| Author: | Olivier Friard |
|---|---|
| Author: | Marco Gamba |
Behavioral sequences analysis with random permutations test
Behatrix is free and open-source software available for GNU/Linux, Windows and MacOS.
Behatrix was formerly named BSA (Behavioral Strings Analysis)
The details of modifications are available in the revision history .
Behatrix can be downloaded from the GiHub repository
All versions are portable, they do not need to be installed on your system.
All previous versions of Behatrix are available in the GitHub repository.
Download the behatrix-x.y.z-x86_64.tar.gz file, unzip it, go to the bin directory and launch the start_behatrix.
Download the behatrix-x.y.z-win64-portable.zip file, unzip it and launch start_behatrix.bat.
Download the behatrix-x.y.z.dmg image file, mount it and launch the behatrix program.
You will need a working installation of Python >=3.6.
- Create a virtual environment (to isolate Behatrix from your system):
python3 -m venv behatrix_venv- Activate the virtual environment
source behatrix_venv/bin/activateThe prompt should now be prefixed by behatrix_venv
- Install Behatrix
pip install behatrix- Launch Behatrix
python3 -m behatrixFor flow diagrams generation you must install the Graphviz package.
Go to the Graphviz web site and download the version corresponding to your system.
If the dot program is not on the path you will have to indicate the complete path to the dot program.
The behavioral sequences can be directly written, paste or loaded from file in the Behavioral strings edit box.
See the BORIS user guide for exporting behavioral strings.
In a behavioral sequence, the successive behaviors can be separated by any character or group of characters. By default BORIS uses the pipe character (|). If no separator is used each different character of the sequence will be interpreted as a behavior.
The Clear strings button allows to eliminate all the sequences put in the edit box.
Eventually repeated behaviors in the sequences can be removed by clicking on the Remove repeated behaviors button.
Below, click on the Generate statistics button to obtain the statistical values and to Transition matrix to generate the transition matrix related to the behavioral sequences.
Some statistics can be obtained for various n-gram by clocking on the Generate statistics button.
In the results box Behatrix will list all the behaviors present in the sequences in alphabetical order, the total number of behaviors, the total number of transitions, the number of different transitions and the behaviors frequencies.
Use the Save results button for both the statistics and the transition matrix.
Example of statistics for 1-gram:
Number of sequences: 3
Statistics
==========
Number of different behaviours: 7
Total number of behaviours: 23
Number of different transitions: 12
Total number of transitions: 20
Behaviours list:
================
Alert
Locomotion
Manipulate
Play in the water
Play on the ground
Roll objects
Swim
Behaviours frequencies:
=======================
Alert 0.304 7 / 23
Locomotion 0.087 2 / 23
Manipulate 0.174 4 / 23
Play in the water 0.043 1 / 23
Play on the ground 0.043 1 / 23
Roll objects 0.261 6 / 23
Swim 0.087 2 / 23
Example of statistics for 2-gram:
(...)
Frequencies of 2-grams:
=======================
Alert|Locomotion 0.050 1 / 20
Alert|Manipulate 0.050 1 / 20
Alert|Roll objects 0.250 5 / 20
Manipulate|Alert 0.100 2 / 20
Manipulate|Locomotion 0.050 1 / 20
Manipulate|Roll objects 0.050 1 / 20
Play in the water|Swim 0.050 1 / 20
Play on the ground|Manipulate 0.050 1 / 20
Roll objects|Alert 0.200 4 / 20
Roll objects|Manipulate 0.050 1 / 20
Swim|Alert 0.050 1 / 20
Swim|Play in the water 0.050 1 / 20
Example of observed transition matrix:
Alert Locomotion Manipulate Play in the water Play on the ground Roll objects Swim
Alert 0 1 1 0 0 5 0
Locomotion 0 0 0 0 0 0 0
Manipulate 2 1 0 0 0 1 0
Play in the water 0 0 0 0 0 0 1
Play on the ground 0 0 1 0 0 0 0
Roll objects 4 0 1 0 0 0 0
Swim 1 0 0 1 0 0 0
Click the Generate GraphViz script button to obtain the script then click the Generate flow diagram button to visualize the flow diagram.
From version 0.9.1 the binary version for Microsoft-Windows can use the multiprocessing module, the permutations test is able to use many cores.
