TreePar: Estimating birth and death rates based on phylogenies

(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.

Author
Tanja Stadler
Date of publication
2015-01-02 17:48:44
Maintainer
Tanja Stadler <tanja.stadler@bsse.ethz.ch>
License
GPL-2
Version
3.3

View on CRAN

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

Files in this package

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