Analyse Biological Time-Series Data
Computes, tabulates and plots day-time and night-time onset of sleep b...
Generate actograms
Periodogram analysis for activity data
Periodogram analysis for sleep data
Generate actograms for sleep data (Somnograms)
Compute anticipation for activity data
Bin activity data to desired intervals
Objectively quantify and visualise phases and calculate consolidation ...
Plot actogram of individual fly
Periodogram plot for activity data of individual flies
Periodogram plot for sleep data of individual flies
Generate actograms for sleep data (Somnograms) for individual flies
Phase identifier for activity data
Compute and plot activity profiles
Compute and plot sleep profiles
Generate rose plots for averaged activity data
Generate rose plots for averaged sleep data
Equivalent of binData() but for sleep data
Plot sleep stages in individual flies
Computes and tabulates day-time and night-time sleep statistics
Plot and generate data for transition frequencies between sleep stages
Trim data for downstream analyses
Compiles functions to trim, bin, visualise, and analyse activity/sleep time-series data collected from the Drosophila Activity Monitor (DAM) system (Trikinetics, USA). The following methods were used to compute periodograms - Chi-square periodogram: Sokolove and Bushell (1978) <doi:10.1016/0022-5193(78)90022-X>, Lomb-Scargle periodogram: Lomb (1976) <doi:10.1007/BF00648343>, Scargle (1982) <doi:10.1086/160554> and Ruf (1999) <doi:10.1076/brhm.30.2.178.1422>, and Autocorrelation: Eijzenbach et al. (1986) <doi:10.1111/j.1440-1681.1986.tb00943.x>. Identification of activity peaks is done after using a Savitzky-Golay filter (Savitzky and Golay (1964) <doi:10.1021/ac60214a047>) to smooth raw activity data. Three methods to estimate anticipation of activity are used based on the following papers - Slope method: Fernandez et al. (2020) <doi:10.1016/j.cub.2020.04.025>, Harrisingh method: Harrisingh et al. (2007) <doi:10.1523/JNEUROSCI.3680-07.2007>, and Stoleru method: Stoleru et al. (2004) <doi:10.1038/nature02926>. Rose plots and circular analysis are based on methods from - Batschelet (1981) <ISBN:0120810506> and Zar (2010) <ISBN:0321656865>.