rstatisticslme4longitudinalmultilevel-analysis

lme4 1.1-27.1 error: pwrssUpdate did not converge in (maxit) iterations


Sorry that this error has been discussed before, each answer on stackoverflow seems specific to the data

I'm attempting to run the following negative binomial model in lme4:

Model5.binomial<-glmer.nb(countvariable ~ waves + var1 + dummycodedvar2 + dummycodedvar3 + (1|record_id), data=datadfomit) 

However, I receive the following error when attempting to run the model:

Error in f_refitNB(lastfit, theta = exp(t), control = control) :pwrssUpdate did not converge in (maxit) iterations

I first ran the model with only 3 predictor variables (waves, var1, dummycodedvar2) and got the same error. But centering the predictors fixed this problem and the model ran fine.

Now with 4 variables (all centered) I expected the model to run smoothly, but receive the error again.

Since every answer on this site seems to point towards a problem in the data, data that replicates the problem can be found here:

https://file.io/3vtX9RwMJ6LF

Solution

  • Your response variable has a lot of zeros:

    enter image description here

    I would suggest fitting a model that takes account of this, such as a zero-inflated model. The GLMMadaptive package can fit zero-inflated negative binomial mixed effects models:

    ## library(GLMMadaptive)
    ## mixed_model(countvariable ~ waves + var1 + dummycodedvar2 + dummycodedvar3, ##   random = ~ 1 | record_id, data = data,
    ##   family = zi.negative.binomial(), 
    ##   zi_fixed = ~ var1,
    ##   zi_random = ~ 1 | record_id) %>% summary()
    
    Random effects covariance matrix:
                    StdDev    Corr
    (Intercept)     0.8029        
    zi_(Intercept)  1.0607 -0.7287
    
    Fixed effects:
                   Estimate Std.Err z-value  p-value
    (Intercept)      1.4923  0.1892  7.8870  < 1e-04
    waves           -0.0091  0.0366 -0.2492 0.803222
    var1             0.2102  0.0950  2.2130 0.026898
    dummycodedvar2  -0.6956  0.1702 -4.0870  < 1e-04
    dummycodedvar3  -0.1746  0.1523 -1.1468 0.251451
    
    Zero-part coefficients:
                Estimate Std.Err z-value    p-value
    (Intercept)   1.8726  0.1284 14.5856    < 1e-04
    var1         -0.3451  0.1041 -3.3139 0.00091993
    
    log(dispersion) parameter:
      Estimate Std.Err
        0.4942  0.2859
    
    Integration:
    method: adaptive Gauss-Hermite quadrature rule
    quadrature points: 11
    
    Optimization:
    method: hybrid EM and quasi-Newton
    converged: TRUE