save_tipranges_to_LagrangePHYLIP: Save a tipranges object to a LAGRANGE PHYLIP-style file...
In BioGeoBEARS: BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts

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

Given some geographic range data for tips in the tipranges object, this function exports them to an ASCII text file in the Lagrange C++/PHYLIP format (Smith et al. (2010)). This file can then be read by getranges_from_LagrangePHYLIP.

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  save_tipranges_to_LagrangePHYLIP(tipranges_object,
    lgdata_fn = "lagrange_area_data_file.data",
    areanames = colnames(tipranges_object@df))

`tipranges_object`	An object of class `tipranges`.
`lgdata_fn`	The LAGRANGE geographic data file to be output.
`areanames`	A list of the names of the areas.

LAGRANGE C++ geographic range files are ASCII text files with the format:

19 4 (A B C D)
P_mariniana_Kokee2 1000
P_mariniana_Oahu 0100
P_mariniana_MauiNui 0010
P_hawaiiensis_Makaopuhi 0001
P_wawraeDL7428 1000
[...]

The first row specifies the number of taxa (here, 19), the number of areas (here, 4), and finally, the names/abbreviations of the areas. The rest of the rows give the taxon names, followed by a tab and then the presence/absence in each range with 1s/0s.

The file above is part of the geographic range data for the Hawaiian Psychotria dataset used by Ree et al. (2008).

tipranges_object An object of class tipranges

Go BEARS!

Nicholas J. Matzke matzke@berkeley.edu

http://phylo.wikidot.com/matzke-2013-international-biogeography-society-poster https://code.google.com/p/lagrange/

SmithRee2010_CPPversion

ReeSmith2008

Matzke_2012_IBS

define_tipranges_object, getranges_from_LagrangePHYLIP

testval=1

# Create an example tipranges object
tipranges = define_tipranges_object()

# See current directory
getwd()

## Not run: 
# Save the file
# Set the filename
fn = "example_tipranges.data"
save_tipranges_to_LagrangePHYLIP(tipranges_object=tipranges, lgdata_fn=fn)

# Show the file
tmplines = scan(file=fn, what="character", sep="\n")
cat(tmplines, sep="\n")

# Again, with areanames
save_tipranges_to_LagrangePHYLIP(tipranges_object=tipranges,
lgdata_fn=fn, areanames=c("area1","area2","area3"))

# Show the file
tmplines = scan(file=fn, what="character", sep="\n")
cat(tmplines, sep="\n")

## End(Not run) # End dontrun