Hi,
I am attempting to use a PLMM through asreml-R with a series of closely
related pairs in a phylogeny where one lineage may be involved in several
near-sister pairs. I would like to include information about the most
recent common ancestor of the two lineages in a pair as a random effect,
however I am having difficulty.
I have tried to represent the most recent common ancestor by including a
factor in my data frame with the corresponding node of the MRCA of the
pair, however when I do this, I get an error message I don't know how to
interpret. See below:
Where tree is a phylogenetic tree in phylo format and small is a dataframe
with species pairs (species1, species2), color as a factor, node of MRCA as
a factor and a quantitative variable x.
Ainv <- inverseA(tree)$Ainv
fit <- asreml(x ~color, random=~giv(MRCA)+species1+species2,
ginverse=list(MRCA=sm2asreml(Ainv)), data=small)
With this, I get the error message:
Error in asreml.giv(MRCA, data = data, Rcov = 0) :
MRCA has levels in data missing in ginverse
I would appreciate any help in understanding this error message and (more
importantly), how to account for species pairs sharing the same MRCA in a
PLMM.
Thank you for any help!
- Libby
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