[R-sig-ME] glmer and influence.me - complaining about nAGQ==0
bbo|ker @end|ng |rom gm@||@com
Sat Apr 24 23:08:14 CEST 2021
Don't have much to add to John's comments. You can see
vignette("lmerperf") for a few suggestions on improving performance.
I'm a little surprised that your response variable is "logRT" *and*
you have a log-link; that seems like double-logging? (I was going to
suggest that if you aren't wedded to the Gamma model, a log-Normal model
(lmer(log(logRT) ~ ...) would probably be a lot faster ...)
It's possible that other platforms (glmmTMB, Julia::MixedModels.jl)
would be faster ... but then you might be stuck without influence
diagnostics again ...
On 4/24/21 3:52 PM, John Fox wrote:
> Dear Catia,
> I believe I understand what's going on: influence.merMod() works by
> updating the model -- it calls update() -- using the parameter estimates
> for the fit to the full data as start-values. The idea is to decrease
> the computation necessary for each re-fit.
> It probably would have been better if I had made this an option, with
> using the start-values as the default, but perhaps there's a work-around:
> You may be able to fit your model without specifying nACQ by instead
> specifying the estimates that you obtained as start-values. Then glmer()
> may converge quickly. If it doesn't, that would, I suppose, indicate
> some sort of ill-conditioning.
> Ben might well have something to add.
> I hope this helps,
> John Fox, Professor Emeritus
> McMaster University
> Hamilton, Ontario, Canada
> web: https://socialsciences.mcmaster.ca/jfox/
> On 2021-04-24 2:29 p.m., Cátia Ferreira De Oliveira via
> R-sig-mixed-models wrote:
>> Dear Professor Bolker,
>> I am really sorry for bothering you but I have been quite stuck and have
>> posted my question both on reddit and cross validated but nothing has
>> from it. Do you know if there is a good way of running dfbetas for glmer
>> with a gamma distribution? The model runs without issues,
>> lmer_log11 <- glmer(logRT ~ Probability*Block*Session*testing + (1 +
>> Block * Probability * Session|Participant), data= Data, family =
>> Gamma(link = "log"),
>> nAGQ = 0)
>> yet when I run the influence function I get this error:
>> influentialcases <- influence(glmer_log11, "Participant")
>> Error in glmer(formula = RT ~ Probability * Block * Session * testing
>> + :
>> should not specify both start$fixef and nAGQ==0
>> I have tried to remove the "nAGQ==0" but the model is now taking 10
>> days to
>> converge, a lot more than usual. Given this, I haven't been able to check
>> if the influential cases will run normally.
>> Do you have any idea why this is happening? I would very much
>> appreciate your help!
>> Thank you so much!
>> Best wishes,
>> [[alternative HTML version deleted]]
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