phy.nodetimes: finding splitting times for nodes In spacodiR: Spatial and Phylogenetic Analysis of Community Diversity

Description

`phy.nodetimes` is a function to collect all nodes (and times) that are within a particular time fraction of the total temporal extent of a phylogeny

Usage

 `1` ```phy.nodetimes(phy, time.range = c(0, 0), proportion = TRUE) ```

Arguments

 `phy` a phylogenetic tree of class `phylo`; see `read.tree` `time.range` the temporal slice of the tree defining the bounds for extracted nodes `proportion` Boolean; whether `time.range` is regarded as proportions of tree height

Details

Given a temporal fraction of a phylogeny, this function will return all contained nodes (and branching times if desired). If used with `spacodi.by.nodes`, one could conduct significance testing of `Bst` through particular time slices of the phylogeny. Note: when using `proportion=TRUE`, '0' is regarded as the present, '1' as the root of the tree (e.g., `start.time=1.0` and `stop.time=0.8` gathers nodes for the basalmost or most rootward 20 percent of the temporal extent of the tree).

Value

A named vector of times (whose names are node labels; see `nodelabels` for the function used to label nodes).

Jonathan Eastman

Examples

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20``` ```## an example of comparing observed and expected Bst at nodes ## data(sp.example) attach(sp.example) s=spl p=phy # get nodes for a time-slice n.t=phy.nodetimes(phy=p,time.range=c(0.25,0.75)) # get Bsts for nodes o=spacodi.by.nodes(sp.plot=s, phy=p, obs.only=TRUE)[[1]] obs=o[!is.na(match(o[,"node.ID"], names(n.t))),1] # compile expected Bst-values from data reshuffling spacodi.by.nodes(sp.plot=s, phy=p, n.rep=5, method="1s")[[2]]->exps e=exps[!is.na(match(row.names(exps), names(n.t))),] exp=unname(unlist(e)) # randomization test of observed and expected Bst resamp.test(obs=obs, exp=exp, iter=100, two.tailed=TRUE) ```

spacodiR documentation built on May 29, 2017, 10:10 p.m.