[R-sig-ME] [R] Different random intercepts but same random slope for groups

Wed Jun 10 18:45:02 CEST 2015

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

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.
>>> 
>> 
> 
> _______________________________________________ 
> R-sig-mixed-models at r-project.org mailing list 
> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> 

-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.11 (GNU/Linux)

iQEcBAEBAgAGBQJVeGmOAAoJEOCV5YRblxUH+sQIANQ/wAdPE8ERp95iEKqmpK2B
FFCL7pBIGbO/mEry3GHk57v9h5QR0FhFwsRClJ6zrxXDCpsRW4juaulsqXGQog5Q
aI6WwMyime/pdIQgSozKCTVnpPBPWY6BNs9ZWcR1zwt6oPnwBGtDEcfKS2I6c2cw
Zi0OIoWf8xbD9Oujup7WrLG3RCPu/nS+UlaNxl/h6sFM7dHzhXXDsbaS9B2rwY3n
lkmE+bbHb6UuZJ7NVA5B+F17av7GeTF5F+M6AHH8z5XutnLHCb74CFgpsaCZkQo0
fMdOYAVmcp1hXAaGVsi6nBTXiomnGqfOGmbzCwSw5vQvzy8XCpeh1AUWpxwnugE=
=9z6N
-----END PGP SIGNATURE-----