Description Usage Arguments Details Value Author(s) References Examples

calculating and plotting disparity-through-time for a phylogenetic tree and phenotypic data

1 2 3 |

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

`data` |
a named vector or matrix of continuous trait values, associated with species in |

`index` |
disparity index to use (see |

`mdi.range` |
time range over which to calculate MDI statistic |

`nsim` |
number of simulations used to calculate null disparity-through-time plot (see |

`CI` |
confidence level from which to plot simulated disparities |

`plot` |
whether to plot disparities through time |

`calculateMDIp` |
calculate p-value for MDI compared to null; only valid if nsim is not zero |

The most complete implementation of `dtt`

(where `nsim`

is greater than 0) carries out the entire disparity-through-time (DTT) procedure described in Harmon et al. 2003, where simulated data are used to construct a null DTT distribution. The function `disparity`

simply computes the morphological disparity for a set of species. Note that for `mdi.range`

, time is relative to a total tree length of 1. The default `mdi.range`

is the entire temporal span of the tree, from 0 (root) to 1 (tips).

For either function, the disparity index can be one of the following:

**avg.sq**is average squared Euclidean distance among all pairs of points; this is the most common distance metric for disparity in macroevolution**avg.manhattan**is average Manhattan distance among all pairs of points**num.states**is number of unique character states; this is currently the only option for discrete character data

The function `disparity`

returns the disparity of the supplied `data`

. If given a tree, `disparity`

will return
disparities computed for each subtree. The vector of disparities is indexed based on the numeric node-identifier of the subtending subtree (e.g., the
root is indexed by N+1, where N is the number of species in the tree; see `read.tree`

).

The function `dtt`

returns elements from the list below:

**dtt**is average disparity for clades whose stem crosses each time interval in the tree**times**are times for each value in disparity-through-time calculation; these are just the branching times of the phylogeny**sim**are disparities at time intervals for each simulated dataset**MDI**is the value of the MDI statistic, which is the area between the DTT for the data and the median of the simulations

If results are plotted, the mean DTT from the simulated datasets appears in dashed line and the empirical DTT in solid line.

LJ Harmon and GJ Slater

Foote M. 1997. The evolution of morphological diversity. *ARES* 28:129-152.

Harmon LJ, JA Schulte, JB Losos, and A Larson. 2003. Tempo and mode of evolutionary radiation in iguanian lizards. *Science* 301:961-964.

Slater GJ, SA Price, F Santini, and MA Alfaro. 2010. Diversity vs disparity and the evolution of modern cetaceans. *PRSB* 277:3097 -3104.

1 2 3 4 5 6 7 8 9 10 11 12 13 | ```
geo=get(data(geospiza))
## disparity -- not tree-based
disparity(data=geo$dat) # not tree-based
## cladewise disparities
disparity(phy=geo$phy, data=geo$dat)
## disparity through time of culmen length
dttcul<-dtt(phy=geo$phy, data=geo$dat[,"culmenL"], nsim=100, plot=TRUE)
## disparity through time of entire dataset -- without simulated data
dttgeo<-dtt(phy=geo$phy, data=geo$dat, nsim=0, plot=TRUE)
``` |

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