[R] New version of coxme / lmekin

[Terry Therneau]

Version 2.2 of coxme has been posted to CRAN, Windows versions and
mirrors should appear in due course.  This is a major update with three
features of note:

1. A non-upwardly compatable change:

Extractor functions: beta= fixed effects, b=random effects
             nlme    lme4     coxme <2.2   coxme 2.2   lmekin 2.2
           ------------------------------------------------------
beta        fixef    fixef     fixef       fixef         fixef
b           ranef    ranef     ----        ranef         ranef
var(beta)   vcov     vcov      ----        vcov          vcov
var(b)      VarCorr  VarCorr   ranef       VarCorr       VarCorr

  Notice that "ranef" in the prior release was out of step with everyone
else, which became obvious when working on lmekin. Also, the constructs
"fit$coef$random" and "fit$coef$fixed" no longer work due to some
internal rearrangments.


2. The lmekin function is now part of the package.  This is the last
portion of the older "kinship" package to be updated; I will be talking
to the current maintainer of kinship about making it depreciated. This
version of lmekin is both more stable and more capable than the old
one.  
  Why use lmekin?  It can fit most of the models that lme or lmer can,
and uses the same formula notation as lmer.  However, if lmer can fit
your needs I see no good reason to use lmekin and lots of reasons not to
use it (plots, residuals, documentation, ...).  The lmekin routine can
also fit models with complex user-specified variance structures,
however, of which familial kinship correlation matrices are the
principle example.

3. More vignettes.

Terry Therneau