[R-sig-ME] Kinship vs. Pedigreemm

[Joehanes, Roby (NIH/NHLBI) [F]]

Hi David and lmers:

Thank you. Pedigreemm, whose backend is lmer, also can fit mixed model with a kinship matrix. I think both packages can.

I did a little bit of experiment with both packages and found that the -2 log likelihood value (-2LL) of pedigreemm output is consistently smaller than that of kinship, suggesting better convergence. This is perhaps reflected by the backend numerical optimizers used by the package. Moreover, in pedigreemm, I could specify which random effects are affected by the pedigree factor and which ones are not. I could not find such option in kinship package.

Other than these, I am not aware of any differences---especially on models that can or cannot be specified by either package. I wonder if any of you know of this.

Thank you again,
Roby


On Apr 9, 2012, at 10:36 PM, David Duffy wrote:

> On Mon, 9 Apr 2012, Joehanes, Roby (NIH/NHLBI) [F] wrote:
> 
>> Yes, you are right. It appears that package kinship is now broken into 
>> several packages: coxme, kinship2, bdsmatrix, among others. Are you 
>> aware of the difference between them and pedigreemm?
> 
> Terry Therneau wrote in the lmekin vignette:
> 
> "Let me emphasis this: most models that can be fit with the lmekin 
> function can also be fit with lme and/or lmer. For any such model the 
> lme/lmer functions will be faster and have superior support routines 
> (residuals, printing, plotting, etc.) The solution code for lmer is likely 
> also more reliable since it has been exercised on a much wider variety of 
> data sets.
> 
> "However, there are models that lmekin will fit which lme will not. The 
> most obvious of these are models with a random genetic effect, e.g. a 
> kinship matrix. The second class will be models for which the user has 
> written their own variance extension, as described in the variance 
> vignette."
> 
> 
> -- 
> | David Duffy (MBBS PhD)                                         ,-_|\
> | email: davidD at qimr.edu.au  ph: INT+61+7+3362-0217 fax: -0101  /     *
> | Epidemiology Unit, Queensland Institute of Medical Research   \_,-._/
> | 300 Herston Rd, Brisbane, Queensland 4029, Australia  GPG 4D0B994A v