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addroot adds a root edge ancestral to the first branching event.
● Data Source:
CranContrib
● Keywords:
● Alias: addroot
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LikDD calculates the likelihood of speciation and extinction rates for a phylogeny under a density-dependent speciation model. Speciation rate is a function of the number of species N, lambda(N) = max(0,lambda(1-N/K)), where K is the carying capacity and lambda the speciation rate when N<<K. Extinction rate is mu (constant). For a computationally much faster implementation, please use function runExpoTree in R package expoTree. In contrast to LikDD, runExpoTree can handle trees with tips sampled sequentially through time.
● Data Source:
CranContrib
● Keywords:
● Alias: LikDD
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bd.shifts.plot plots the diversification rate estimates obtained with the function bd.shifts.optim.
● Data Source:
CranContrib
● Keywords:
● Alias: bd.shifts.plot
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LikShiftsSTT calculates likelihood of piecewise constant birth and death rates for a given phylogenetic tree with sequentially sampled tips, conditioning on the age of the tree.
● Data Source:
CranContrib
● Keywords:
● Alias: LikShiftsSTT
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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. Speciation rate is constant. Time to extinction is a Gamma distribution.
● Data Source:
CranContrib
● Keywords:
● Alias: LikAge
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create.mat generates input for LikAge and bd.age.optim.matlab.
● Data Source:
CranContrib
● Keywords:
● Alias: create.mat
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(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.
● Data Source:
CranContrib
● Keywords:
● Alias: TreePar, TreePar-package
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bd.age.optim.matlab estimates the maximum likelihood speciation and extinction rates in a (possibly incomplete sampled) phylogeny. Speciation rate is constant, time to extinction is assumed to be a Gamma distribution.
● Data Source:
CranContrib
● Keywords:
● Alias: bd.age.optim.matlab
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LikTypesSTT calculates the likelihood of the 2-type birth-death model parameters given a tree, conditioning on the age of the tree. For obtaining the maximum likelihood parameter estimates use the R function optim (see example below).
● Data Source:
CranContrib
● Keywords:
● Alias: LikTypesSTT
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LikShiftsPP calculates the likelihood of speciation and extinction rates and shift times given a phylogenetic tree, conditioning on the age of the tree. This function uses the point process theory (Lambert and Stadler, 2013).
● Data Source:
CranContrib
● Keywords:
● Alias: LikShiftsPP
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providing 
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