https://github.com/dombennett/predicts-pd
:evergreen_tree::house: Response of phylogenetic diversity to human impacts in terrestrial ecosystems
https://github.com/dombennett/predicts-pd
Last synced: 8 months ago
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:evergreen_tree::house: Response of phylogenetic diversity to human impacts in terrestrial ecosystems
- Host: GitHub
- URL: https://github.com/dombennett/predicts-pd
- Owner: DomBennett
- Created: 2014-11-25T18:31:14.000Z (over 11 years ago)
- Default Branch: master
- Last Pushed: 2015-09-28T14:29:40.000Z (over 10 years ago)
- Last Synced: 2025-08-17T03:42:52.577Z (10 months ago)
- Language: R
- Homepage:
- Size: 777 KB
- Stars: 0
- Watchers: 4
- Forks: 0
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
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README
# Response of phylogenetic diversity to human impacts in terrestrial ecosystems
All code is made available for reproducing the analyses as described in
[insert paper URL here]. This is code only, for full completed dataset click
here (not yet available).
## Pipeline
The analysis comes in four stages:
Each stage is run once with the exception of `B1_parse.R`, `B2_compare.R` and `B3_metrics.R`
which are each run twice for comparing the results from unconstrained and constrained
pG-lt trees and testing whether there is a difference between total and age
branch length normalisation.
## Running
Make sure all relevant packages are installed:
```{bash}
Rscript x_install_deps.R
```
Additionally, you will need a compiled version of [pathD8](http://www2.math.su.se/PATHd8/)
in your working directory.
To run entire automated pipeline (UNIX OS):
```{bash}
sh x_run.sh
```
pG-lt step can only be run separately. It was originally run on Imperial's HPC.
Make sure you have `0_pglt/` before running the calculate step.
`C1_analysis.R` is an interactive script and it not part of the pipeline.
Note, setup will take a long time to run as they interact
with the [GNR](http://resolver.globalnames.biodinfo.org/).
## Stage details
### Setup
This is run with the `x_setup.sh` script. You can run pG-lt after it is run.
* `A1_presolve.R`: read in published trees and PREDICTS data, search names
against [GNR](http://resolver.globalnames.biodinfo.org/).
* `A2_parse.R`: read in published trees and rate-smooth
* `A3_pgltsetup.R`: identify suitable PREDICTS studies, output into pG-lt friendly
format. You can run pG-lt with the resulting folder.
* `A4_map.R`: use published phylogenies in `0_data` to generate study-level
phylogenies
### Calculate
This is run with the `x_calculate.R` script.
* `B1_parse.R`: read in pG-lt and mapped phylogenies, check and rate-smooth
* `B2_compare.R`: compare mapped and pG-lt phylogenies
* `B3_metrics.R`: generate PD, PSV and PSE values per site using both pG-lt and
mapped trees.
* `B4_plots.R`: community plot PREDICTS data onto pG-lt consensus phylogenies
## Directory (after complete run)
```
-- 0_data/
-- PREDICTS-DATA/
-- [site-level PREDICTS data]
-- raw_trees/
-- [downloaded published trees]
-- 0_pglt/
-- A1_preresolve/
-- A2_parse/
-- A3_pgltsetup/
-- A4_map/
-- B1_parse/
-- B2_compare/
-- B3_metrics/
-- B4_plots/
-- C1_analysis/
-- stages/
-- [all R stages files]
-- tools/
-- [all custom R functions]
-- sanity_checks/
-- [demonstrations of code accuracy]
-- other/
-- [misc non-essential items]
```
## Data
After cloning this repo to your machine, you can download all missing data files
with this link (not yet available).
Uncompress files:
```{bash}
sh x_uncompress.sh
```
And compress again:
```{bash}
sh x_compress.sh
```
## Authors
[Bennett D.J.](https://github.com/DomBennett),
[De Palma A.](https://github.com/adrianadepalma),
[Pearse W.D.](https://github.com/willpearse)
and [Purvis A](https://github.com/AndyPurvis).