> lmm0 <- lmer(logRT ~ condition * NumSpk * Group + (1 | Participant), data = Bar_data_RT)
> anova(lmm0, lmm1)
refitting model(s) with ML (instead of REML)
Data: Bar_data_RT
Models:
lmm0: logRT ~ condition * NumSpk * Group + (1 | Participant)
lmm1: logRT ~ condition * NumSpk * Group + (condition * NumSpk | Participant)
     Df    AIC    BIC logLik deviance Chisq Chi Df          Pr(>Chisq)    
lmm0 20 -13831 -13685   6936   -13871                                     
lmm1 40 -14058 -13766   7069   -14138   267     20 <0.0000000000000002 ***
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  • $\begingroup$ Thanks. I downgraded my lme4 version to yours - and still I get this singular fit message. Now I am just curious as to what is going on here. Could there be another relevant package that has a different version from yours? Also, I would like to know in principle if different versions provide different results - which veresion should we "trust"? What are they doing differently? $\endgroup$ – Galit Feb 17 '19 at 7:09
  • $\begingroup$ Do you get the warning without random slopes too ? Obviously something is different. Have you looked at the rest of the sessioninfo we have in common ? $\endgroup$ – Robert Long Feb 17 '19 at 10:57
  • $\begingroup$ I don't get a warning when I remove the random slopes. I tried to figure out what other differences relevant to lmer were betewen our sessioninfo. I thought maybe it was because I have lmerTest and you don't. I removed lmerTest, but still - singular fit. New R session - same error. However, when I restarted my computer and allowed for updates (Windows) - error disappeared. I find this puzzling, I would assume that Windows updates have no impact on R's internal algorithms. Do you have an idea or an explanation for this situation? $\endgroup$ – Galit Feb 18 '19 at 21:19

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