ips (version 0.0.11)

pathd8: PATHd8

Description

This function is a wrapper for PATHd8 and can be used for phylogenetic dating, especially of large trees

Usage

pathd8(phy, exec = "/Applications/PATHd8/PATHd8", seql, calibration)

Arguments

phy

An object of class phylo.

exec

A character string giving the path to the PATHd8 program.

seql

sequence length of alignment

calibration

A data frame with 4 columns and as many rows as calibration points. Columns are: taxon 1; taxon 2; one of c("minage", "maxage", "fixage"); age.

Value

tree list of ultrametric trees returned from PATHd8 of class phylo. First tree is PATHd8 chronogram, which is a calibrated ultrametric tree. Second is a PATH tree, which is a ultrametric tree without calibration.

References

Britton et al (2006). PATHd8---a new method for estimating divergence times in large phylogenetic trees without a molecular clock. Available from the authors (www.math.su.se/PATHd8)

Britton et al. (2007). Estimating divergence times in large phylogenetic trees. Systematic biology. 56:741--752

Examples

# NOT RUN {
## This example is taken from the PATHD8 manual
cal <- rbind(cal1 = c("Rat", "Ostrich", "minage", 260), 
cal2 = c("Human", "Platypus", "fixage", 125),
cal3 = c("Alligator", "Ostrich", "minage", 150))
colnames(cal) = c("tax1", "tax2", "age_type", "age")
phy <- read.tree(text = paste0("((((Rat:0.007148,Human:0.001808):0.024345,",
                               "Platypus:0.016588):0.012920,(Ostrich:0.018119,",
                               "Alligator:0. 006232):0.004708):0.028037,Frog:0);")
seql <- 1823
pathd8(phy, exec = "/Applications/PATHd8/PATHd8", seql = seql, calibration = cal)
# }