# plotAncClim: Chronograms with Climatic Data on the Y-Axis In phyloclim: Integrating Phylogenetics and Climatic Niche Modeling

## Description

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

## Usage

 ```1 2``` ```plotAncClim(x, clades = NULL, col, density = TRUE, tipmode = 1, nchar = 3, cex, tipspace, cladespace = 1, lwd, ylab = "") ```

## Arguments

 `x` A list with elements `tree`, `data`, and (optional) `central.density` (see details). `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 `TRUE`, the central density intervals for recent species are plotted. `tipmode` Integer: `tipmode = 0` means no tiplabels (and no central density intervals) are plotted; values `1`, `2`, and `3` define different ways of plotting the tiplabels (see Examples). `nchar` An integer giving the number of characters to which the tiplabels are truncated. `cex` Numeric character expansion factor for tiplabels; multiplied by `par`(`"cex"`) yields the final character size. `NULL` is are equivalent to `1.0`. `tipspace` The fraction of the x-axis that is reserved for tiplabel plotting. If no value is given (default), `plotAncClim` calculates the fraction as 1 - (4 / nbtips), but this can be overridden by specifiying a fixed value for `tipspace` in ]0, 1[. `cladespace` A positive reel number; tentative: a factor controlling the space between tiplabels of different clades. `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.

## Details

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

## References

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`

## Examples

 ``` 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) ```

### Example output

```Loading required package: ape