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https://github.com/dombennett/om..pathd8
outsider-module: pathd8
https://github.com/dombennett/om..pathd8
Last synced: 9 days ago
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outsider-module: pathd8
- Host: GitHub
- URL: https://github.com/dombennett/om..pathd8
- Owner: DomBennett
- Created: 2019-11-12T12:59:19.000Z (almost 5 years ago)
- Default Branch: master
- Last Pushed: 2020-01-16T10:41:03.000Z (almost 5 years ago)
- Last Synced: 2023-10-20T19:24:33.476Z (about 1 year ago)
- Language: R
- Homepage:
- Size: 66.4 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.Rmd
Awesome Lists containing this project
README
---
output: github_document
---
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "README-"
)
```
# Run [`pathd8`](https://www2.math.su.se/PATHd8/) with `outsider` in R
[](https://travis-ci.org/dombennett/om..pathd8)
> Date phylogenetic trees without a molecular clock.
## Install and look up help
```{r install-snippet, eval=TRUE, include=TRUE}
library(outsider)
module_install(repo = "dombennett/om..pathd8")
# module_help(repo = "dombennett/om..pathd8")
```
## Detailed example
```{r detailed-example, eval=TRUE, include=TRUE}
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)
```
```{R uninstall, eval=TRUE, include=FALSE}
module_uninstall(repo = 'dombennett/om..pathd8')
```
### Key arguments
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.
## Links
Find out more by visiting the [PATHD8 homepage](https://www2.math.su.se/PATHd8/)
## Please cite
* 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](http://www.math.su.se/PATHd8/PATHd8-abstract.doc).)
* 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
---
**An `outsider` module**
Learn more at [outsider website](https://docs.ropensci.org/outsider/). Want to build your own module? Check out [`outsider.devtools` website](https://docs.ropensci.org/outsider.devtools/).