ElstonStewart-package {ElstonStewart}R Documentation

Elston-Stewart package

Description

A flexible implementation of the Elston-Stewart algorithm

Details

The Elston-Stewart algorithm allows to compute probability functions in pedigrees.

The function 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 kinship2.

The algorithm itself is run by two functions, Elston and Likelihood. 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). Likelihood 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 es.stopCluster.

Two small data sets are provided for illustration, conrad2 and fams. The Elston-Stewart vignette gives commented examples.

Author(s)

Herve Perdry herve.perdry@u-psud.fr


[Package ElstonStewart version 1.1 Index]