TreePar (version 2.1.2)

bd.groups.optim: bd.groups.optim: Estimating speciation and extinction rates in higher-taxonomic-level phylogenies

Description

bd.groups.optim estimates the maximum likelihood speciation and extinction rates under a constant rate speciation and extinction model based on a phylogeny on higher taxa, where the number of species within each taxa are known.

Usage

bd.groups.optim(phy, S, xcut=0)

Arguments

phy

Phylogenetic tree on higher taxa.

S

Vector of number of species for each higher taxa.

xcut

Each species extant at cutoff time xcut in the past defines a higher taxa (implying that xcut must be after the most recent branching time in phi). xcut=0 is used if no xcut is specified and means that higher taxa are not defined using a cutoff, but highe

Value

• res[[1]]
  First row: Maximum likelihood estimate for turnover (mu/lambda) with 95 per cent confidence intervals. Second row: Maximum likelihood estimate for diversification rate (lambda-mu) with 95 per cent confidence intervals.
• res[[2]]$value
  - Log Likelihood value
• res[[2]]$convergence
  Convergence information. 0 is successful. For other output see man for subplex.

References

T. Stadler, F. Bokma: Estimating speciation and extinction rates for phylogenies of higher taxa. Submitted, 2011.

Examples

### An example from Paradis (2003) using the avian orders:
data(bird.orders)
### Number of species in each order from Sibley and Monroe (1990):
S <- c(10, 47, 69, 214, 161, 17, 355, 51, 56, 10, 39, 152, 6, 143, 358, 103, 319, 23, 291, 313, 196, 1027, 5712)
xcut<-95*0.207407
out<-bd.groups.optim(bird.orders, S, xcut)
### Not accounting for the cutoff when defining the bird taxa estimates 0 extinction:
out1<-bd.groups.optim(bird.orders, S, 0)
### xcut=0 produces almost the same results as the following ape function
bd.ext(bird.orders, S)