behavr - Canonical Data Structure for Behavioural Data

Implements an S3 class based on 'data.table' to store and process efficiently ethomics (high-throughput behavioural) data.

Last updated 4 years ago

biological-data-analysisdata-structuresethomics

5.84 score 6 stars 6 dependents 64 scripts 675 downloads

zeitgebr - Analysis of Circadian Behaviours

Use behavioural variables to compute period, rhythmicity and other circadian parameters. Methods include computation of chi square periodograms (Sokolove and Bushell (1978) <DOI:10.1016/0022-5193(78)90022-X>), Lomb-Scargle periodograms (Lomb (1976) <DOI:10.1007/BF00648343>, Scargle (1982) <DOI:10.1086/160554>, Ruf (1999) <DOI:10.1076/brhm.30.2.178.1422>), and autocorrelation-based periodograms.

Last updated 11 months ago

5.15 score 11 stars 1 dependents 43 scripts 524 downloads

ggetho - Visualisation of High-Throughput Behavioural (i.e. Ethomics) Data

Extension of 'ggplot2' providing layers, scales and preprocessing functions useful to represent behavioural variables that are recorded over multiple animals and days. This package is part of the 'rethomics' framework <https://rethomics.github.io/>.

Last updated 2 years ago

biological-data-analysisggplot2visualization

4.98 score 9 stars 1 dependents 71 scripts 697 downloads

damr - Interface to Drosophila Activity Monitor System Result Files

Loads behavioural data from the widely used Drosophila Activity Monitor System (DAMS, TriKinetics <https://trikinetics.com/>) into the rethomics framework.

Last updated 11 months ago

biological-data-analysisparsing

4.92 score 6 stars 1 dependents 31 scripts 496 downloads

sleepr - Analyse Activity and Sleep Behaviour

Use behavioural variables to score activity and infer sleep from bouts of immobility. It is primarily designed to score sleep in fruit flies from Drosophila Activity Monitor (TriKinetics) and Ethoscope data. It implements sleep scoring using the "five-minute rule" (Hendricks et al. (2000) <DOI:10.1016/S0896-6273(00)80877-6>), activity classification for Ethoscopes (Geissmann et al. (2017) <DOI:10.1371/journal.pbio.2003026>) and a new algorithm to detect when animals are dead.

Last updated 3 years ago

biological-data-analysisneuroscience

4.27 score 6 stars 62 scripts 308 downloads

scopr - Read Ethoscope Data

Handling of behavioural data from the Ethoscope platform (Geissmann, Garcia Rodriguez, Beckwith, French, Jamasb and Gilestro (2017) <DOI:10.1371/journal.pbio.2003026>). Ethoscopes (<http://gilestrolab.github.io/ethoscope/>) are an open source/open hardware framework made of interconnected raspberry pis (<https://www.raspberrypi.org>) designed to quantify the behaviour of multiple small animals in a distributed and real-time fashion. The default tracking algorithm records primary variables such as xy coordinates, dimensions and speed. This package is part of the rethomics framework <http://rethomics.github.io/>.

Last updated 3 years ago

biological-data-analysisparsing

3.18 score 3 stars 370 downloads