TreePar: Estimating birth and death rates based on phylogenies
Version 3.3

(i) For a given species phylogeny on present day data which is calibrated to calendar-time, a method for estimating maximum likelihood speciation and extinction processes is provided. The method allows for non-constant rates. Rates may change (1) as a function of time, i.e. rate shifts at specified times or mass extinction events (likelihood implemented as LikShifts, optimization as bd.shifts.optim and visualized as bd.shifts.plot) or (2) as a function of the number of species, i.e. density-dependence (likelihood implemented as LikDD and optimization as bd.densdep.optim) or (3) extinction rate may be a function of species age (likelihood implemented as LikAge and optimization as bd.age.optim.matlab). Note that the methods take into account the whole phylogeny, in particular it accounts for the "pull of the present" effect. (1-3) can take into account incomplete species sampling, as long as each species has the same probability of being sampled. For a given phylogeny on higher taxa (i.e. all but one species per taxa are missing), where the number of species is known within each higher taxa, speciation and extinction rates can be estimated under model (1) (implemented within LikShifts and bd.shifts.optim with groups !=0). (ii) For a given phylogeny with sequentially sampled tips, e.g. a virus phylogeny, rates can be estimated under a model where rates vary across time using bdsky.stt.optim based on likelihood LikShiftsSTT (extending LikShifts and bd.shifts.optim). Furthermore, rates may vary as a function of host types using LikTypesSTT (multitype branching process extending functions in R package diversitree). This function can furthermore calculate the likelihood under an epidemiological model where infected individuals are first exposed and then infectious.

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AuthorTanja Stadler
Date of publication2015-01-02 17:48:44
MaintainerTanja Stadler <tanja.stadler@bsse.ethz.ch>
LicenseGPL-2
Version3.3
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("TreePar")

Man pages

addroot: addroot: Adds a root edge ancestral to the first branching...
bd.age.optim.matlab: bd.age.optim.matlab: Estimating speciation rate and...
bd.densdep.optim: bd.densdep.optim: Estimating maximum likelihood speciation...
bd.shifts.optim: bd.shifts.optim: Estimating speciation and extinction rate...
bd.shifts.plot: bd.shifts.plot: Plots the diversification rate estimates...
bdsky.stt.optim: bdsky.stt.optim: Estimating piecewise constant birth and...
create.mat: create.mat: Generates input for LikAge and...
get.groups: get.groups: Generates input for bd.shifts.optim when...
LikAge: LikAge: Calculates the likelihood of speciation and...
LikConstant: LikConstant: Calculates the likelihood of constant birth and...
LikConstantn: LikConstantn: Calculates the likelihood of constant birth and...
LikDD: LikDD: Calculates the likelihood of speciation and extinction...
LikShifts: LikShifts: Calculates the likelihood of time-dependent birth...
LikShiftsPP: LikShiftsPP: Calculates the likelihood of time-dependent...
LikShiftsSTT: LikShiftsSTT: Calculates likelihood of piecewise constant...
LikTypesSTT: LikTypesSTT: Calculates the likelihood of the 2-type...
TreePar-package: Estimating birth and death rates based on phylogenies

Functions

BDSSanal Source code
BDSSnum.help Source code Source code
Fderifuncshift Source code
Fderifuncshifth Source code
Ffuncshift Source code
Ffuncshifth Source code
HelpShiftsPPn Source code
LikAge Man page Source code
LikConstant Man page Source code
LikConstantn Man page Source code
LikDD Man page Source code
LikShifts Man page Source code
LikShiftsPP Man page Source code
LikShiftsSTT Man page Source code
LikTypesSTT Man page Source code
R0types Source code
TreePar Man page
TreePar-package Man page
addroot Man page Source code
ai Source code
bd.ME.optim Source code
bd.ME.optim.rho Source code
bd.ME.optim.rho.all Source code
bd.MEyule.optim Source code
bd.age.optim.matlab Man page Source code
bd.densdep.optim Man page Source code
bd.densdep.optim.discrete Source code
bd.groups.conf Source code
bd.groups.optim Source code
bd.shifts.optim Man page Source code
bd.shifts.plot Man page Source code
bdsky.stt.optim Man page Source code
bdtypes.stt.lik.orig Source code
bi Source code
c1 Source code
c2 Source code
const Source code
create.mat Man page Source code
g Source code
get.groups Man page Source code
get.times2 Source code
getmatrix Source code
integrator Source code Source code
integrator2 Source code Source code
inter Source code
interstt Source code
lambFun Source code
lineages Source code
p Source code
p0 Source code
p0sersamp Source code
p1 Source code
partransform Source code
partransformvector Source code
pn Source code
pnshift Source code
q2 Source code
qfunc Source code
qfuncsky Source code
qfuncskylog Source code
qhelp Source code
treemrcabdtreepar Source code

Files

NAMESPACE
R
R/bd.MEyule.optim.R
R/p.R
R/integrator2.R
R/partransform.R
R/BDSSanal.R
R/Fderifuncshifth.R
R/interstt.R
R/bd.ME.optim.rho.R
R/bd.shifts.optim.R
R/partransformvector.R
R/inter.R
R/bdsky.stt.optim.R
R/LikShiftsSTT.R
R/bd.groups.conf.R
R/integrator2-orig.R
R/bd.densdep.optim.discrete.R
R/LikDD.R
R/qhelp.R
R/bdtypes.stt.lik.orig.R
R/p1.R
R/bd.densdep.optim.R
R/getmatrix.R
R/create.mat.R
R/ai.R
R/integrator.R
R/integrator-orig.R
R/Ffuncshift.R
R/bd.ME.optim.rho.all.R
R/bd.shifts.plot.R
R/bi.R
R/p0.R
R/lambFun.R
R/HelpShiftsPPn.R
R/LikShifts.R
R/LikAge.R
R/Fderifuncshift.R
R/BDSSnum.help.R
R/BDSSnum.help-orig.R
R/g.R
R/LikConstant.R
R/lineages.R
R/q2.R
R/R0types.R
R/qfuncsky.R
R/LikTypesSTT.R
R/pnshift.R
R/bd.age.optim.matlab.R
R/addroot.R
R/get.times2.R
R/bd.groups.optim.R
R/Ffuncshifth.R
R/pn.R
R/qfuncskylog.R
R/get.groups.R
R/treemrcabdtreepar.R
R/const.R
R/LikShiftsPP.R
R/bd.ME.optim.R
R/LikConstantn.R
MD5
DESCRIPTION
man
man/addroot.Rd
man/LikDD.Rd
man/bd.shifts.plot.Rd
man/LikShiftsSTT.Rd
man/LikAge.Rd
man/create.mat.Rd
man/TreePar-package.Rd
man/bd.age.optim.matlab.Rd
man/LikTypesSTT.Rd
man/LikShiftsPP.Rd
man/get.groups.Rd
man/bd.shifts.optim.Rd
man/bd.densdep.optim.Rd
man/bdsky.stt.optim.Rd
man/LikShifts.Rd
man/LikConstantn.Rd
man/LikConstant.Rd
TreePar documentation built on May 19, 2017, 10 a.m.