[R-sig-ME] "parm" parameter in lme4::confint.merMod

Ben Bolker bbolker at gmail.com
Sun May 18 16:21:00 CEST 2014

On 14-05-18 07:34 AM, Henrik Singmann wrote:
> Hi Jake,
> I think fixef() or names(fixef()) gives you what you want:

  I don't think it gets you everything.  Your solution works
in the method="Wald" case because method="Wald" only returns
the fixed effects, so one only has to keep track of those
positions.  method="profile" and "boot" include both
variance-covariance and fixed effect parameters, in that order.
Some possibilities are

## this gives names of 'theta' parameters (i.e. Cholesky factors)
## rather than standard deviations/correlations, but I believe
## the order is the same

## theta parameters only (hidden function)

data(md_16.4, package = "afex")
m1 <-  lmer(induct ~ cond*cog + (cog|room:cond), md_16.4)

## I actually had some problems with profiling this example --
## not quite sure why.  Will have to look into it.
pp <- profile(m1)

> fixef(m1)
> ## (Intercept)       cond1         cog   cond1:cog
> ## -6.14153043 10.32001485  0.66722061 -0.02520666
> confint(m1, parm = c(3,2), method="Wald")
> ##             2.5 %    97.5 %
> ## cog     0.2498764  1.084565
> ## cond1 -18.4845630 39.124593
> I hope I didn't misunderstand your question,
> Henrik
> Am 18.05.2014 08:03, schrieb Jake Westfall:
>> Hi all,
>> According to the documentation, in confint.merMod() you can use the
>> "parm" parameter to get confidence intervals for only a specified
>> subset of parameters by indicating the integer positions of the
>> desired parameters. But how is one supposed to know which integer
>> positions correspond with which parameters? I poked around a little
>> but found nothing in the methods or slots of the merMod object that
>> indicates this, and nothing in the documentation detailing this. Have
>> I missed something? I guess you can call the function leaving that
>> argument at its default, and the order of the parameters in that
>> output will correspond with the integer positions, but this approach
>> would seem to defeat the point of being able to specify particular
>> subsets of parameters...
>> Jake                        
>>     [[alternative HTML version deleted]]

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