[R-sig-ME] [R] Different random intercepts but same random slope for groups
li li
hannah.hlx at gmail.com
Wed Jun 10 19:39:44 CEST 2015
2015-06-10 12:45 GMT-04:00, Ben Bolker <bbolker at gmail.com>:
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> Li li: *please* stop cc'ing r-help on the reply.
>
> If group2 and group3 are numeric dummy variables you can add a
> difference in the residual variance as follows ...
>
> alldata$obs <- factor(seq(nrow(alldata)))
>
> ... + (group2|obs) + (group3|obs) + ...
>
> you may need to use lmerControl() to override some of the
> warnings/errors about having as many levels of the random effect as
> there are observations.
>
> Or you could do this in lme and use weights=varIdent(form=~1|group)
>
>
> On 15-06-10 12:40 PM, li li wrote:
>> Thanks all for the reply,
>>
>> I think what Bert specified is what I wanted. Thanks very much. So
>> this model allows different random intercept term but the same
>> random slope term for the three methods.
>>
>> I have an additional question. I would like to require differnt
>> residual variance also for the three groups. Is that possible?
>>
>> Thanks!!
>>
>> 2015-06-09 17:25 GMT-04:00, Bert Gunter <bgunter.4567 at gmail.com>:
>>> Thierry:
>>>
>>> I don't think so. It looks to me like her syntax/understanding is
>>> confused. I think the call should be:
>>>
>>> mod2 <- lmer(result ~ group*time+(group + time|lot),
>>> na.action=na.omit, data=alldata)
>>>
>>> Her request for "the same random slope for each group" -- I
>>> assume it's for time -- means to me that the time slope will vary
>>> "randomly" by lot only, the slope would be the same for all
>>> groups within the lot.
>>>
>>> Of course, I may be wrong also. If so, I suggest that she follow
>>> the posting guide and post at least head(alldata) using dput() to
>>> enable folks to understand the structure of her data. And only on
>>> r-sig-mixed-models -- crossposting is frowned upon here and the
>>> mixed models list is the best bet for this sort of question
>>> anyway.
>>>
>>> As always, corrections and criticism welcome.
>>>
>>> Cheers, Bert
>>>
>>> Bert Gunter
>>>
>>> "Data is not information. Information is not knowledge. And
>>> knowledge is certainly not wisdom." -- Clifford Stoll
>>>
>>> On Tue, Jun 9, 2015 at 1:49 PM, Thierry Onkelinx
>>> <thierry.onkelinx at inbo.be> wrote:
>>>
>>>> Your model is too complex for the data. This gives you two
>>>> options: a) simplify the model and b) get more data.
>>>>
>>>> Best regards,
>>>>
>>>> ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek /
>>>> Research Institute for Nature and Forest team Biometrie &
>>>> Kwaliteitszorg / team Biometrics & Quality Assurance
>>>> Kliniekstraat 25 1070 Anderlecht Belgium
>>>>
>>>> To call in the statistician after the experiment is done may be
>>>> no more than asking him to perform a post-mortem examination:
>>>> he may be able to say what the experiment died of. ~ Sir Ronald
>>>> Aylmer Fisher The plural of anecdote is not data. ~ Roger
>>>> Brinner The combination of some data and an aching desire for
>>>> an answer does not ensure that a reasonable answer can be
>>>> extracted from a given body of data. ~ John Tukey
>>>>
>>>> 2015-06-09 21:57 GMT+02:00 li li <hannah.hlx at gmail.com>:
>>>>
>>>>> Hi all, I'd like to fit a random intercept and random slope
>>>>> model. In my data, there are three groups. I want to have
>>>>> different random intercept for each group but the same random
>>>>> slope effect for all three groups. I used the following R
>>>>> command. However, there seems to be some problem. Any
>>>>> suggestions?
>>>>>
>>>>>
>>>>>
>>>>> mod2 <- lmer(result ~ group*time+(0+group1+ group2 +
>>>>> group3+time|lot), na.action=na.omit, data=alldata)
>>>>>
>>>>>> summary(mod2)
>>>>> Model is not identifiable... summary from lme4 is returned
>>>>> some computational error has occurred in lmerTest Linear
>>>>> mixed model fit by REML ['merModLmerTest'] Formula: result ~
>>>>> group * time + (0 + group1 + group2 + group3 + time | lot)
>>>>> Data: alldata
>>>>>
>>>>> REML criterion at convergence: 807.9
>>>>>
>>>>> Scaled residuals: Min 1Q Median 3Q Max -3.0112
>>>>> -0.3364 0.0425 0.2903 3.2017
>>>>>
>>>>> Random effects: Groups Name Variance Std.Dev. Corr lot
>>>>> group1 0.00000 0.000 group2 86.20156 9.284 NaN
>>>>> group3 55.91479 7.478 NaN 0.06 time 0.02855 0.169
>>>>> NaN -0.99 0.10 Residual 39.91968 6.318 Number of
>>>>> obs: 119, groups: lot, 15
>>>>>
>>>>> Fixed effects: Estimate Std. Error t value (Intercept)
>>>>> 100.1566 2.5108 39.89 group group2 -2.9707
>>>>> 3.7490 -0.79 group group3 -0.0717 2.8144
>>>>> -0.03 time -0.1346 0.1780
>>>>> -0.76 group group2 :time 0.1450 0.2939 0.49 group
>>>>> group3:time 0.1663 0.2152 0.77
>>>>>
>>>>> Warning messages: 1: In checkConv(attr(opt, "derivs"),
>>>>> opt$par, ctrl = control$checkConv,
>>>> :
>>>>> Model failed to converge with max|grad| = 0.147314 (tol =
>>>>> 0.002, component 2) 2: In checkConv(attr(opt, "derivs"),
>>>>> opt$par, ctrl = control$checkConv,
>>>> :
>>>>> Model failed to converge: degenerate Hessian with 2
>>>>> negative
>>>> eigenvalues
>>>>>
>>>>> ______________________________________________
>>>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more,
>>>>> see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do
>>>>> read the posting guide
>>>>> http://www.R-project.org/posting-guide.html and provide
>>>>> commented, minimal, self-contained, reproducible code.
>>>>>
>>>>
>>>> [[alternative HTML version deleted]]
>>>>
>>>> ______________________________________________
>>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more,
>>>> see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read
>>>> the posting guide http://www.R-project.org/posting-guide.html
>>>> and provide commented, minimal, self-contained, reproducible
>>>> code.
>>>>
>>>
>>
>> _______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>>
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