pathd8: PATHd8

In DomBennett/om..pathd8: Outsider module for running pathd8

Description

Run PATHd8, see https://www2.math.su.se/PATHd8/PATHd8manual.pdf for more information.

Usage

pathd8(input_file, output_file)

Arguments

input_file	File path to input file containing tree and constraint information.
output_file	File path to output file.

Examples

library(outsider)
pathd8 <- module_import('pathd8', repo = 'dombennett/om..pathd8')
# Taken from manual
# https://www2.math.su.se/PATHd8/PATHd8manual.pdf
input_text <- "
Sequence length = 1823;

((((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);

mrca: Rat, Ostrich, minage=260;
mrca: Human, Platypus, fixage=125;
mrca: Alligator, Ostrich, minage=150;
name of mrca: Platypus, Rat, name=crown_mammals;
name of mrca: Human, Rat, name=crown_placentals;
name of mrca: Ostrich, Alligator, name=crown_Archosaurs;

# my own notes, not executed by PATHd8
# fossil Archosaurus minage=260
# fossil Archaeopteryx minage=150
# fossil Eomaia minage=125
"

# write out input file as binary
input_file <- file.path(tempdir(), 'pathd8_input.txt')
input_connection <- file(input_file, 'wb')
write(x = input_text, file = input_connection)
close(input_connection)

# run pathd8
output_file <- file.path(tempdir(), 'pathd8_output.txt')
pathd8(input_file = input_file, output_file = output_file)

# check output
cat(readLines(con = output_file), sep = '\n')

# clean up
file.remove(input_file)
file.remove(output_file)

DomBennett/om..pathd8 documentation built on Jan. 20, 2020, 10:36 a.m.