find_peaks: Find peaks in a periodogram

In zeitgebr: Analysis of Circadian Behaviours

Description

This function locates the peaks in a pregenerated periodogram. Detection is based on pracma::findpeaks. Only the significant (i.e. power > signif_threshold) peaks are extracted.

Usage

find_peaks(data, n_peaks = 3)

Arguments

data	behavr::behavr table representing a periodogram, as returned by periodogram
n_peaks	maximal numbers of peak to be detected

Value

behavr::behavr table that is data with an extra column peak. peak is filled with zeros except for rows match a peak. In which case, rows have an integer value corresponding to the rank of the peak (e.g. 1 for the first peak).

References

• zeitgebr tutorial – the relevant rehtomics tutorial

See Also

• periodogram – to generate a periodogram in a first place

• ggetho::geom_peak – a layer to show peaks on a periodogram

Examples

data(dams_sample)
# only four ndividuals for the sake of the example
dt <- dams_sample[xmv(region_id) %in% c(1, 7, 21, 31)]
per_dt_xs <- periodogram(activity, dt, FUN = chi_sq_periodogram)
per_dt_xs_with_peaks <- find_peaks(per_dt_xs)
per_dt_xs_with_peaks[peak == 1]

Example output

Loading required package: behavr
Loading required package: data.table

 ==== METADATA ====

                                       id file_info region_id
                                   <fctr>    <list>     <int>
1: 2017-01-16 08:00:00|dams_sample.txt|01 <list[2]>         1
2: 2017-01-16 08:00:00|dams_sample.txt|07 <list[2]>         7
3: 2017-01-16 08:00:00|dams_sample.txt|21 <list[2]>        21
4: 2017-01-16 08:00:00|dams_sample.txt|31 <list[2]>        31
                         experiment_id      start_datetime       stop_datetime
                                <char>              <POSc>              <fctr>
1: 2017-01-16 08:00:00|dams_sample.txt 2017-01-16 08:00:00 2017-01-26 00:09:00
2: 2017-01-16 08:00:00|dams_sample.txt 2017-01-16 08:00:00 2017-01-26 00:09:00
3: 2017-01-16 08:00:00|dams_sample.txt 2017-01-16 08:00:00 2017-01-26 00:09:00
4: 2017-01-16 08:00:00|dams_sample.txt 2017-01-16 08:00:00 2017-01-26 00:09:00
   period_group
         <fctr>
1:         long
2:         long
3:        short
4:           wt

 ====== DATA ======

                                       id period    power signif_threshold
                                   <fctr>  <num>    <num>            <num>
1: 2017-01-16 08:00:00|dams_sample.txt|01  99720 276.4555         177.4971
2: 2017-01-16 08:00:00|dams_sample.txt|07  98640 200.8368         176.2397
3: 2017-01-16 08:00:00|dams_sample.txt|21  68040 170.8709         132.6670
4: 2017-01-16 08:00:00|dams_sample.txt|31  86040 294.5654         158.5068
        p_value  peak
          <num> <int>
1: 4.100760e-16     1
2: 2.809713e-07     1
3: 2.936584e-09     1
4: 4.913109e-22     1

zeitgebr documentation built on April 25, 2020, 5:07 p.m.