sim.age simulates stochastic trees conditioned on the time since origin of the extant tips under a general model (i.e. any given distribution for speciation and extinction). The method allows for symmetric and asymmetric binary split speciation mode. To keep all extinct trees use complete=TRUE, if complete=FALSE the tree is pruned, resulting on a so called reconstructed tree.
is the total age until each tree will be simulated (e.g. age=3). Time since origin / most recent common ancestor
numbsim
is the number of simulated trees
distributionspname
is the name of the desired probability function that will be used for the speciation process (e.g. distributionspname="rexp"). Note that the name should contain an 'r' before it, since it refers to the randon number of the desired function (e.g. "rweibull", "runif")
distributionspparameters
are the parameters for the specific function desired for speciation.
# IMPORTANT: this vector of function parameters must *start by the second one, since the first parameter will always be one for all the function and is added already by this function*. HINT: see the help of the desired function for more details (e.g. ?rexp) Example of parameter for a exponential distribution with lambda of one is: (distributionspparameters = c(1)). Entry in the distributionparameters can be "#", # or c(#,#) in case of more characters
distributionextname
is the same as the distributionspname but for the probability of extinction (e.g. distributionextname = "rexp")
distributionextparameters
is the same as the distributionspparameters but for the extinction probability function. By default extinction is set to ZERO, i.e. no extinction (i.e. distributionextparameters = c(0)). Entries can be "#", # or c(#,#) in case of more characters
symmetric
tells which macroevolutionary model should be used. If symmetric=TRUE the symmetric model will be used; if FALSE, the asymmetric model will be used. By default symmetric=TRUE
complete
if complete = TRUE, the tree with the extinct and non-sampled lineages is returned. If complete = FALSE, the extinct and non-sampled lineages are suppressed. complete=FALSE by default
labellivingsp
is the label that will be drawn on each tip surviving until the present. An automatic sequential number will be added to the chosen name. By default labellivingsp="sp."
labelextinctsp
is the label that will be drawn on each extinct tip. By default labelextinctsp="ext."
Value
treearray
Array of numbsim trees with the time since origin / most recent common ancestor being age. If tree goes extinct (only possible when mrca = FALSE), returns 0. If only one extant and no extinct tips, returns 1.
Author(s)
Oskar Hagen, Tanja Stadler
References
O. Hagen, K. Hartmann, M. Steel and T. Stadler (2014). Age-dependent speciation explains empirical tree shape distribution. Manuscript.
T. Stadler: Simulating trees on a fixed number of extant species. Syst. Biol. (2011) 60: 676-684.
See Also
sim.taxa
Examples
# One tree with age 3 without extinction and weibull
# disribution for the waiting time until speciation
sim.age(3,1,"rweibull", c(0.4,3))
# Plot one of ten trees
# uniform distribution for speciation and
# exponential distribution for extinction
leo <- sim.age(age=3,10,"runif", c(0,2), "rexp", c(0.1) )
# note that for runif, the first argument is omitted and 0 stands for the
# min parameter of this specific function as 2 stands for max.
plot(leo[[1]])
providing 
.