Simulating Phylogenetic Trees

Documentation for package ‘TreeSim’ version 2.4

TreeSim-package	TreeSim: Simulating Phylogenetic Trees
corsim	corsim: Simulating the missing speciation events in an incomplete phylogenies.
cuttree	cuttree: Cutting off the tree to prune recent branches.
getx	getx: Calculating the vector of speciation / transmission times and sampling times for a phylogenetic tree.
LTT.plot	LTT.plot: Plots the lineages through time of a set of phylogenetic trees.
LTT.plot.gen	LTT.plot.gen: Calculates the number of lineages through time for each input tree, as well as the average number of lineages over all trees.
sim.bd.age	sim.bd.age: Simulating birth-death trees of a fixed age.
sim.bd.taxa	sim.bd.taxa: Simulating birth-death trees on a fixed number of extant taxa.
sim.bd.taxa.age	sim.bd.taxa.age: Simulating birth-death trees with a given age on a fixed number of extant taxa.
sim.bdsky.stt	sim.bdsky.stt: Simulating sequentially sampled birth-death, SIS, SIR or SIRS trees where birth and death rates are changing through time.
sim.bdtypes.stt.taxa	sim.bdtypes.stt.taxa: Simulating multitype birth-death trees with a fixed number of tips sampled through time.
sim.genespeciestree	sim.genespeciestree: Simulating birth-death species trees with nested coalescent gene trees.
sim.genetree	sim.genetree: Simulating coalescent gene trees.
sim.gsa.taxa	sim.gsa.taxa: Sampling trees on n tips from bigger trees.
sim.rateshift.taxa	sim.rateshift.taxa: Simulating trees incorporating mass extinction events and rate shifts.
TreeSim	TreeSim: Simulating Phylogenetic Trees