lagtime {PhySim} | R Documentation |
Each node is classified as an interspecific or intraspecific phylogenetic split by drawing a lag-time to speciaton randomly from a exponential distribution of lag-times. Beginning from the root, once a node is classified as a intraspecific split all of its daughter lineages keep the same classification in order to maintain species as monophyletic. All nodes classified as intra-specific splits are pruned.
lagtime(phy, rate)
phy |
a phylogenetic tree of class phylo |
rate |
the average lag-time to speciation. 1 / rate is the rate parameter of the exponential distribution used to model speciation along a phylogenetic tree. |
returns a phylogenetic tree of class phylo, possessing only inter-specific splits.
Jason T. Weir
Weir, J. T. and Schluter, D. 2007. Science in press
lagtime.batch
, to model a lag-time to speciation for a batch of phylogenetic trees
#Apply an average lag-time of 1 tree <- birthdeath.tree(b=0.3, d=0, T=10) tree2 <- lagtime(phy=tree, rate = 1)