NichePy: a collection of Python scripts for estimating overlap of ecological niche and species distribution models.
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NichePy version 1.1 QUICK INSTALL $ git clone https://github.com/bastodian/NichePy.git $ sudo python3 setup.py install If python3 -V < 3.2 choose option 2 else option 1 GET NICHEPY To download a zip archive of the NichePy repository: https://github.com/bastodian/NichePy/zipball/master To download a tar.gz archive of the NichePy repository: https://github.com/bastodian/NichePy/tarball/master Alternatively: $ git clone https://github.com/bastodian/NichePy.git This will download the contents of the NichePy repository into a folder called NichePy. Prerequisite for this to work is that you install git if you haven't already installed it on your machine (http://git-scm.com/download). INSTALLATION Refer to the MANUAL for additional details. In short, all Python scripts require Python version 3 (ideally >= 3.2). The functions required by NichePy scripts are contained in the nichefunc.py module. In addition Python versions 3 < 3.2 require the argparse.py module. Simply run setup.py or keep these module files in the same directory as the resampling scripts, nicheIdentity.py and nicheBackground.py, and the getMetric.py script. Included is an installation script that places a link from the location of the getMetric, nicheIdentity, and nicheBackground scripts to the folder /usr/bin and makes the scripts executable. In addition, the nichefunc and/or argparse modules will be installed using Python's built-in installer. After running the installation script the scripts can be called from anywhere in the file-system hierarchy. To install using our installation script change to root (su root) and: $ python3 setup.py install or if you have sudo set up (default on Ubuntu and many other Linux distros) $ sudo python3 setup.py install After installing the scripts using setup.py the scripts can be executed as follows: $ nicheIdentity $ nicheBackground $ getMetric If the scripts were not installed using setup.py use: $ python3 path/to/nicheIdentity.py $ python3 path/to/nicheBackground.py $ python3 path/to/getMetric.py EXAMPLES The folder Examples contains example occurrence data sets and models. Please refer to the README in the Example folder to learn more about the input/output datastructure for NichePy. BATCH SCRIPTS AND WRAPPERS We included example batch scripts that show how ENMs/SDMs may be generated with OpenModeller or Maxent in batch mode. Also included is a script that converts the output from nicheIdentity and/or nicheBackground into a format suitable as input for OpenModeller. In addition, we included the scripts we used to generate simple consensus models by averaging. BUGS AND HELP We made every effort to track down and fix bugs in our scripts. If you discover what you believe to be a bug, please send an email to email@example.com and/or firstname.lastname@example.org. If you have trouble using our scripts don't hesitate to contact us. Please include a brief description of the problem in the email that includes any messages that the scripts printed to the screen. Please also include (a subset) of the files you were trying to run the scripts on, so that we can replicate the problem. Lastly, please include the version number of your Python installation (type python -V or python3 -V in the shell) and Operating system in your email to us.