Estimating birth and death rates based on phylogenies

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Documentation for package ‘TreePar’ version 3.3

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TreePar-package Estimating birth and death rates based on phylogenies
addroot addroot: Adds a root edge ancestral to the first branching event.
bd.age.optim.matlab bd.age.optim.matlab: Estimating speciation rate and age-dependent extinction rate in phylogenies.
bd.densdep.optim bd.densdep.optim: Estimating maximum likelihood speciation and extinction rates in phylogenies under a density-dependent speciation model.
bd.shifts.optim bd.shifts.optim: Estimating speciation and extinction rate changes and mass extinction events in phylogenies.
bd.shifts.plot bd.shifts.plot: Plots the diversification rate estimates obtained with the function bd.shifts.optim.
bdsky.stt.optim bdsky.stt.optim: Estimating piecewise constant birth and death rates in phylogenies with sequentially sampled tips.
create.mat create.mat: Generates input for LikAge and bd.age.optim.matlab.
get.groups get.groups: Generates input for bd.shifts.optim when groups!=0.
LikAge LikAge: Calculates the likelihood of speciation and extinction rates for an ultrametric phylogeny under an age-dependent extinction model conditioning on the age of the tree.
LikConstant LikConstant: Calculates the likelihood of constant birth and death rates for a given phylogenetic tree.
LikConstantn LikConstantn: Calculates the likelihood of constant birth and death rates for a given phylogenetic tree.
LikDD LikDD: Calculates the likelihood of speciation and extinction rates for an ultrametric phylogeny under a density-dependent speciation model conditioning on the age of the tree.
LikShifts LikShifts: Calculates the likelihood of time-dependent birth and death rates given a phylogenetic tree.
LikShiftsPP LikShiftsPP: Calculates the likelihood of time-dependent birth and death rates given a phylogenetic tree.
LikShiftsSTT LikShiftsSTT: Calculates likelihood of piecewise constant birth and death rates for a given phylogenetic tree with sequentially sampled tips.
LikTypesSTT LikTypesSTT: Calculates the likelihood of the 2-type birth-death model parameters for a given tree.
TreePar Estimating birth and death rates based on phylogenies