https://github.com/dombennett/project-edbmm
:evergreen_tree::ghost: Testing the phylogenetic reality of the living fossil with an EDBMM
https://github.com/dombennett/project-edbmm
evolutionary-distinctness living-fossil markov-model phylogeny pipeline r
Last synced: 3 months ago
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:evergreen_tree::ghost: Testing the phylogenetic reality of the living fossil with an EDBMM
- Host: GitHub
- URL: https://github.com/dombennett/project-edbmm
- Owner: DomBennett
- Created: 2014-06-19T17:01:03.000Z (almost 11 years ago)
- Default Branch: master
- Last Pushed: 2017-01-07T19:41:14.000Z (over 8 years ago)
- Last Synced: 2025-02-08T06:13:03.734Z (4 months ago)
- Topics: evolutionary-distinctness, living-fossil, markov-model, phylogeny, pipeline, r
- Language: R
- Homepage: https://www.cambridge.org/core/journals/paleobiology/article/div-classtitleevolutionarily-distinct-living-fossils-require-both-lower-speciation-and-lower-extinction-ratesdiv/895514AC2A88019CB206CC6D83C11943
- Size: 28.3 MB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# Evolutionary Distinctness Biased Markov Model (EDBMM)
An R pipeline for exploring how an evolutionary distinctness bias in a tree-growth Markov model affects tree shape in order to test the reality of the living fossil, see the published article ['Evolutionarily distinct “living fossils” require both lower speciation and lower extinction rates'](https://doi.org/10.1017/pab.2016.36).
The pipeline uses a Markov-Model to grow trees with extinction and speciation rates determined by a tip's evolutionary distinctness.
Data and results files are not provided in this repository, only the code is.
All results and starting datasets can be found in the [Dryad repository](https://datadryad.org/resource/doi:10.5061/dryad.hm55b). The repository
holds a large (5GB) compressed file in five parts. These parts must all be downloaded,
combined and then uncompressed to produce the folders.
```{bash}
# recombine and uncompress (UNIX)
cat xaa xab xac xad xae > data_results.tar.gz
tar zxvf data_results.tar.gz
```
**System requirements**
Run the `install_deps.R` script to install all dependent packages automatically.
* OS
+ UNIX (but readily modifiable for Windows)
* R version
+ 3+
* R packages (version used)
+ `plyr` (1.8.1)
+ `ape` (3.2)
+ `geiger` (2.0.3)
+ `apTreeshape` (1.4.5)
+ `ggplot2` (1.0.0)
+ `MoreTreeTools` (0.0.1)
+ `outliers` (0.14)
+ `doMC` (1.3.3, not for Windows)
+ `foreach` (1.4.2)
+ `test_that` (0.9.1, optional)
* External
+ [PATHd8](http://www2.math.su.se/PATHd8/)
Please note, [MoreTreeTools](https://github.com/DomBennett/MoreTreeTools) is in development and can only be installed via GitHub.
It is best to install using the EDBMM branch:
```{R}
library(devtools)
install_github('DomBennett/MoreTreeTools', ref='edbmm') # install edbmm branch
```
**Directory structure**
```
-- data/
---- raw_trees/
------ literature/
-------- [manually added]
------ treebase/
---- parsed_trees/
---- treestats/
-- parameters/
---- [all analysis parameters]
-- stages/
---- [all stage .R scripts]
-- tools/
---- [all tool .R scripts]
-- results/
----- [all folders named by analysis as specified in run.R]
-- other/
-- sanity_checks/
-- PATHd8
----- [excutable if parsing trees]
```
**Pipeline**
The pipeline works by calling the pipeline scripts `setup.R` and `run.R`. These scripts call
stage scripts which can be found in [`/stages`](https://github.com/DomBennett/Project-EDBMM/tree/master/stages).
The stages scripts depend on custom functions found in the [`/tools`](https://github.com/DomBennett/Project-EDBMM/tree/master/tools) folder.
**setup.R**
This phase of the pipeline sources and calculates statistics from empirical
trees:
1. Download trees from TreeBase
2. Parse trees (make ultramteric using different methods)
3. Calculate tree shape statistics
4. Determine the taxonomic identities of downloaded trees
**run.R**
This phase models trees for determining how model parameters affect tree shape:
1. Read in parameters from [`parameters/`](https://github.com/DomBennett/Project-EDBMM/tree/master/parameters)
2. Model trees according to parameters in `run.R`
3. Calculate tree shape statistics
**Analysis**
The final stage script is user interactive. All plots and analysis presented in the publication
are generated with this script.
**Clade analysis**
In addition to setup and run, there are additional clade analysis stages: `clade.R` and `analyse_clades.R`.
**Testing**
Run `test.R` to make sure core functions are working.
**Reference**
Bennett, D.J., Sutton, M.D. & Turvey, S.T., 2016. Evolutionarily distinct “living fossils” require both lower speciation and lower extinction rates. Paleobiology, pp.1–15. Available at: http://www.journals.cambridge.org/abstract_S0094837316000361.
**Author**
Dom Bennett