[R-sig-ME] Patch for pedigreemm 0.3-3 plus questions

[Roby Joehanes]

Dear all:

Attached please find the patch for pedigreemm 0.3-3, with the following changes:
1. Control options are now passed through to the optimizeLmer / optimizeGlmer, including optimizer, calc.derivs, etc. This saves about 15% of time.
2. Allowing direct matrix specification on pedigree. This will allow broader application in genetics, such as allowing cryptic relatedness to stand in as pedigree matrix.

A few questions from me. I think pedigreemm tries to call lmer / glmer once to get @pp (for Zt, primarily, but also X, Lambdat, and Lind), @resp (only for REML), @flist and @Gp, then followed up with optimizeLmer or optimizeGlmer. I think it is a big waste of time since most of these can be constructed offline (i.e., without actually computing the results), like in pedigreemm version 1.1 or so. Is there a way in lme4 package to do that instead of calling lmer / glmer? Is lme4::lFormula / lme4::glFormula the right way? Did I overlook something?

Thank you!

Sincerely,
Roby



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