A python package for summarizing the output of Ecoevolity
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README.md

Table of Contents

Pycoevolity

A package for summarizing the output of Ecoevolity.

Installation

Prerequisites

For some of the plots that pycoevolity produces, it uses the R packages ggplot2 and ggridges. So, if you want plotting by pycoevolity to be fully functional, and you don't already have R installed, you'll need to install it. Once R is in place, you can install the necessary packages from the R prompt using:

install.packages(c("ggplot2", "ggridges"))

Installing pycoevolity with pip

If you have the Python package manager pip installed, you should be able to install pycoevolity using:

pip install git+git://github.com/phyletica/pycoevolity.git

Manual install

If you don't have pip, I recommend you install it and use the command above to install pycoevolity. If that is not an option, you can download and install manually:

git clone https://github.com/phyletica/pycoevolity.git
cd pycoevolity
python setup.py install

If the last command fails with a "permission denied" error, and you have admin privileges on your computer, try:

sudo python setup.py install

If you don't have admin privileges, try:

python setup.py install --user

If you use the last command, pycoevolity will be installed in a directory within your home directory. Specifically, the command-line tools will probably be installed to a .local/bin directory within your home folder. You will probably have to add this directory to your PATH for your shell to find and run the pycoevolity tools.

Usage

pyco-sumtimes --help

Acknowledgments

This work was supported by funding provided to Jamie Oaks from the National Science Foundation (grant numbers DBI 1308885 and DEB 1656004).

License

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

See "LICENSE.txt" for full terms and conditions of usage.