R2G2 (version 1.0-2)

Phylo2GE: Producing 3D Phylogenies in Google Earth

Description

The function converts a phylogenetic tree and the corresponding geographical coordinates of its taxa into a KML that can be displayed into Google Earth.

Usage

Phylo2GE(geo, phy, resol = 0.1, minAlt = 1e+04, maxAlt = 2e+06, goo = "Phylo2GE.kml")

Arguments

geo

Matrix of geographical centroids for each taxa. Lines = taxa, columns = species name (as in phylogeny), lon and lat in decimal degrees.

phy

Phylogenetic tree, as imported using read.tree (ape).

resol

Drawing resolution of arcs in the phylogeny. Each horizontal arc will be divided in 1/resol subarcs.

minAlt

Altitude of tips, as displayed in Google Earth (in meters).

maxAlt

Altitude of root ancestral node, as displayed in Google Earth (in meters).

goo

Name of the KML file to that will be saved into the working directory (use getwd() to find it).

Value

A KML file is produced in the current working directory.

Details

Phylo2GE matches the phy and geo objects, according to taxa names. This matching cares for differential sorting of the phy and geo objects. This property also allows focusing on tree subclades without needing to update the geo array.

References

KML conversions of phylogenies were first seen in Mesquite (http://mesquiteproject.org/mesquite/mesquite.html) and on Rod Page's blog http://iphylo.blogspot.com/

See Also

aggregate curvy

Examples

# uncomment to use
# require(ape)
# require(picante)
# geo = data.frame(taxa = c("D", "E", "A", "B", "C", "F"), 
#	 lon = c(9.291113, 23.18146, 75.274541, -8.653739, 11.622450, 12.622450),
#	 lat = c(8.774068, 4.581856, 48.078570, 10.966451, 28.722732, 29.722732))
# geo

# phy = "(((B:0.41,C:0.31):0.65,(D:0.21,E:0.11):0.75):0.85,A:0.51);"
# phy = read.tree(text = phy)

# Phylo2GE(geo, phy, resol = .05, goo = 'Phylo2GE.kml')