expoTree: Calculate density dependent likelihood of a phylogenetic tree
Version 1.0.1

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.

Browse man pages Browse package API and functions Browse package files

AuthorGabriel 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 publication2013-09-03 14:12:55
MaintainerGabriel E Leventhal <gabriel@leventhal.ch>
LicenseBSD_3_clause + file LICENCE
Version1.0.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("expoTree")

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.

Functions

ape2time Man page Source code
epi.coords Source code
epi2tree Man page Source code
expoTree Man page
expoTree-package Man page
expoTree.optim Man page Source code
expoTreeSurvival Source code
get.age Source code
get.tips Source code
infExpoTree Man page Source code
node.age Source code
plotLTT Man page Source code
runExpoTree Man page Source code
sim.epi Man page Source code

Files

src
src/Makevars
src/expoTree.h
src/theta_taylor_half.h
src/expo.c
src/expmv.c
src/expoTree.c
src/expmv.h
src/simulate_trees.cpp
src/RsimTrees.cpp
src/stdeg.c
src/expo_type.h
src/expomv.c
src/dlapst.f
src/theta_taylor_single.h
src/normAm.c
src/simulate_trees.h
src/dlarpc.f
src/theta_taylor.h
src/expo.h
src/expomv.h
src/dlacn1.f
NAMESPACE
R
R/plotLTT.R
R/sim.epi.R
R/node.age.R
R/get.tips.R
R/epi2tree.R
R/expoTree.optim.R
R/ape2time.R
R/runExpoTree.R
R/epi.coords.R
R/get.age.R
R/expoTreeSurvival.R
R/zzz.R
R/infExpoTree.R
README.md
MD5
DESCRIPTION
LICENCE
ChangeLog
man
man/runExpoTree.Rd
man/sim.epi.Rd
man/epi2tree.Rd
man/plotLTT.Rd
man/infExpoTree.Rd
man/ape2time.Rd
man/expoTree.optim.Rd
man/expoTree-package.Rd
.Rinstignore
expoTree documentation built on May 29, 2017, 3:49 p.m.