Pedigreemm on lme4-1.0
On 14-02-14 06:07 PM, Joehanes, Roby (NIH/NHLBI) [F] wrote:
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.
I don't think so, I can replicate your first example.
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
Your patch was appreciated, but superseded by fairly major architectural changes we made. There is a fairly straightforward way now to bypass this test: control=lmerControl(check.nobs.vs.nlev="ignore") This really should be done within the call in pedigreemm, but it can be enabled globally as follows: options(lmerControl=list(check.nobs.vs.nlev="ignore"))
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
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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