https://github.com/fastscape-lem/adascape

Simple adaptive speciation model as a component of FastScape-LEM
https://github.com/fastscape-lem/adascape

Last synced: about 1 year ago
JSON representation

Simple adaptive speciation model as a component of FastScape-LEM

• Host: GitHub
• URL: https://github.com/fastscape-lem/adascape
• Owner: fastscape-lem
• License: agpl-3.0
• Created: 2023-04-03T08:22:42.000Z (about 3 years ago)
• Default Branch: master
• Last Pushed: 2024-08-12T08:55:46.000Z (almost 2 years ago)
• Last Synced: 2025-03-27T17:51:53.528Z (about 1 year ago)
• Language: Jupyter Notebook
• Homepage:
• Size: 89.7 MB
• Stars: 3
• Watchers: 2
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

          
[![test build](https://github.com/fastscape-lem/adascape/actions/workflows/test.yml/badge.svg?branch=master)](https://github.com/fastscape-lem/adascape/actions)

[![test notebooks](https://github.com/fastscape-lem/adascape/actions/workflows/test_notebooks.yml/badge.svg?branch=master)](https://github.com/fastscape-lem/adascape/actions)

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7794374.svg)](https://doi.org/10.5281/zenodo.7794374)

# AdaScape: Adaptive speciation and landscape evolution model

The "AdaScape" package contains a simple adaptive speciation model written

in Python that is coupled with the landscape evolution model [FastScape](https://fastscape.readthedocs.io/en/latest/).

## Install

This package depends on Python (3.9 or later is recommended),

[numpy](http://www.numpy.org/),

[scipy](https://docs.scipy.org/doc/scipy/reference/),

[pandas](https://pandas.pydata.org/),

[fastscape](https://github.com/fastscape-lem/fastscape) and 

[orographic precipitation](https://github.com/fastscape-lem/orographic-precipitation) .

This package also provides a [dendropy](https://dendropy.org/) extension and 

uses [toytree](https://toytree.readthedocs.io/en/latest/index.html) 

to plot phylogenetic trees (optional dependencies).

To install the package locally, first clone this repository:

``` shell

$ git clone https://github.com/fastscape-lem/adascape.git

$ cd adascape

```

Then run the command below (this will install numpy, scipy and pandas

if those libraries are not yet installed in your environment):

``` shell

$ pip install .

```

To install the package for development purpose, use the following

command instead:

``` shell

$ pip install -e .

```

## Usage

Some examples are shown in the ``notebooks`` folder (Jupyter Notebooks).

## Tests

To run the tests, you need to have

[pytest](https://docs.pytest.org/en/latest/) installed in your environment.

Then simply run from this repository's root directory:

``` shell

$ pytest adascape -v

```