lagtime.batch {PhySim} | R Documentation |
Each node in a series of phylogenetic trees is classified as an interspecific or intraspecific phylogenetic split by drawing a lag-time to speciation randomly from a exponential distribution of lag-times. Beginning from the root of each tree, 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 intras-specific splits are pruned.
lagtime.batch(b, d, n, T, rate)
b |
birth (speciation) rate under which trees are simulated |
d |
death (extinction) rate under which trees are simulated |
n |
number of trees in simulation |
T |
time units trees simulated for |
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. |
Reads in a file of trees simulated with parameters b, d, n and T using the command 'birthdeath.simulation'. If b and d are a list, then multiple files will be read.
write a series of phylogenetic trees of class phylo, possessing only inter-specific splits, to a file with '.tree\_no\_extinct' extension.
Jason T. Weir
Weir, J. T. and Schluter, D. 2007. Science in press
lagtime
, to model a lag-time to speciation along a single phylogenetic tree.