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

Run `pathd8` with `outsider` in R

Date phylogenetic trees without a molecular clock.

library(outsider)
#> ----------------
#> outsider v 0.1.0
#> ----------------
#> - Security notice: be sure of which modules you install
module_install(repo = "dombennett/om..pathd8")
#> -----------------------------------------------------
#> Warning: You are about to install an outsider module!
#> -----------------------------------------------------
#> Outsider modules install and run external programs
#> via Docker <https://www.docker.com>. These external
#> programs may communicate with the internet and could
#> potentially be malicious.
#> 
#> Be sure to know the module you are about to install:
#> Is it from a trusted developer? Are colleagues using
#> it? Is it supposed to download lots of data? Is it
#> well used (e.g. check number of stars on GitHub)?
#> -----------------------------------------------------
#>  Module information
#> -----------------------------------------------------
#> program: pathd8
#> details: Estimating divergence times in large phylogenetic trees.
#> docker: dombennett
#> github: dombennett
#> url: https://github.com/dombennett/om..pathd8
#> image: dombennett/om_pathd8
#> container: om_pathd8
#> package: om..pathd8
#> Travis CI: Passing
#> -----------------------------------------------------
#> Enter any key to continue or press Esc to quit
# module_help(repo = "dombennett/om..pathd8")

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)
#> Calculation finished.

# check output
cat(readLines(con = output_file), sep = '\n')
#> 
#> 
#> ************************************************************************************************
#> *  d 8   C A L C U L A T I O N                                                                 *
#> ************************************************************************************************
#> 
#> Number of informative fixnodes:   1
#> Number of informative minnodes:   2
#> Number of informative maxnodes:   0
#> 
#> d8 tree    : ((((Rat:22.388060,Human:22.388060)crown_placentals:102.611940,Platypus:125.000000)crown_mammals:135.000000,(Ostrich:150.000000,Alligator:150.000000)crown_Archosaurs:110.000000):166.742712,Frog:426.742712);
#> 
#> Ancestor of          Ancestor of          Name                        Age  #Terminals              MPL         Rate *      minage      maxage
#> Rat                  Frog                 -                       426.743           6           86.333       0.202308           -           - 
#> Rat                  Alligator            -                       260.000           5           52.600       0.202308       260.0           - 
#> Rat                  Platypus             crown_mammals           125.000           3           44.667       0.357333       125.0       125.0 
#> Rat                  Human                crown_placentals         22.388           2            8.000       0.357333           -           - 
#> Ostrich              Alligator            crown_Archosaurs        150.000           2           22.000       0.146667       150.0           - 
#> 
#> 
#>   *) Rate = MPL / Age
#> 
#> 
#> ************************************************************************************************
#> *  M P L  C A L C U L A T I O N                                                                *
#> ************************************************************************************************
#> 
#> Clock test confidence: 0.950000
#> Clock tests          : 5   (one for each node)
#> Accepted             : 1
#> Rejected             : 4
#> 
#> MPL tree   : ((((Rat:8.000000,Human:8.000000)crown_placentals:36.666667,Platypus:44.666667)crown_mammals:7.933333,(Ostrich:22.000000,Alligator:22.000000)crown_Archosaurs:30.600000):33.733333,Frog:86.333333);
#> 
#> Ancestor of          Ancestor of          Name                            MPL             #Terminals      Clock test: Acc/Rej
#> Rat                  Frog                 -                        86.333 +/- 13.772               6      Acc
#> Rat                  Alligator            -                        52.600 +/- 8.803                5      Rej, prob=0.000004
#> Rat                  Platypus             crown_mammals            44.667 +/- 9.727                3      Rej, prob=0.012738
#> Rat                  Human                crown_placentals          8.000 +/- 3.917                2      Rej, prob=0.012419
#> Ostrich              Alligator            crown_Archosaurs         22.000 +/- 6.496                2      Rej, prob=0.000911
#> 
#> 
#> ************************************************************************************************
#> *  E N D  C A L C U L A T I O N                                                                *
#> ************************************************************************************************

# clean up
file.remove(input_file)
#> [1] TRUE
file.remove(output_file)
#> [1] TRUE

The pathd8 function takes just two arguments: input_file which specifies the tree and the run parameters and output_file where the resulting tree is saved.

Find out more by visiting the PATHD8 homepage

Estimating divergence times in large phylogenetic trees by Tom Britton, Cajsa Lisa Anderson, David Jacquet, Samuel Lundqvist and Kåre Bremer, found in Systematic Biology 56:5, pp 741 - 752 . (The abstract can be found here.)
Britton, T., B. Oxelman, A. Vinnersten, and K. Bremer. 2002. Phylogenetic dating with confidence intervals using mean path lengths. Molecular Phylogenetics and Evolution 24:58-65.
Bennett et al. (2020). outsider: Install and run programs, outside of R, inside of R. Journal of Open Source Software, In review