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

[Mario Garrido]

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

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