Abstract
Behavioural studies provide insights into normal and disrupted biological mechanisms. In many research areas, a growing spectrum of animal models—particularly small organisms—is used for high-throughput studies with infrared-based activity monitors, generating counts per time data. The freely available software to analyse such data, however, are primarily optimized for drosophila and circadian analysis. Researchers investigating other species or non-circadian behaviour would thus benefit from a more versatile software. Here we report the development of a free and open-source software—Rtivity—allowing customisation of species-specific parameters, and offering a versatile analysis of behavioural patterns, biological rhythms, stimulus responses, and survival. Rtivity is based on the R language and uses Shiny and the recently developed Rethomics package for a user-friendly graphical interface without requiring coding skills. Rtivity automatically assesses survival, computes various activity, sleep, and rhythmicity parameters, and performs fractal analysis of activity fluctuations. Rtivity generates multiple informative graphs, and exports structured data for efficient interoperability with common statistical software. In summary, Rtivity facilitates and enhances the versatility of the behavioural analysis of diverse animal species (e.g. drosophila, zebrafish, daphnia, ants). It is thus suitable for a broad range of researchers from multidisciplinary fields such as ecology, neurobiology, toxicology, and pharmacology.
Highlights
Behavioural studies provide insights into normal and disrupted biological mechanisms
The Drosophila Activity Monitor (DAM) and the Locomotor Activity Monitor (LAM) are IR-based activity monitors developed by Trikinetics (TriKinetics, Waltham, MA), which automatically count the number of IR beam crossings by small organisms
Rtivity uses data obtained from infrared activity monitors, or from other sources where activity is expressed in a counts per time format
Summary
The Rtivity (R + acTIVITY) software is based on the R programming language[17], using Shiny and the recently published Rethomics packages[18,19]. We detail the major advantages of Rtivity, namely: (1) Data pre-processing to check file format and missing values, allowing their imputation; (2) the customization of activity and sleep parameters to different species, and survival analysis; (3) the analysis of diverse biological rhythms and transient responses; and (4) the integrated analysis of multiple experiments and software interoperability. Previous software defined 5 min as the minimum period of time to consider that an animal is a sleep[15,16] This definition suits drosophila[32], different species have diverse sleep. Rtivity allows users to adjust the minimum inactivity period required to consider that an animal is asleep (Fig. 2Bi) This allows species-specific evaluation of sleep-related parameters: sleep ratio, duration of sleep bouts (uninterrupted periods of sleep; Fig. 2Bii), sleep latency, total sleep time, and wake after sleep onset (Table 1). Researchers may be interested in the time of death, or in the behavioural
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