lme4, failure to converge with a range of optimisers, trust the fitted model anyway?
One of the problems is that you have a relatively high random effects variance. A standard deviation of the intercept of 3 is a huge amount, it means that there is massive variation in the random effect value needed to model each cluster, to the point that some clusters will be all zeros and some will be all ones. In this situation the assumption of approximate normality of the likelihood around the nodes which is required for using Laplace's method is very far from met. I would find a spare computer and increase nAGQ to say 5. It might take a while to run but hopefully it will be enough to make it converge. Then increase nAGQ until the logLikelihood doesn't change. I have a preference for nlminb. Programs that do random effects logistic with more than one random effect are scarce. I can try Latent Gold with Syntax Module but I'm not certain what limit it has on number of observations.
On 4 April 2015 at 20:29, Hans Ekbrand <hans.ekbrand at gmail.com> wrote:
Dear list,
I know, the failure to converge problem is boring, but still I would
like your input on my situation.
I have tried four optimizers/methods, and they all fail; glmer used.
1. Nelder_Mead: Model failed to converge with max|grad| = 0.00116526
(tol = 0.001, component 6)
2. bobyqa: Model failed to converge with max|grad| = 0.00117064 (tol =
0.001, component 7)
3. optimx, nlminb: Model failed to converge: degenerate Hessian with 4
negative eigenvalues
4. optimx, L-BFGS-B: Model failed to converge with max|grad| =
0.012963 (tol = 0.001, component 7)" "Model failed to converge:
degenerate Hessian with 3 negative eigenvalues
The sample size is large: 1.833.793
The estimates resulting from fitting the model to data with the
different optimizers are similar:
NM bobyqa nlmin BFGS
(Intercept) 4.9857379 3.7283744 4.9477121 3.2138480
QoG 0.7866227 0.5962816 0.7534208 0.5991817
GDPLog -1.5161825 -1.3643422 -1.5111097 -1.2940261
Ruralyes 4.3436228 4.3422641 4.3419199 4.3415551
KilledPerMillion5Log 0.6632158 0.6005677 0.6276264 0.5216984
Ruralyes:KilledPerMillion5Log 0.7313136 0.7316543 0.7314746 0.7329137
My theoretical focus is on the last two rows.
1. Is this likely to be a false positive? I'm willing to share data if
that can help the development of lme4.
2. If the fits are bad, then what are my alternatives? continue with
glmer and increase nAGQ? Other ideas? Or do I need to use other
packages? I really love lme4, so I hope this will not be necessary.
Kind regards,
Hans Ekbrand
Postscript.
Here is the output of summary for the Nelder_Mead fit:
Generalized linear mixed model fit by maximum likelihood (Laplace
Approximation) ['glmerMod']
Family: binomial ( logit )
Formula: SanitationDeprivation ~ (1 | Country) + (1 | ClusterID) + QoG +
GDPLog + Rural * KilledPerMillion5Log
Data: my.df.aid
AIC BIC logLik deviance df.resid
1013298.5 1013397.9 -506641.2 1013282.5 1833785
Scaled residuals:
Min 1Q Median 3Q Max
-9.6390 -0.2883 -0.0508 0.0666 14.6730
Random effects:
Groups Name Variance Std.Dev.
ClusterID (Intercept) 9.675 3.110
Country (Intercept) 11.115 3.334
Number of obs: 1833793, groups: ClusterID, 38177; Country, 65
Fixed effects:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 4.98574 0.08764 56.89 < 2e-16 ***
QoG 0.78662 0.13190 5.96 2.46e-09 ***
GDPLog -1.51618 0.04841 -31.32 < 2e-16 ***
Ruralyes 4.34362 0.04655 93.31 < 2e-16 ***
KilledPerMillion5Log 0.66322 0.15070 4.40 1.08e-05 ***
Ruralyes:KilledPerMillion5Log 0.73131 0.06059 12.07 < 2e-16 ***
---
Signif. codes: 0 ?***? 0.001 ?**? 0.01 ?*? 0.05 ?.? 0.1 ? ? 1
Correlation of Fixed Effects:
(Intr) QoG GDPLog Rurlys KlPM5L
QoG -0.042
GDPLog -0.153 0.129
Ruralyes -0.020 0.067 -0.037
KlldPrMll5L -0.081 -0.113 -0.091 -0.131
Rrlys:KPM5L -0.007 -0.088 -0.044 -0.426 0.205
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