README.md

In edpclau/circadian-dynamics: Period and Rythm Analysis of Timeseries Data

circadian-dynamics

A repository for analyzing circadian data

1. To install in R use:

devtools::install_github("edpclau/circadian-dynamics")

2. Example script for TriKinetics monitors

a) Import Trikinetics data into R (opens a GUI)

monitor <- read_trikinetics()

b) Change bin size (in this case its a 1hr bin)

monitor_downsampled <- downsample_time_series(monitor[-2], amount = 1, units = "hour", method = "sum")

c) Set window size, steps and data filtering options

monitor_processed <- multivariate_process_timeseries(
  df = monitor_downsampled,
  sampling_rate = '1 hour',
  window_size_in_days =3,
  window_step_in_days = 1, 
  detrend_data = TRUE,
  butterworth = TRUE,
  f_low=1/4,
  f_high=0,
  plot = TRUE
  )

d) Data analysis and period determination steps

monitor_analysis <- multivariate_rythm_analysis(
  monitor_processed,
  sampling_rate = "1 hour",
  alpha=0.000000001,
  autocorrelation = TRUE,
  lomb_scargle = TRUE,
    from = 16, to = 32,
  ofac =60)

e) Export data and figures

export_all(raw_data = monitor_downsampled,
           processed_data = monitor_processed,
           rythm_analysis_data = monitor_analysis,
         autocorrelation = TRUE,
           new_dir_name = "Monitor_40")

edpclau/circadian-dynamics documentation built on March 18, 2023, 10:22 p.m.