Description Usage Arguments Details Author(s) References See Also Examples

This function can be used to plot the history of climatic tolerance for a clade *sensu* Evans et al. (2009).

1 2 |

`x` |
A list with elements |

`clades` |
A list containing vectors of tip labels which define the clades to highlight. |

`col` |
A vector containing colors for different clades (see Examples). |

`density` |
Logical, if |

`tipmode` |
Integer: |

`nchar` |
An integer giving the number of characters to which the tiplabels are truncated. |

`cex` |
Numeric |

`tipspace` |
The fraction of the x-axis that is reserved for tiplabel plotting. If no value is given (default), |

`cladespace` |
A positive reel number; |

`lwd` |
The line width, a positive number, defaulting to 1. |

`ylab` |
A character string, giving a label for the y-axis, i.e., for the bioclimatic dimension of the plot. |

The main argument `x`

is a list consisting of at least the first two of the following elements: (1) `tree`

is an ultrametric phylogenetic tree stored as object of class `phylo`

; (2) `data`

is an object of class `matrix`

; its columns correspond to bioclimatic variables and its rows corresond to node numbers such as defined by class `phylo`

objects; (3) `central.density`

must only be included if `density = TRUE`

– it is a list, which for every bioclimatic variable, contains a matrix that contains the some minimum and maximum quantile of the respective bioclimatic variable for every tip in the tree.

Christoph Heibl

Evans, M. E. K., S. A. Smith, R. S. Flynn, and M. J. Donoghue. 2009. Climate, niche evolution,
and diversification of the 'bird-cage evening primroses' (*Oenothera*, sections *Anogra* and
*Kleinia*). *Am. Nat.* **173**: 225-240.

`pno`

, `pno.weighted.mean`

, `anc.clim`

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | ```
# load phylogeny and PNOs of Oxalis sect. Palmatifoliae
data(tree)
data(PNO)
# choose summer precipitation for analysis
clim <- PNO$PrecipitationWarmestQuarter
# estimate ancestral tolerances
ac <- anc.clim(target = tree, pno = clim, n = 100)
# visualize results with default branch coloration
plotAncClim(ac)
# alternative clade colors are given according to the order
# in which tip labels appear from left to right
plotAncClim(ac, col = c("red", "purple", "blue"))
# the 'tipmode' argument
plotAncClim(ac, tipmode = 0)
plotAncClim(ac, tipmode = 1)
plotAncClim(ac, tipmode = 2, nchar = 5)
plotAncClim(ac, tipmode = 3, nchar = 4)
``` |

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