View source: R/diversification.R

bd.ms | R Documentation |

estimating net diversification rate with confidence limits and testing diversities

```
bd.ms(phy=NULL, time, n, missing = 0, crown=TRUE, epsilon = 0)
bd.km(phy=NULL, time, n, missing = 0, crown=TRUE)
crown.p(phy=NULL, time, n, r, epsilon)
stem.p(phy=NULL, time, n, r, epsilon)
crown.limits(time, r, epsilon, CI=0.95)
stem.limits(time, r, epsilon, CI=0.95)
```

`phy` |
a phylogenetic tree of class 'phylo' (see |

`time` |
time interval (can be a vector) |

`n` |
number of extant species |

`r` |
net diversification rate, birth - death |

`epsilon` |
extinction rate as a fraction of speciation rate |

`missing` |
number of taxa missing from tree |

`crown` |
whether time is treated as crown age (or otherwise as stem age) |

`CI` |
confidence level for estimated parameters |

`bd.ms`

uses the Magallon and Sanderson (2000) method to calculate net diversification rate for a clade given extant diversity and age. `bd.km`

computes the Kendall-Moran estimate of speciation rate, which assumes a complete phylogenetic tree.

Associated functions `crown.p`

and `stem.p`

also calculate the probability of obtaining a clade with at least `n`

species given
a net diversification rate (`r`

), extinction fraction (`epsilon`

), and `time`

interval. Associated functions `stem.limits`

and
`crown.limits`

generate confidence limits on extant diversity given a net diversification rate (`r`

), extinction fraction (`epsilon`

),
and `time`

interval.

Where a function calls for a `time`

and an `n`

element, a tree may be given instead (as argument `phy`

). The argument `n`

is taken from the number of tips in the tree. The method
will attempt to discern whether the model should be fitted assuming `crown`

or `stem`

. If the tree has a non-NULL `phy$root.edge`

element, the length will be assumed for the stem and `crown`

is assumed to be `FALSE`

(see also `read.tree`

).

**bd.ms**returns net diversification rate (`r`

=`lambda`

-`mu`

)**bd.km**returns speciation rate assuming a completely sampled tree**crown.p**and**stem.p**return the probability of obtaining a clade as big as (or bigger than) size`n`

, given`time`

,`r`

, and`epsilon`

**crown.limits**and**stem.limits**return lower (`lb`

) and upper (`ub`

) confidence intervals for clade size given`time`

,`r`

, and`epsilon`

LJ Harmon and C Brock

Magallon S and MJ Sanderson. 2000. Absolute diversification rates in angiosperm clades. *Evolution* 55:1762-1780.

```
geo=get(data(geospiza))
# Assuming no extinction
bd.ms(phy=geo$phy, missing=1, epsilon=0)
# Assuming high extinction
bd.ms(phy=geo$phy, missing=1, epsilon=0.9)
```

geiger documentation built on April 4, 2023, 1:07 a.m.

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