[R-sig-ME] Convergence Issue
Phillip Alday
me @end|ng |rom ph||||p@|d@y@com
Thu Sep 2 17:04:01 CEST 2021
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)
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