This R-package contains various functions to clean, visualize and analyze the dynamics of circadian parameters from time series of several types of data. The types of data and formats supported in the package include: 1) temperature, humidity, and light from the HOBO sensors (U12-012); 2) barometric pressure, wind speed and direction from the HOBO Micro weather station (H21-USB); 3) colony weight from the Brushy Mountain Hive Scales (714 – Hive Scale); 4) locomotor activity from all DAM and LAM series of Activity Monitors from Trikinetics (http://trikinetics.com/) and; 4) time stamp annotated events from videos of the hive entrance. The unique feature of this package compared to existing tools, is the ability to quantify the dynamics of circadian parameters over time rather than assuming static rhythms. In general, this package estimates the period, amplitude, phase and rhythm strength of a sliding window from the time series inputted using 3 different methods that are well establish in the circadian field (references). In addition, functions to upload and fix common issues such as date, temporal formats, gaps and changes in sampling rate from each of these types of files are also included in the package.
Credits: Jonathan Aleman Rios, Jose L. Agosto-Rivera, Rémi Mégret, Tugrul Giray, Edgar Acuña.
License: BSD
Download: CircadianDynamics_scripts