TimeTraits: extracting functional traits from biological time-series in R.

MOTIVATION: It is currently challenging for scientists to extract meaningful parameters from circadian rhythms that dynamically change over time (i.e. non-stationary rhythms). Circadian rhythms may be non-stationary due to dynamic conditions, such as changes in photoperiod. Circadian rhythms are also nonstationary when plants are suddenly placed under continuous light conditions after a period of entrainment, as their clocks slowly drift without external entrainment signals. RESULTS: TimeTraits provides a series of functions to enable the extraction of parameters from time series data using Functional Data Analysis methods. We demonstrate its utility in dissecting the changes in curve shape of a circadian clock bioluminescence marker, following a photoperiod shift in wildtype and phyB Arabidopsis. AVAILABILITY AND IMPLEMENTATION: TimeTraits is available in CRAN: https://cran.r-project.org/web/packages/TimeTraits.