cbtb

Collective behaviour and bio-hybrid results analysis

• A python package that includes:

  • Analysis of experimental results
  • Includes loaders for experimental results generated with assisipy_utils exec tools
  • Also includes loader for the built-in assisipy.casu logfile
  • code to compute indices including:
    • collective decision index
    • volatility index

• v0.6

• author: rob.mills@fc.ul.pt

How do I get set up?

• Install with pip

  $ pip install --user --upgrade cbtb-0.6.tar.gz

• Install editable with pip

  $ git clone <repo.git> <the_path> $ cd !$ $ pip install --editable .

• Dependencies: numpy, scipy, yaml

• For info_theory/libinfo, JIDT must be installed (the infodynamics.jar is needed). See guide [https://github.com/jlizier/jidt/wiki/Installation]. jpype is also needed (e.g. sudo apt-get install python-jpype)

  (pip doesn't well handle the fact that ubuntu's apt has installed python-numpy -- if that is how obtained... so these are not declared in the setup.py)