[R-sig-ME] help: error in (function...): Downdated VtV is not positive definite and convergence problems

[Mario Garrido]

Thanks again Dr. Rizopoulos,
i cannot find the command initial values in the Package 'lme4' PDF here:
https://cran.r-project.org/web/packages/lme4/lme4.pdf

Where can I look how to use it?

thanks!

2018-10-08 14:09 GMT+03:00 Mario Garrido <gaadio using post.bgu.ac.il>:

> Thanks so much Dimitris,
> in any case, now I have recieved another warning
>
> fm <- mixed_model(countMyc.qPCR ~ sp + day, random = ~ 0+day | exp.ID,
> data = MycGLMM, family = poisson())
> Error in optim(par = b_i, fn = log_post_b, gr = score_log_post_b, method =
> "BFGS",  :
>   non-finite value supplied by optim
>
> Any idea why?
>
> Thanks!
>
> PS, sorry to insist, but is not a problem what I said in the mail
> before? due the differences in scales between the minimum and maximum value
>
>
>
>
> El sáb., 6 oct. 2018 19:56, D. Rizopoulos <d.rizopoulos using erasmusmc.nl>
> escribió:
>
>> You could give a try to the GLMMadaptive package that can fit the same
>> model using the adaptive Gaussian quadrature, i.e.,
>>
>> library(GLMMadaptive)
>> fm <- mixed_model(countMyc.qPCR ~ sp + day, random = ~ 0 day | exp.ID,
>> data = your_data, family = poisson())
>> summary(fm)
>>
>> Best,
>> Dimitris
>>
>>
>> - - - - - -
>> Dimitris Rizopoulos
>> Professor of Biostatistics
>> Erasmus University Medical Center
>> The Netherlands
>>
>> *From: *Mario Garrido <gaadio using post.bgu.ac.il>
>> *Date: *Saturday, 06 Oct 2018, 4:26 PM
>> *To: *r-sig-mixed-models using r-project.org <r-sig-mixed-models using r-project.org>
>> *Subject: *[R-sig-ME] help: error in (function...): Downdated VtV is not
>> positive definite and convergence problems
>>
>> Hello,
>> I tried to fit a GLMM and I get the following error. I know that my data
>> is
>> probably more negative binomial than Poisson (sd>>mean), but I want to
>> understand where this problem comes from
>>
>> glmer(countMyc.qPCR ~ sp+day +(0+day|exp.ID), family=poisson)
>>
>> Error in (function (fr, X, reTrms, family, nAGQ = 1L, verbose = 0L, maxit
>> =
>> 100L,  :
>>   Downdated VtV is not positive definite
>>
>> *countMyc.qPCR*:amount of bacteria ina particualr individual     Numeric
>> discrete value
>> *sp*:species each individual vbelongs to Factor w/ 3 levels "GA","GG","GP"
>> *day*: day of infection    Numeric discrete value
>> *exp.ID*: number of individual under experiment  Factor w/ 33 levels
>> "EA1","EA10","EA12",..: 3 6 7 10 11 14 18 21 22 31 ...
>>
>> I fixed the random factor as 0+day|exp.ID cause at day zero the amount of
>> bacteria is zero
>>
>> Can be the error due the differences in scales between the minimum and
>> maximum value
>> > describe.by(countMyc.qPCR)
>>    vars   n     mean       sd       median   trimmed     mad      min
>>    max      range       skew      kurtosis       se
>> X1  1    363  127789.2  783829.6      6      455.65      8.9       0
>>  8434322   8434322     7.84        67.75      41140.39
>>
>> In addition, when I tried to fix an simpler data I have also warnings, but
>> other kinds
>>
>> glmer(countMyc.qPCR ~day +(0+day|exp.ID), family=poisson)
>> Generalized linear mixed model fit by maximum likelihood (Laplace
>> Approximation) ['glmerMod']
>>  Family: poisson  ( log )
>> Formula: countMyc.qPCR ~ day + (0 + day | exp.ID)
>>        AIC        BIC     logLik   deviance   df.resid
>>  213021061  213021073 -106510528  213021055        360
>> Random effects:
>>  Groups Name Std.Dev.
>>  exp.ID day  0.1742
>> Number of obs: 363, groups:  exp.ID, 33
>> Fixed Effects:
>> (Intercept)          day
>>     13.3201      -0.1898
>> convergence code 0; 1 optimizer warnings; 0 lme4 warnings
>> Warning message:
>> In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
>>   Model is nearly unidentifiable: very large eigenvalue
>>  - Rescale variables?
>>
>>
>> PS. I saw a similar question before (19th July) but cannot find a solution
>> there
>> --
>> Mario Garrido Escudero, PhD
>> Dr. Hadas Hawlena Lab
>> Mitrani Department of Desert Ecology
>> Jacob Blaustein Institutes for Desert Research
>> Ben-Gurion University of the Negev
>> Midreshet Ben-Gurion 84990 ISRAEL
>>
>> gaiarrido using gmail.com; gaadio using post.bgu.ac.il
>> phone: (+972) 08-659-6854
>>
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>>
>> _______________________________________________
>> R-sig-mixed-models using r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>>
>
>
>
> --
> Mario Garrido Escudero, PhD
> Dr. Hadas Hawlena Lab
> Mitrani Department of Desert Ecology
> Jacob Blaustein Institutes for Desert Research
> Ben-Gurion University of the Negev
> Midreshet Ben-Gurion 84990 ISRAEL
>
> gaiarrido using gmail.com; gaadio using post.bgu.ac.il
> phone: (+972) 08-659-6854
>
>
>


-- 
Mario Garrido Escudero, PhD
Dr. Hadas Hawlena Lab
Mitrani Department of Desert Ecology
Jacob Blaustein Institutes for Desert Research
Ben-Gurion University of the Negev
Midreshet Ben-Gurion 84990 ISRAEL

gaiarrido using gmail.com; gaadio using post.bgu.ac.il
phone: (+972) 08-659-6854

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