lumpedMatrix | R Documentation |
Reduce a mutation matrix by combining a set of alleles into one "lump", if this can be done without distorting the mutation process of the remaining alleles. Such "allele lumping" can give dramatic efficiency improvements in likelihood computations with multi-allelic markers, in cases where only some of the alleles are observed in the pedigree.
lumpedMatrix(mutmat, lump, afreq = NULL, check = TRUE, labelSep = NULL)
lumpedModel(mutmod, lump, afreq = NULL, check = TRUE)
mutmat |
A |
lump |
A nonempty subset of the alleles (i.e., the column names of
|
afreq |
A vector with frequency vector, of the same length as the size
of |
check |
A logical indicating if lumpability should be checked before lumping. Default: TRUE. |
labelSep |
((For debugging) A character used to name lumps by pasting allele labels. |
mutmod |
A |
A reduced mutation model. If the original matrix has dimensions
n\times n
, the result will be k\times k
, where k
= n - length(lump) + 1
.
mutationModel()
, mutationMatrix()
### Example 1: Lumping a mutation matrix
mat = mutationMatrix("eq", alleles = 1:5,
afreq = rep(0.2, 5), rate = 0.1)
mat
# Lump alleles 3, 4 and 5
mat2 = lumpedMatrix(mat, lump = 3:5)
mat2
# Example 2: Full model, proportional
mutrate = list(male = 0.1, female = 0.2)
mod = mutationModel("prop", alleles = 1:4,
rate = mutrate, afreq = c(.1,.2,.3,.4))
mod
# Lump alleles 3 and 4
mod2 = lumpedModel(mod, lump = 3:4)
mod2
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