sim.bdsky.stt
(Package: TreeSim) :
sim.bdsky.stt: Simulating sequentially sampled birth-death, SIS, SIR or SIRS trees where birth and death rates are changing through time.
sim.bdsky.stt simulates birth-death trees with tips being sampled sequentially. The birth and death rates may change in a piecewise fashion. The birth rates may additionally depend on the number of susceptible individuals in an epidemic, corresponding to epidemiological SIS, SIR or SIRS dynamics. The trees are conditioned on a fixed number of tips or a fixed age.
● Data Source:
CranContrib
● Keywords:
● Alias: sim.bdsky.stt
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LTT.plot
(Package: TreeSim) :
LTT.plot: Plots the lineages through time of a set of phylogenetic trees.
LTT.plot plots the lineages through time (LTT) for a set of phylogenetic trees in black (complete or reconstructed; with or without polytomies) together with the average LTT plot in red. The trees may be simulated using any function in TreeSim, or may be empirical trees. The method works for ultrametric and non-ultrametric trees which are binary or have polytomies. NOTE: you probably need to adapt the code such that the plot is pretty for your particular data (range of axes etc).
● Data Source:
CranContrib
● Keywords:
● Alias: LTT.plot
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sim.bdtypes.stt.taxa
(Package: TreeSim) :
sim.bdtypes.stt.taxa: Simulating multitype birth-death trees with a fixed number of tips sampled through time.
sim.bdtypes.stt.taxa simulates trees on n tips sampled through time under a multitype birth-death process.
● Data Source:
CranContrib
● Keywords:
● Alias: sim.bdtypes.stt.taxa
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Simulation methods for phylogenetic trees where (i) all tips are sampled at one time point or (ii) tips are sampled sequentially through time. (i) For sampling at one time point, simulations are performed under a constant rate birth-death process, conditioned on having a fixed number of final tips (sim.bd.taxa()), or a fixed age (sim.bd.age()), or a fixed age and number of tips (sim.bd.taxa.age()). When conditioning on the number of final tips, the method allows for shifts in rates and mass extinction events during the birth-death process (sim.rateshift.taxa()). The function sim.bd.age() (and sim.rateshift.taxa() without extinction) allow the speciation rate to change in a density-dependent way. The LTT plots of the simulations can be displayed using LTT.plot(), LTT.plot.gen() and LTT.average.root(). TreeSim further samples trees with n final tips from a set of trees generated by the common sampling algorithm stopping when a fixed number m>>n of tips is first reached (sim.gsa.taxa()). This latter method is appropriate for m-tip trees generated under a big class of models (details in the sim.gsa.taxa() man page). For incomplete phylogeny, the missing speciation events can be added through simulations (corsim()). (ii) sim.rateshifts.taxa() is generalized to sim.bdsky.stt() for serially sampled trees, where the trees are conditioned on either the number of sampled tips or the age. Furthermore, for a multitype-branching process with sequential sampling, trees on a fixed number of tips can be simulated using sim.bdtypes.stt.taxa(). This function further allows to simulate under epidemiological models with an exposed class. The function sim.genespeciestree() simulates coalescent gene trees within birth-death species trees, and sim.genetree() simulates coalescent gene trees.
● Data Source:
CranContrib
● Keywords:
● Alias: TreeSim, TreeSim-package
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sim.bd.age
(Package: TreeSim) :
sim.bd.age: Simulating birth-death trees of a fixed age.
sim.bd.age simulates trees conditioned on (i) the time since origin or (ii) the time since the most recent common ancestor of the extant tips. The method allows for incomplete sampling: only a fixed fraction of all tips is included in the sampled tree. The method assumes constant birth and death rates, or allows for a density-dependent birth rate. If you want to have species-age dependent rates, use sim.age in R package TreeSimGM.
● Data Source:
CranContrib
● Keywords:
● Alias: sim.bd.age
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sim.genetree
(Package: TreeSim) :
sim.genetree: Simulating coalescent gene trees.
sim.genetree simulates a gene tree assuming the coalescent with coalescent rate being 1. The method returns summary statistics of the gene tree.
● Data Source:
CranContrib
● Keywords:
● Alias: sim.genetree
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sim.rateshift.taxa
(Package: TreeSim) :
sim.rateshift.taxa: Simulating trees incorporating mass extinction events and rate shifts.
sim.rateshift.taxa simulates trees on n species under the constant rate birth-death process. At user-specified points in the past, the rates can shift. Further, mass extinction events can be incorporated. The method further allows for incomplete sampling, i.e. only a fixed fraction of all tips is included in the sampled tree. The tree is conditioned to have n tips after sampling.
● Data Source:
CranContrib
● Keywords:
● Alias: sim.rateshift.taxa
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cuttree takes as input a tree and a cuttime, and then prunes all lineages more recent than cuttime.
● Data Source:
CranContrib
● Keywords:
● Alias: cuttree
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getx calculates the vector of branching (speciation / transmission) times and sampling times for a phylogenetic tree (which may have polytomies). This vector is the input for the TreePar methods.
● Data Source:
CranContrib
● Keywords:
● Alias: getx
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sim.bd.taxa.age
(Package: TreeSim) :
sim.bd.taxa.age: Simulating birth-death trees with a given age on a fixed number of extant taxa.
sim.bd.taxa.age simulates trees on n species with a (i) fixed time since origin or (ii) fixed time since the most recent common ancestor of the sampled species under the constant rate birth-death process. The method allows for incomplete sampling, i.e. each extant tip from a complete tree is included with a fixed probability. The tree is conditioned to have n tips after sampling and a fixed time since origin or since the most recent common ancestor of the sampled species.
● Data Source:
CranContrib
● Keywords:
● Alias: sim.bd.taxa.age
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