[R-sig-ME] blme optimizer warnings
Sijia Huang
hu@ng@jcc @end|ng |rom gm@||@com
Thu May 14 04:57:54 CEST 2020
Thank you so much, Vincent!
On Wed, May 13, 2020 at 7:54 PM Vincent Dorie <vdorie using gmail.com> wrote:
> A couple of guesses here in addition to what Ben mentioned, but you
> likely don't want a prior on the covariance of the random effects and
> the weights should be on the scale of inverse variances. The following
> replicates the numbers for the CCREM column from table 1:
>
> blmer(g ~ 1 + (1 | Study) + (1 | Subscale) + (1 | Outcome:Study:Subscale),
> data = meta, weights = Precision, control =
> lmerControl(optimizer = "bobyqa"),
> resid.prior = point(1), cov.prior = NULL)
>
>
> On Wed, May 13, 2020 at 10:04 PM Sijia Huang <huangsjcc using gmail.com> wrote:
> >
> > Here it is. Thanks!
> >
> > A demonstration and evaluation of the use of cross-classified
> > random-effects models for meta-analysis
> >
> > On Wed, May 13, 2020 at 6:57 PM Ben Bolker <bbolker using gmail.com> wrote:
> >
> > >
> > > Can you give a more specific reference? I can't immediately guess
> from
> > > Fernández-Castilla's google scholar page which article it is ...
> > > On 5/13/20 9:36 PM, Sijia Huang wrote:
> > >
> > > Thanks for the quick reply, Ben!
> > >
> > > I am replicating the Fernández-Castilla et al. (2018) article. Below
> are
> > > the data they have in the article. Anything I can do to resolve the
> issue?
> > > Thanks!
> > >
> > > > meta
> > > Study Outcome Subscale g Variance Precision
> > > 1 1 1 1 -0.251 0.024 41.455
> > > 2 2 1 1 -0.069 0.001 1361.067
> > > 3 3 1 5 0.138 0.001 957.620
> > > 4 4 1 1 -0.754 0.085 11.809
> > > 5 5 1 1 -0.228 0.020 49.598
> > > 6 6 1 6 -0.212 0.004 246.180
> > > 7 6 2 7 0.219 0.004 246.095
> > > 8 7 1 1 0.000 0.012 83.367
> > > 9 8 1 2 -0.103 0.006 162.778
> > > 10 8 2 3 0.138 0.006 162.612
> > > 11 8 3 4 -0.387 0.006 160.133
> > > 12 9 1 1 -0.032 0.023 44.415
> > > 13 10 1 5 -0.020 0.058 17.110
> > > 14 11 1 1 0.128 0.017 59.999
> > > 15 12 1 1 -0.262 0.032 31.505
> > > 16 13 1 1 -0.046 0.071 14.080
> > > 17 14 1 6 -0.324 0.003 381.620
> > > 18 14 2 6 -0.409 0.003 378.611
> > > 19 14 3 7 0.080 0.003 385.319
> > > 20 14 4 7 -0.140 0.003 385.542
> > > 21 15 1 1 0.311 0.005 185.364
> > > 22 16 1 1 0.036 0.005 205.063
> > > 23 17 1 6 -0.259 0.001 925.643
> > > 24 17 2 7 0.196 0.001 928.897
> > > 25 18 1 1 0.157 0.013 74.094
> > > 26 19 1 1 0.000 0.056 17.985
> > > 27 20 1 1 0.000 0.074 13.600
> > > 28 21 1 6 -0.013 0.039 25.425
> > > 29 21 2 7 -0.004 0.039 25.426
> > > 30 22 1 1 -0.202 0.001 1487.992
> > > 31 23 1 1 0.000 0.086 11.628
> > > 32 24 1 1 -0.221 0.001 713.110
> > > 33 25 1 1 -0.099 0.001 749.964
> > > 34 26 1 5 -0.165 0.000 6505.024
> > > 35 27 1 1 -0.523 0.063 15.856
> > > 36 28 1 1 0.000 0.001 1611.801
> > > 37 29 1 6 0.377 0.045 22.045
> > > 38 29 2 7 0.575 0.046 21.677
> > > 39 30 1 1 0.590 0.074 13.477
> > > 40 31 1 1 0.020 0.001 1335.991
> > > 41 32 1 1 0.121 0.043 23.489
> > > 42 33 1 1 -0.101 0.003 363.163
> > > 43 34 1 1 -0.101 0.003 369.507
> > > 44 35 1 1 -0.104 0.004 255.507
> > > 45 36 1 1 -0.270 0.003 340.761
> > > 46 37 1 1 0.179 0.150 6.645
> > > 47 38 1 2 0.468 0.020 51.255
> > > 48 38 2 4 -0.479 0.020 51.193
> > > 49 39 1 5 -0.081 0.024 42.536
> > > 50 40 1 1 -0.071 0.043 23.519
> > > 51 41 1 1 0.201 0.077 13.036
> > > 52 42 1 6 -0.070 0.006 180.844
> > > 53 42 2 7 0.190 0.006 180.168
> > > 54 43 1 1 0.277 0.013 79.220
