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-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.
