read.phylip.data {PHYLOGR}

Read Phylip Infile Data Files

Description

Reads one file with tip data, such as a PHYLIP infile, and returns an R data frame. The files have to follow the PHYLIP standard of having a first line with the number of species and traits. There can be multiple traits, as allowed in PHYLIP. Data for a species can extend over several lines, as for PHYLIP's sequential data format for continuous traits. It is assumed that all traits are cuantitative.

Usage

read.phylip.data(input.phylip.file, variable.names=NULL)

Arguments

input.phylip.file

the name, with path if necessary, of the infile.

variable.names

an optional vector with the new names for the variables.

Value

A data frame (with class phylip.file and data frame) with first column the names of tips and remaining columns the data columns from the phylip file.

Note

The format of PHYLIP's infiles is not exactly the same as the TIP files produced from PDTREE. First, PHYLIP's infiles can contain an arbitrary number of traits, whereas PDTREE's TIP files only have two. Second, PHYLIP's infiles have a first line with the number of tips and the number of traits, separated by blanks. Third, the first field or column of PHYLIP's infiles must be ten characters wide; if the tips names are shorter, they must be padded with blanks (see PHYLIP's documentation). This limitation does not apply to read.phylip.data, but you might want to follow it if you plan to use PHYLIP.

Author(s)

Diaz-Uriarte, R., and Garland, T., Jr.

References

Diaz-Uriarte, R., and Garland, T., Jr., in prep. PHYLOGR: an R package for the analysis of comparative data via Monte Carlo simulations and generalized least squares approaches.

See Also

read.inp.data, read.pdi.data, read.sim.data,

Examples

# This works under both Unix and Windows.
# First need to find out where the ''Examples'' directory is located.
path.to.example <- paste(path.package(package="PHYLOGR"),"Examples/",sep="/") 



lacertid.data.name <- paste(path.to.example,"LacertidData.PhylipInfile",sep="")
lacertid.data <- read.phylip.data(lacertid.data.name,variable.names=c("svl", "svl.matur",
                                  "hatsvl", "hatweight", "clutch.size",
                                  "age.mat", "cl.freq", "xx"))
lacertid.data

# You could jump directly to the call to the function if you
# are willing to enter the path explicitly.
# For example in some Linux systems the following works
# read.phylip.data("/usr/lib/R/library/PHYLOGR/Examples/LacertidData.PhylipInfile")
# In Windows, maybe do:
# read.pdi.data("c:\\progra~1\\rw1001\\library\\PHYLOGR\\Examples\\LacertidData.PhylipInfile")