> > > 55 44 1 5 -0.086 0.001 903.924
> > > 56 45 1 5 -0.338 0.002 469.260
> > > 57 46 1 1 0.262 0.003 290.330
> > > 58 47 1 5 0.000 0.003 304.959
> > > 59 48 1 1 -0.645 0.055 18.192
> > > 60 49 1 5 -0.120 0.002 461.802
> > > 61 50 1 5 -0.286 0.009 106.189
> > > 62 51 1 1 -0.124 0.006 172.261
> > > 63 52 1 1 0.023 0.028 35.941
> > > 64 53 1 5 -0.064 0.001 944.600
> > > 65 54 1 1 0.000 0.043 23.010
> > > 66 55 1 1 0.000 0.014 72.723
> > > 67 56 1 5 0.000 0.012 85.832
> > > 68 57 1 1 0.000 0.012 85.832
> > >
> > >
> > > On Wed, May 13, 2020 at 6:00 PM Ben Bolker <bbolker using gmail.com> wrote:
> > >
> > >> Without looking very carefully at this:
> > >>
> > >> * unless your response variable is somehow already centered at zero by
> > >> design, a model with no intercept at all is going to be
> > >> weird/problematic (random effects are always zero-centered by
> definition).
> > >>
> > >> * is it really OK to have an infinite scale in your wishart prior?
> (It
> > >> may be fine, I'm not immediately familiar with the blme
> > >> parameterizations, it just looks weird)
> > >>
> > >> * the fact that your standard devs are all exactly 1 suggests that the
> > >> optimizer bailed out before actually doing anything (these are the
> > >> default starting values).
> > >>
> > >> Can you provide a reproducible example?
> > >>
> > >> On 5/13/20 8:53 PM, Sijia Huang wrote:
> > >> > Hi everyone,
> > >> > I am fitting a cross-classified model with blme, but getting 1
> optimizer
> > >> > warning. The code and output are shown below. Any suggestions
> regarding
> > >> > fixing the estimation issue? Thanks!
> > >> >
> > >> >
> > >> >> meta.example <- blmer(g~0+(1|Study)+(1|Subscale)+
> > >> > 1|Outcome:Study:Subscale),
> > >> > + data=meta, weights = Variance,
> > >> > + resid.prior = point(1),
> > >> > + control = lmerControl(optimizer="bobyqa"))
> > >> >
> > >> >> meta.example
> > >> > Cov prior : Outcome:Study:Subscale ~ wishart(df = 3.5, scale = Inf,
> > >> > posterior.scale = cov, common.scale = TRUE)
> > >> > : Study ~ wishart(df = 3.5, scale = Inf,
> posterior.scale =
> > >> cov,
> > >> > common.scale = TRUE)
> > >> > : Subscale ~ wishart(df = 3.5, scale = Inf,
> posterior.scale
> > >> =
> > >> > cov, common.scale = TRUE)
> > >> > Resid prior: point(value = 1)
> > >> > Prior dev : NaN
> > >> >
> > >> > Linear mixed model fit by maximum likelihood ['blmerMod']
> > >> > Formula: g ~ 0 + (1 | Study) + (1 | Subscale) + (1 |
> > >> Outcome:Study:Subscale)
> > >> > Data: meta
> > >> > Weights: Variance
> > >> > AIC BIC logLik deviance df.resid
> > >> > Inf Inf -Inf Inf 64
> > >> > Random effects:
> > >> > Groups Name Std.Dev.
> > >> > Outcome:Study:Subscale (Intercept) 1
> > >> > Study (Intercept) 1
> > >> > Subscale (Intercept) 1
> > >> > Residual 1
> > >> > Number of obs: 68, groups: Outcome:Study:Subscale, 68; Study, 57;
> > >> > Subscale, 7
> > >> > No fixed effect coefficients
> > >> > convergence code 0; 1 optimizer warnings; 0 lme4 warnings
> > >> >
> > >> >
> > >> >
> > >> >
> > >> > Best,
> > >> > Sijia
> > >> >
> > >> > [[alternative HTML version deleted]]
> > >> >
> > >> > _______________________________________________
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> > >>
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> > >>
> > >
> >
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> >
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