phylo3D: 3D Geophylogenies for GIS Applications
In fmichonneau/phyloch: Tools for phylogenetics and taxonomy

Description Usage Arguments Value Author(s) References See Also

Given an ultametric phylogeny and locality data for each of its tips, this function constructs a three-dimensional vector map that can be displayed in GIS applications on raster surfaces or topological maps (e.g. via the NVIZ model in GRASS GIS).

1	geophylo(phy, file = "", loc, z_exag = 1000)

`phy`	An object of class `phylo`, must be ultrametric.
`file`	A character string giving the filename; if `file = ""`, the file is written on the standard output connection (i.e. the console).
`loc`	A matrix with locality data for the tips of the phylogeny; rows are assumed to correspond to tips as numbered in objects of class `phylo`; the first column must contain longitudinal values, the second column latitudinal values.
`z_exag`	Integer; used for superelevation of the internal nodes.

none; a vector map in ASCII format in printed to the given directory

Christoph Heibl

This function is inspired by GeoPhyloBuilder, a plug-in developed for ArcGIS by David Kidd and Xianhua Liu, available at https://www.nescent.org/wg_EvoViz/GeoPhyloBuilder.

Kidd, D. & X. Lui. 2008. GEOPHYLOBUILDER 1.0: an ArcGIS extension for creating 'geophylogenies'. Molecular Ecology Resources 8:88-91.

read.tree

fmichonneau/phyloch documentation built on May 16, 2019, 1:45 p.m.