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Create and plot the wavelet power spectrum

Source: R/2_create_wavelet.R
create_wavelet.Rd

create_wavelet creates the a wavelet spectrum using WaveletComp package. Optionally loads and plots an existing my.w object.

Usage

create_wavelet(
  archive,
  tag_ID,
  wv_period_hours = 24,
  sampling_frequency = NULL,
  load_existing_wavelet = FALSE,
  suboctaves = 12,
  lower_period_mins = 5,
  upper_period_hours = 24,
  pval = FALSE,
  output = FALSE,
  output_folder = NULL,
  verbose = FALSE,
  plot_wavelet = TRUE,
  max_period_ticks = 10,
  plot_width = 800,
  plot_height = 400,
  interactive_mode = TRUE
)

Arguments

archive

Data frame containing processed time series depth data

tag_ID

Unique tag identification number in a vector of characters. E.g. "123456"

wv_period_hours

Time resolution in hours to calculate wavelet. Currently only supports the default of 24 hours as this package is created to investigate daily diving behaviour. Defaults to 24.

sampling_frequency

Sampling frequency of depth data in seconds. Defaults to time between first and second depth record. Recommended to leave blank.

load_existing_wavelet

Load an existing my.w wavelet object from the output_folder. Defaults to FALSE.

suboctaves

number of suboctaves between each logarithmic period. E.g. between 24 and 12 hours. Highly recommended to use 12, for easy of interpretation of hours and signal present (daily, diel, tidal).

lower_period_mins

Lower period of the wavelet sampling in minutes. Cannot be less than sampling frequency. Defaults to 5 minutes.

upper_period_hours

Upper period of the wavelet sampling in days. Defaults to 24 hours.

pval

Produce p-values or not. True or False. Default set to FALSE, see WaveletComp::analyze.wavelet() for further details. P-values not used in further analysis, and increase computation time and file size.

output

Logical. If TRUE, output is saved to output_folder. Defaults to FALSE.

output_folder

Output folder path. If output = TRUE, output_folder must be provided. Defaults to NULL.

verbose

Logical. If TRUE, progress messages are shown. Defaults to FALSE.

plot_wavelet

TRUE or FALSE. Plot the wavelet spectrum and mean power?

max_period_ticks

Number of ticks displayed on the period (y) axis in plots.

plot_width

Width of the wavelet spectrum plot output. Defaults to 800.

plot_height

Height of the wavelet spectrum plot output. Defaults to 400.

interactive_mode

Used for testing the package only. Defaults to TRUE.

Value

When output = TRUE, returns an object of class "analyze.wavelet" from package 'WaveletComp'. Additionally outputs a plot of the wavelet spectrum, and a plot of the mean power per period.

Details

Uses WaveletComp::analyze.wavelet() to create a univariate wavelet power spectrum for the depth data imported, see WaveletComp::analyze.wavelet() for more details. Plots mean wavelet power using WaveletComp::wt.avg(). If you have errors allocating large vectors try using library(bigmemory) and create a big matrix with big_mat <- big.matrix(nrow = 1e7, ncol = 10, type = "double") then run your code again. This allows greater range between lower and upper periods

Examples

# Set file path
filepath <- system.file("extdata", package = "FishDiveR")

# Load archive_days
archive_days <- readRDS(file.path(filepath, "data/archive_days.rds"))

# Run create_wavelet function
my.w <- create_wavelet(
  archive = archive_days,
  tag_ID = "data",
  wv_period_hours = 24,
  sampling_frequency = NULL,
  load_existing_wavelet = FALSE,
  suboctaves = 12,
  lower_period_mins = 30,
  upper_period_hours = 24,
  pval = FALSE,
  output = TRUE,
  output_folder = tempdir(),
  verbose = TRUE,
  plot_wavelet = FALSE,
  max_period_ticks = 10,
  plot_width = 800,
  plot_height = 400,
  interactive_mode = FALSE
)
#> 
#> Analysing tag ID data
#> 
#> Creating new wavelet.
#> Starting wavelet transformation...
#> Class attributes are accessible through following names:
#> series loess.span dt dj Wave Phase Ampl Power Power.avg Power.pval Power.avg.pval Ridge Period Scale nc nr coi.1 coi.2 axis.1 axis.2 date.format date.tz 
#> 
#> Wavelet saved to /tmp/RtmpTKWEE7/data/1_Wavelets/data_wavelet.rds