[R-sig-ME] Pedigreemm on lme4-1.0

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

Hi Ben:

The package could install and the examples in the manual could run.
However, all the examples given in the pedigreemm technical paper do not:
milk <- within(milk, sdMilk <- milk / sd(milk))
fm1 <- pedigreemm(sdMilk ~ lact + log(dim) + (1|id) + (1|herd), data =
milk, pedigree = list(id = pedCowsR))

The error message is:
Error in .sortCsparse(.Call(dtCMatrix_sparse_solve, a, b)) :
  Dimensions of system to be solved are inconsistent

The same goes to these examples (same error message):
milk <- within(milk, idPE <- id)
fm2 <- pedigreemm(sdMilk ~ lact + (1|id) + log(dim) + (1|idPE) + (1|herd),
data = milk, pedigree = list(id = pedCows))

fm3 <- pedigreemm(NCM ~ birth + calvingYear + (1|sire) + (1|herd),  data =
mastitis, pedigree = list(sire = pedSires), family = "poisson")

fm4 <- pedigreemm(mastitis ~ birth + calvingYear + (1|sire) + (1|herd),
data = mastitis, pedigree = list(sire = pedSires),


cf: http://www.journalofanimalscience.org/content/88/2/497.full.pdf+html

Updating/recompiling Rcpp, RcppEigen, and lme4 do not help. I see no test
codes at all in pedigreemm-0.3-1 package. As such, pedigreemm at the
present state could only be used for toy examples. Or this could be a
problem exclusively on my side.

Plus, I remember that I submitted a patch to allow specification of one
observation per ID. It seems that the patch did not transfer over. I
always get this error message:
Error in checkNlevels(reTrms$flist, n = n, control) :
  number of levels of each grouping factor must be < number of observations
http://r-forge.r-project.org/tracker/index.php?func=detail&aid=1928&group_i
d=60&atid=300


I can try to fix this problem, but I will need guidance from you and
others since I have been absent from the lme4 development for 1.5 years
now. The patch above is now obsolete with lme4-v1.0.

Sincerely,
Roby





On 2/14/14 5:29 PM, "Ben Bolker" <bbolker at gmail.com> wrote:

>On 14-02-14 12:22 PM, Joehanes, Roby (NIH/NHLBI) [F] wrote:
>> Hi all:
>> 
>> Just wondering if there is any people working on pedigreemm so that
>> it can run on the new lme4 version 1.0? In current version of lme4
>> 1.0, pedigreemm is broken. May I know the latest status on
>> pedigreemm?
>> 
>> Thanks, Roby
>> 
>> _______________________________________________
>> R-sig-mixed-models at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>> 
>
>  I'm a little surprised, because the current CRAN page suggests it's
>OK: http://cran.r-project.org/web/packages/pedigreemm/index.html -- this
>page wouldn't exist, I think, if the package didn't at least pass its
>checks with the new version of lme4 (and it says that it requires lme4
>>= 1.0).
>   Perhaps you could provide a little more information for those of us
>who don't use pedigreemm on a regular basis -- does it fail to install?
> Installs but doesn't pass checks/examples fail?  Examples run but give
>incorrect answers?  Some particular cases don't work?
>   Posting here seems perfectly reasonable, but I would also suggest
>contacting the maintainer (listed at the URL above) as well.  If that
>maintainer is unwilling or unable to fix whatever's broken, then
>presumably someone else will have to step forward to act as maintainer ...
>
>  I'm willing to help fix what's broken, in particular on the
>lme4-interface end, but would need to get *specific* examples of what's
>not working ...
>
>  Ben Bolker