expoTree: Calculate density dependent likelihood of a phylogenetic tree

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Calculates the density dependent likelihood of a phylogenetic tree. It takes branching and sampling times as an argument and integrates the likelihood function over the whole tree.

Author
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.
Date of publication
2013-09-03 14:12:55
Maintainer
Gabriel E Leventhal <gabriel@leventhal.ch>
License
BSD_3_clause + file LICENCE
Version
1.0.1

View on CRAN

Man pages

ape2time
Convert tree from 'phylo' format (ape) to event time format.
epi2tree
Convert an 'epi' object from 'sim.epi' to 'phylo' format...
expoTree.optim
Perform optimization to find a maximum likelihood estimate.
expoTree-package
Calculate density dependent likelihood of a phylogenetic tree
infExpoTree
Likelihood calculation without density dependence.
plotLTT
Plot lineages through time.
runExpoTree
Density-dependent likelihood caluculation
sim.epi
Simulates epidemic outbreaks and sampled transmission trees.

Files in this package

expoTree
expoTree/src
expoTree/src/Makevars
expoTree/src/expoTree.h
expoTree/src/theta_taylor_half.h
expoTree/src/expo.c
expoTree/src/expmv.c
expoTree/src/expoTree.c
expoTree/src/expmv.h
expoTree/src/simulate_trees.cpp
expoTree/src/RsimTrees.cpp
expoTree/src/stdeg.c
expoTree/src/expo_type.h
expoTree/src/expomv.c
expoTree/src/dlapst.f
expoTree/src/theta_taylor_single.h
expoTree/src/normAm.c
expoTree/src/simulate_trees.h
expoTree/src/dlarpc.f
expoTree/src/theta_taylor.h
expoTree/src/expo.h
expoTree/src/expomv.h
expoTree/src/dlacn1.f
expoTree/NAMESPACE
expoTree/R
expoTree/R/plotLTT.R
expoTree/R/sim.epi.R
expoTree/R/node.age.R
expoTree/R/get.tips.R
expoTree/R/epi2tree.R
expoTree/R/expoTree.optim.R
expoTree/R/ape2time.R
expoTree/R/runExpoTree.R
expoTree/R/epi.coords.R
expoTree/R/get.age.R
expoTree/R/expoTreeSurvival.R
expoTree/R/zzz.R
expoTree/R/infExpoTree.R
expoTree/README.md
expoTree/MD5
expoTree/DESCRIPTION
expoTree/LICENCE
expoTree/ChangeLog
expoTree/man
expoTree/man/runExpoTree.Rd
expoTree/man/sim.epi.Rd
expoTree/man/epi2tree.Rd
expoTree/man/plotLTT.Rd
expoTree/man/infExpoTree.Rd
expoTree/man/ape2time.Rd
expoTree/man/expoTree.optim.Rd
expoTree/man/expoTree-package.Rd
expoTree/.Rinstignore