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NichePy: a collection of Python scripts for estimating overlap of ecological niche and species distribution models.

branch: master
README
    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
    bastodian@gmail.com and/or m.shcheglovitova@gmail.com.

    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.
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