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.
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biological-data-analysisdata-structuresethomics
6.20 score 8 stars 7 dependents 95 scripts 453 downloadszeitgebr - 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.
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5.37 score 14 stars 1 dependents 56 scripts 293 downloadsggetho - 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/>.
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biological-data-analysisggplot2visualization
5.25 score 11 stars 1 dependents 108 scripts 326 downloadsdamr - 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.
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biological-data-analysisparsing
5.13 score 7 stars 1 dependents 43 scripts 529 downloadssleepr - 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.
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biological-data-analysisneuroscience
4.42 score 6 stars 87 scripts 332 downloadsscopr - 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/>.
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biological-data-analysisparsing
4.23 score 3 stars 56 scripts 315 downloads