# Analyzing Animal's Rhythmicity

## Documentation for package ‘digiRhythm’ version 2.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

actogram | Plot a an single actogram over a period of time for a specific variable
daily_activity_wrap_plot | Plot daily average over a period of time for a specific variable.
daily_average_activity | Plot daily average over a period of time for a specific variable.
df516b_2 | df516b_2 Activity Data Sets
df603 | df603 Activity Data Sets
df625 | df625 Activity Data Sets
df678_2 | df678_2 Activity Data Sets
df689b_3 | df689b_3 Activity Data Sets
df691b_1 | df691b_1 Activity Data Sets
df759a_3 | df759a_3 Activity Data Sets
dfc | Computes the Degree of Function coupling (DFC), Harmonic Part (HP) and Weekly Lomb-Scargle Spectrum (LSP Spec) for one variable in an activity dataset. The dataset should be digiRhythm friendly.
df_act_info | Outputs some information about the activity dataframe
dgm_periodicity | Returns the periodicity of a digiRhythm dataframe
diurnality | Computes the diurnality index based on an activity dataframe
diurnality_customTimes | Computes the diurnality index, using different start and end definitions for each day and night, based on an activity dataframe

highest_possible_harm_cutoff

Function to calculate the smallest possible harmonic to consider given a sampling frequency. The minimum possible harmonic = 2 x the period of the maximum frequency according to the Shanon theorem. Example: if the sampling period is 15 min, the minimum possible treatable period is 30 minutes and that corresponds to the 48th harmonic (24 hours * 60 minutes / 48 = 30 minutes)

import_raw_activity_data | Reads Raw Activity Data from csv files
is_dgm_friendly | Informs if a dataset is digiRhythm Friendly
levopt | Returns the level given the p-value computed with pbaluev (2008). Copied from the LOMB library.

lomb_scargle_periodogram

Computes the Lomb Scargle Periodogram and returns the information needed for computing the DFC and HP. A plot visualizing the Harmonic Frequencies presence in the spectrum is possible. The function is inspired from the Lomb library in a great part, with modifications to fit the requirements of harmonic powers and computation of the DFC. This function is inspired by the lsp function from the lomb package and adapted to add different colors for harmonic and non harmonic frequencies in the signal. For more information about lomb::lsp, please refer to: https://cran.r-project.org/web/packages/lomb/

pbaluev | Returns p-value of a frequency peak according to pbaluev (2008) given Z, fmax and tm. Reused from the LOMB library (https://rdrr.io/cran/lomb/)
print_v | Print if Verbose is true
remove_activity_outliers | Remove outliers from the data
resample_dgm | Change the sampling of a digiRhythm friendly dataset
timedata | timedata Dataset of start and end of day and night