Some transitions can be excluded from the permutations test:
to be finished...
to be finished...
usage:
python3 -m behatrix [options]
Behatrix command line utility
optional arguments:
-h, --help show this help message and exit
-v, --version Behatrix version
-s SEQUENCES, --sequences SEQUENCES
Path of file containing behavioral sequences
--separator SEPARATOR
Separator of behaviors
-o OUTPUT, --output OUTPUT
Path of output files
--exclusions EXCLUSIONS
Path of file containing exclusions
--n-random NRANDOM Number of permutations
--n-cpu N_CPU Number of CPU to use for permutations test
--block-first block first behavior during permutations test
--block-last block last behavior during permutations test
--no-repetition exclude repetitions during permutations test
--n-gram NGRAM n-gram value
-q, --quiet Do not print results on terminal
See http://www.boris.unito.it/pages/behatrix for details :-)
python3 -m behatrix --sequences behav_sequences.txt --output behav_sequences_results --n_cpu 6 --n_random 10000
Behaviors are separated by the pipe character (|) otherwise each character will be interpreted as a behavior
Swim|Play in the water|Play in the water
Swim|Play in the water|Swim|Swim|Play in the water|Swim|Play in the water|Play in the water|Alert|Locomotion|Swim
Locomotion|Locomotion|Alert|Sniff|Rub|Locomotion
Locomotion|Alert|Alert+Vocalize|Alert+Vocalize|Locomotion
Locomotion|Alert|Sniff|Rub|Rest|Locomotion|Locomotion|Locomotion|Locomotion+Sniff|Sniff|Alert|Drink|Alert
Sniff|Manipulate|Locomotion|Locomotion|Locomotion|Locomotion|Rub|Alert|Sniff|Alert|Manipulate|Locomotion
Manipulate
Play on the ground|Manipulate|Locomotion
Rub|Locomotion|Sniff|Alert|Rub|Locomotion|Rub|Locomotion|Rub|Alert|Locomotion|Rub|Sniff|Rub|Sniff|Dig|Rest|Rub|Locomotion|Rub
Rub|Manipulate|Sniff|Rub|Sniff|Rub|Locomotion|Rub|Locomotion
Play on the ground|Locomotion
Locomotion|Manipulate|Alert|Sniff|Sniff+Locomotion|Sniff|Manipulate|Sniff
Self-groom|Sniff|Locomotion|Locomotion+Sniff|Sniff|Defecate|Defecate+Urinate|Defecate+Urinate+Yawn|Urinate|Locomotion|Locomotion+Sniff|Sniff
Sniff|Sniff|Defecate|Defecate+Urinate|Defecate+Urinate+Stomp|Defecate+Urinate|Defecate+Urinate+Yawn|Urinate|Locomotion|Dig|Locomotion
Play on the ground
Locomotion|Sniff|Locomotion|Locomotion+Sniff|Sniff|Locomotion|Locomotion|Rub|Sniff
Rub|Sniff|Rub|Locomotion
Alert|Alert+Vocalize|Alert+Vocalize|Rub|Rub+Vocalize|Rub+Vocalize|Vocalize|Alert|Alert+Vocalize|Alert+Vocalize|Alert+Vocalize|Rub|Alert|Rub|Alert|Self-groom|Alert|Rub|Locomotion|Locomotion
Locomotion|Alert|Locomotion|Alert|Locomotion|Locomotion|Locomotion|Locomotion+Sniff|Locomotion|Alert|Locomotion|Rub|Alert|Rub|Alert|Rub|Alert|Rub|Allogroom|Rub|Alert|Rub|Alert|Rub|Alert|Locomotion
Alert|Alert+Vocalize|Alert+Vocalize|Alert+Vocalize|Rub|Self-groom|Alert|Alert+Vocalize|Rub|Locomotion|Alert|Locomotion|Alert|Locomotion
Sniff|Alert|Locomotion
Locomotion|Alert|Rub|Self-groom|Alert|Self-groom|Rub|Self-groom|Alert|Rub|Alert|Rub
Rub|Sniff|Alert|Sniff|Alert|Rub|Sniff|Rub|Alert|Locomotion
Rub|Alert|Rub|Sniff|Rub
Rub|Rub|Sniff
Locomotion|Manipulate|Alert|Locomotion|Manipulate|Tear|Manipulate|Tear
Self-groom|Locomotion|Self-groom|Alert|Self-groom|Alert|Locomotion
Alert|Locomotion|Locomotion+Sniff|Sniff|Manipulate|Locomotion|Locomotion+Sniff|Sniff|Manipulate|Sniff|Sniff+Locomotion|Sniff|Manipulate|Locomotion|Manipulate
Locomotion|Alert|Locomotion|Alert|Locomotion
Swim|Swim|Locomotion|Locomotion+Sniff|Locomotion|Locomotion+Sniff|Sniff|Sniff|Swim|Locomotion|Locomotion|Locomotion|Swim|Alert|Swim|Swim|Alert|Eat|Alert|Swim|Alert|Sniff|Eat|Dig|Eat|Locomotion|Dig|Eat|Swim|Alert|Sniff|Alert|Sniff|Dig|Eat|Dig|Eat|Dig|Sniff|Dig|Alert|Dig|Alert|Locomotion
Sniff|Eat|Sniff|Dig|Eat|Dig|Swim
Copyright 2017-2022 Olivier Friard
Behatrix 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 2, or any later version.
Behatrix 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.