[R-sig-ME] Convergence Issue

[Phillip Alday]

I don't have time to give more thorough help at the moment, but look at
the help page on converge, accessible via ?convergence in R or mirrored
online, e.g. https://rdrr.io/cran/lme4/man/convergence.html

Hope that helps

Phillip

On 02/09/2021 09:58, Alex Waldman wrote:
> Dear All,
>
> I have a dataset with 119 individuals with information on the presence of lesions of various types (1,2,3) at various levels (1,2,3) and want to understand the effect of type and location on lesion presence. Therefore, I ran the following:
>
> glmer.model<-glmer(LesionPresence ~ Location*Type + (1 | ID), data=lesion_proportion_staged_level, family="binomial")
>
> Unfortunately, I ran into the following warning:
>
> In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
> Model failed to converge with max|grad| = 0.048092 (tol = 0.002, component 1)
>
> I'm quite new to running mixed models and even with some googling am still unsure why I am running into this issue? Any insight would be much appreciated. I am attaching the model output below and the input data in case that is helpful and do let me know if you need any additional information:
> Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) [
> glmerMod]
> Family: binomial  ( logit )
> Formula: LesionPresence ~ Level * LesionType + (1 | ID)
>    Data: lesion_proportion_staged_level
>
>      AIC      BIC   logLik deviance df.resid
>   1080.4   1129.2   -530.2   1060.4      962
>
> Scaled residuals:
>     Min      1Q  Median      3Q     Max
> -1.6875 -0.5649 -0.3291  0.7170  4.2816
>
> Random effects:
> Groups Name        Variance Std.Dev.
> ID     (Intercept) 1.519    1.232
> Number of obs: 972, groups:  ID, 119
>
> Fixed effects:
>                    Estimate Std. Error z value Pr(>|z|)
> (Intercept)         -1.6081     0.2966  -5.423 5.87e-08 ***
> Level1              -0.6006     0.3900  -1.540 0.123600
> Level2              -0.7270     0.4094  -1.776 0.075782 .
> LesionType1          1.6362     0.3538   4.624 3.76e-06 ***
> LesionType2          1.1659     0.3524   3.309 0.000938 ***
> Level1:LesionType1  -0.3568     0.5022  -0.711 0.477379
> Level2:LesionType1  -0.2015     0.5211  -0.387 0.698986
> Level1:LesionType2   0.4030     0.5004   0.805 0.420607
> Level2:LesionType2   0.1608     0.5229   0.308 0.758387
> ---
> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>
> Correlation of Fixed Effects:
>             (Intr) Level1 Level2 LsnTy1 LsnTy2 L1:LT1 L2:LT1 L1:LT2
> Level1      -0.603
> Level2      -0.574  0.447
> LesionType1 -0.703  0.498  0.475
> LesionType2 -0.694  0.503  0.479  0.582
> Lvl1:LsnTy1  0.480 -0.766 -0.339 -0.691 -0.400
> Lvl2:LsnTy1  0.461 -0.344 -0.775 -0.665 -0.385  0.466
> Lvl1:LsnTy2  0.468 -0.772 -0.344 -0.392 -0.692  0.598  0.268
> Lvl2:LsnTy2  0.453 -0.344 -0.773 -0.379 -0.665  0.267  0.607  0.468
> optimizer (Nelder_Mead) convergence code: 0 (OK)
> Model failed to converge with max|grad| = 0.048092 (tol = 0.002, component 1)
> _______________________________________________
> R-sig-mixed-models using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models