R: Calculate density dependent likelihood of a phylogenetic tree
expoTree-package
R Documentation
Calculate density dependent likelihood of a phylogenetic tree
Description
Calculates the density dependent likelihood of a phylogenetic tree.
It takes branching and sampling times as an argument and integrates the
likelihoood function over the whole tree.
Details
Package:
expoTree
Type:
Package
Version:
1.0.1
Date:
2013-09-03
License:
BSD 3 clause
Author(s)
Gabriel E Leventhal, partly adapted from MATLAB code by Awad H. Al-Mohy and
using the routines DLNAC1 and DLARPC by Sheung Hun Cheng, and DLAPST from
ScaLAPACK.
References
Leventhal, Guenthard, Bonhoeffer & Stadler, (2013) "Using an epidemiological
model for phylogenetic inference reveals density-dependence in HIV
transmission".
Al-Mohy & Higham (2011) "Computing the Action of the Matrix Exponential, with
an Application to Exponential Integrators". SIAM Journal on Scientific
Computing, 33.
Cheng & Highami (2001) "Implementation for LAPACK of a Block Algorithm for
Matrix 1-Norm Estimation". Numerical Analysis Report No. 393, Manchester
Centre for Computational Mathematics, Manchester, England, August 2001, and
LAPACK Working Note 152.
Blackford et al. (1997) "ScaLAPACK Users' Guide". Society for Industrial and
Applied Mathematics, Philadelphia, PA.