[R-sig-ME] Likelihood drops on adding random effect
Murray Jorgensen
maj at waikato.ac.nz
Fri May 18 01:36:04 CEST 2012
I guess we may have a case of a sort of spike in the loglikelihood that
indicates that the MLE (or at least the lmer estimate) for the model
without the 'tree' effect is spurious. (Probably the sort of thing that
would be smoothed away by any reasonable prior.) I really was looking
more closely at the other fixed effect parameters, regarding the
intercept as a bit of a nuisance. I hope to say more about the data set
later. Maybe I will do a sort of profile around the intercept value and
just fit the other parameters.
I would like to ask the list for some more help with the 'start ='
parameter though because I don't seem to be quite using it correctly.
> ip2 = c(0, 8.29931, 2.56368e-06, 0.00000)
> f0128bit = lmer(fincr ~ icfac + (1|gap) + (1|box)+ (1|gap:box) +
(1|tree), family = binomial,
+ verbose = TRUE, start = ip2)
0: 775.67797: 0.00000 8.29931 2.56368e-06 0.00000 -3.22238
1.44743 -2.20257 1.02515
1: 747.52247: 0.00000 5.04306 6.75518e-05 0.00000 -4.34098
2.12417 -3.74289 -0.121576
2: 736.84946: 0.00000 4.55878 0.000215665 0.00000 -4.39655
1.52182 -3.63273 -0.115459
...
45: 671.01076: 4.57910e-09 0.287720 0.350164 0.711054 -3.43481
1.45346 -2.57398 0.293897
46: 671.01076: 0.00000 0.287721 0.350162 0.711064 -3.43483
1.45346 -2.57397 0.293955
That works well for initialising the variance parameters only.
> f0128bit = lmer(fincr ~ icfac + (1|gap) + (1|box)+ (1|gap:box) +
(1|tree), family = binomial,
+ verbose = TRUE, start = list( fixef = list( -9.28405,
2.81300, -4.75935, 2.91080),
+ ST = list(0, 8.29931, 2.56368e-06, 0.00000))
+ )
Error: class(STnew[[i]]) == class(ST[[i]]) is not TRUE
In addition: Warning message:
In sort(names(start)) == sort(names(FL)) :
longer object length is not a multiple of shorter object length
A failed attempt to initialise both fixed and random parameters.
> f0128bit = lmer(fincr ~ icfac + (1|gap) + (1|box)+ (1|gap:box) +
(1|tree), family = binomial,
+ verbose = TRUE, start = list( fixef = c( -9.28405,
2.81300, -4.75935, 2.91080),
+ ST = c(0, 8.29931, 2.56368e-06, 0.00000))
+ )
Error: is.list(STnew) is not TRUE
In addition: Warning message:
In sort(names(start)) == sort(names(FL)) :
longer object length is not a multiple of shorter object length
Another failure.
> initpar = c(0, 8.29931, 2.56368e-06, 0.00000, -9.28405, 2.81300,
-4.75935, 2.91080)
> f0128bit = lmer(fincr ~ icfac + (1|gap) + (1|box)+ (1|gap:box) +
(1|tree), family = binomial,
+ verbose = TRUE, start = initpar)
0: 696.35176: 1.15470 0.222222 0.182574 0.157135 -3.22238
1.44743 -2.20257 1.02515
1: 687.88422: 0.646498 0.349241 0.199295 0.375671 -4.02981
1.29061 -2.23330 1.01588
...
26: 671.01076: 0.00000 0.287718 0.350162 0.711060 -3.43482
1.45346 -2.57397 0.293937
27: 671.01076: 0.00000 0.287721 0.350163 0.711061 -3.43482
1.45346 -2.57398 0.293936
Runs, but does not seem to use the supplied starting parameters.
Thanks, for your comments.
Murray
On 18/05/2012 5:48 a.m., Douglas Bates wrote:
> Look at the values of the coefficients and standard deviations that
> you are "converging" to. Your intercept is -9.28, which, with a
> binomial family, corresponds to probabilities below 1e-4. With icfac
> = fem the linear predictor is -9.28 - 4.76 = -14.04 corresponding to a
> probability of 8e-07.
>
> You are going to need to look at the data and the proportions of
> positives for different levels of icfac to see what would make sense.
> This problem will create a very ill-defined likelihood surface because
> the fitted values will lose sensitivity to the parameters when the
> probabilities are so extreme. If you start extreme values you will
> never be able to converge.
>
> On Thu, May 17, 2012 at 12:37 AM, Murray Jorgensen<maj at waikato.ac.nz> wrote:
>> PS I also tried
>>
>> start = list( fixef = c( -9.28405, 2.81300, -4.75935, 2.91080),
>> ST = c(0, 8.29931, 2.56368e-06, 0.00000))
>>
>> and
>>
>> start = list( fixef = list( -9.28405, 2.81300, -4.75935, 2.91080),
>> ST = list(0, 8.29931, 2.56368e-06, 0.00000))
>>
>> to no avail.
>>
>>
>> _______________________________________________
>> R-sig-mixed-models at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
--
Dr Murray Jorgensen http://www.stats.waikato.ac.nz/Staff/maj.html
Department of Statistics, University of Waikato, Hamilton, New Zealand
Email: maj at waikato.ac.nz majmurr at gmail.com Fax 7 838 4155
Phone +64 7 838 4773 wk Home +64 7 825 0441 Mobile 021 0200 8350
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