A flexible implementation of the Elston-Stewart algorithm
The Elston-Stewart algorithm allows to compute probability functions in pedigrees.
es.pedigree allows to create S3 objects for pedigrees. They can be
plotted with a S3 method
plot.es.pedigree which is simply a wrapper for the
method provided in
The algorithm itself is run by two functions,
Elston computes a probability for a single pedigree, given a probability model (similar
to the one given in
modele.di). It relies on memoization (or dynamic programming)
and allows vectorization (computing a vector of probabilities at once).
is similar, but runs on pedigrees lists: it computes (the sum of) the logarithms of the probabilities
for each pedigree. It allows parallelization, running the computation for the various
pedigrees on different nodes of a cluster. The cluster is left opened for being re-used
(with memoization) on the same set of pedigrees. It can be closed with
Two small data sets are provided for illustration,
The Elston-Stewart vignette gives commented examples.
Herve Perdry [email protected]
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