Marxan Connect
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README.md

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Marxan Connect
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NEW The Marxan Connect bioRxiv preprint is now available!

Marxan Connect (henceforth the "app") is a Graphical User Interface (GUI) to help conservationists include "connectivity" in their protected area network planning.

The term "connectivity" has a variety of definitions (i.e. larval connectivity, genetic connectivity, landscape connectivity, etc) and protected area networks can be optimized for various connectivity objectives. The app is intended to guide conservationists through the process of identifying important aspects of connectivity for their conservation scenarios as well as highlighting the necessary data.

The app also includes a fully functional Python module that is operated via command line. The Python module, marxanconpy, can be used to reproduce an analysis using the project file (.MarCon) generated by the GUI (in progress).

To use this software, please visit the Tutorial and the Glossary (both in progress). Otherwise, if you would just like to get started, please install the app and proceed through all the tabs from left to right starting the "Spatial Input". After calculating the "Connectivity Metrics", you can choose to conduct a Marxan analysis in the app, export the connectivity metrics for use in a standalone custom Marxan analysis, or you can visualize the Connectivity Metrics using the "Plotting Options" tab

If you would like to report any bugs or request a missing feature, please post an issue on the GitHub repository or email (although GitHub is preferred). Please provide as much information as possible, such as: detailed description, app version, operating system, even a link to your data if relevant (also, see Contributing).

Authors

  • Remi Daigle - App design, programming, development, maintenance - remi-daigle
  • Anna Metaxas - Initial conception, Acquisition of funding, App improvements and development
  • Arieanna Balbar - App improvements, testing, and development - abalbar
  • Jennifer McGowan - App improvements, design for discrete conservation features
  • Eric Anton Treml - App improvements, input to connectivity definitions and metrics
  • Caitie Kuempel - App improvements - cdkuempel
  • Hugh Possingham - App improvements
  • Maria Beger - Initial conception, Acquisition of funding, App improvements and development

See also the list of contributors who participated in this project on Github and the Acknowledgments section.

Installing

Marxan Connect was built for Windows 10. Users may find compatibility issues with Windows 7 or 8 (the app may not be able to run Marxan, but can create Marxan files to run manually). The app is currently not compatible with Linux and Mac although the python processing script (marxanconpy) and GUI scripts (gui and MarxanConnectGUI) were designed with interoperability in mind.

Windows Installer

(WARNING! Marxan Connect is in 'beta' release and is not yet fully tested.)

Please download the latest MarxanConnect-vX-Y-Z-windows-setup.exe installer file, run it, and follow the instructions. Alternatively (for advanced users only), follow the Building from source instructions to use the latest bleeding edge version of the app.

Windows Zipped Bundle

If you cannot use the installer because you do not have administrative privileges, we've provided a zipped bundle of the app to allow users to bypass that problem. To use, download the latest MarxanConnect.zip, unzip it to your preferred destination (e.g. ~/Desktop), and double-click MarxanConnectGUI.exe. In this case you will have to generate any start menu shortcuts, or file associations (i.e. .MarCon) manually.

Building from source

Not for the typical user. Building from source is only necessary if you plan to contribute to the project (see Contributing section below) or if you want to use the bleeding edge version of the app.

  • Download this repository
  • If necessary, edit the hard coded file paths in setup.py and WindowsSetupBuilder.iss
  • open a terminal or cmd window (or git bash) in the project directory and type:
make

Alternatively, you can compile the website with make web, the Marxan Connect executable with make exe, the windows installer make win, and the zip with make zip

Prerequisites (for building from source)

It also assumes you have all the pre-requisite python modules installed, i.e.:

#!/bin/bash
# for basic GUI
pip install wxpython
pip install matplotlib
pip install matplotlib.basemap
pip install geopandas
pip install descartes
pip install python-igraph
pip install shapely
pip install pandas
pip install numpy
pip install bs4


# for compiling executable
pip install cx_Freeze

Built With

The gui.py file was built using the fantastic wxFormBuilder.

The windows installer was built using Inno Setup.

THe documentation and website was built with R and the rmarkdown package

Contributing

Please read CONTRIBUTING.md for details on our code of conduct, and the process for submitting pull requests or issues to us.

Versioning

We use SemVer for versioning. For the versions available, see the tags on this repository.

License

This project is licensed under the MIT License - see the LICENSE.md file for details

Acknowledgments

References

Ball, I.R., H.P. Possingham, and M. Watts. 2009. Marxan and relatives: Software for spatial conservation prioritisation. Chapter 14: Pages 185-195 in Spatial conservation prioritisation: Quantitative methods and computational tools. Eds Moilanen, A., K.A. Wilson, and H.P. Possingham. Oxford University Press, Oxford, UK.