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Extract a signal in between tracked boundaries in a wavelet scalogram

Source: R/dynamic_extraction.R
dynamic_extraction.Rd

Interactively select points in a wavelet scalogram to trace the upper and lower period of an cycle. The dynamic_extraction function plots a wavelet scalogram in which points peaks can selected allowing one to track the lower and upper period of a cycle. First track the upper or lower period of the to be extracted cycle and then track the other boundary. Tracking points can be selected in the Interactive interface and will be shown as white dots connected by a black line. When one wants to deselect a point the white dots can be re-clicked/re-selected and will turn red which indicates that the previously selected point is deselected. Deselecting points can be quite tricky. After tracking the lower and upper boundaries of the cycle the dynamic_extraction function will extract the signal in between the boundaries. the output can then used as input for the minimal_tuning function to create an age model.

Usage

dynamic_extraction(
  wavelet = NULL,
  n.levels = 100,
  add_peaks = FALSE,
  periodlab = "Period (metres)",
  x_lab = "depth (metres)",
  palette_name = "viridis",
  color_brewer = "viridis",
  plot_horizontal = TRUE,
  smooth = FALSE,
  add_mean = TRUE,
  colour_brewer = NULL
)

Arguments

wavelet

Wavelet object (list) created with analyse_wavelet; its scalogram is plotted for the tracking and its reconstructed components are summed between the tracked boundaries. Required (Default=NULL).

n.levels

Number of colour levels of the power scale (integer, > 1); the levels are quantiles of the power. Default=100.

add_peaks

Add the spectral peaks (local power maxima along the period axis of each column of the scalogram) as points to the tracking plot, to help the tracking (logical, TRUE or FALSE). Default=FALSE.

periodlab

Label of the period axis (character). Default="Period (metres)".

x_lab

Label of the depth/time axis (character). Default="depth (metres)".

palette_name

Name of the colour palette of the power (colour) scale, a character string. Which names are valid depends on color_brewer:

  • color_brewer = "grDevices": "rainbow", "heat.colors", "terrain.colors", "topo.colors", "cm.colors", or any of the 115 hcl.colors palettes (list them with grDevices::hcl.pals()), for example "viridis", "Plasma", "Inferno", "YlOrRd", "Spectral", "Blue-Red", "Zissou 1".

  • color_brewer = "viridis": "viridis", "magma", "inferno", "plasma", "cividis", "rocket", "mako", "turbo".

  • color_brewer = "RColorBrewer": "BrBG", "PiYG", "PRGn", "PuOr", "RdBu", "RdGy", "RdYlBu", "RdYlGn", "Spectral", "Accent", "Dark2", "Paired", "Pastel1", "Pastel2", "Set1", "Set2", "Set3", "Blues", "BuGn", "BuPu", "GnBu", "Greens", "Greys", "Oranges", "OrRd", "PuBu", "PuBuGn", "PuRd", "Purples", "RdPu", "Reds", "YlGn", "YlGnBu", "YlOrBr", "YlOrRd" (also listed by wr_brewer_palettes()).

  • color_brewer = "colorRamps": "blue2green", "blue2green2red", "blue2red", "blue2yellow", "cyan2yellow", "green2red", "magenta2green", "matlab.like", "matlab.like2", "ygobb".

  • color_brewer = "scico" (all except "batlowK" need the scico package): "acton", "bam", "bamako", "bamO", "batlow", "batlowK", "batlowW", "berlin", "bilbao", "broc", "brocO", "buda", "bukavu", "cork", "corkO", "davos", "devon", "fes", "glasgow", "grayC", "hawaii", "imola", "lajolla", "lapaz", "lipari", "lisbon", "managua", "navia", "nuuk", "oleron", "oslo", "roma", "romaO", "tofino", "tokyo", "turku", "vanimo", "vik", "vikO".

Low power is drawn with the first colour of the palette and high power with the last. Default="viridis".

color_brewer

Palette family from which palette_name is taken, a character string: "grDevices", "viridis", "RColorBrewer", "colorRamps" or "scico" (the last one, except for "batlowK", needs the scico package). See palette_name for the palette names of each family. Default="viridis".

plot_horizontal

Orientation of the tracking plot (logical): TRUE draws depth/time on the x-axis and period on the y-axis, FALSE draws period on the x-axis and depth/time on the y-axis. Default=TRUE.

smooth

Smooth each of the two tracked boundaries with loess_auto after interpolating them to the depth/time grid of the wavelet (logical, TRUE or FALSE). Default=FALSE.

add_mean

Add the mean of the original data series to the extracted signal (logical, TRUE or FALSE); FALSE returns the signal centred on zero. Default=TRUE.

colour_brewer

British spelling of color_brewer, with the same options; if given (not NULL) it overrides color_brewer. Default=NULL.

Value

Results of the tracking of a cycle in the wavelet spectra is a matrix with 3 columns. The first column is depth/time The second column is the extracted tracked cycle The third column is upper tracked period The fourth column is lower tracked period

References

Routines for astrochronologic testing, astronomical time scale construction, and time series analysis <doi:10.1016/j.earscirev.2018.11.015>

Author

The function is based/inspired on the traceFreq function of the 'astrochron' R package

Examples

if (FALSE) { # \dontrun{
#Track the 405kyr upper and lower periods of the eccentricity cycle in the
#magnetic susceptibility record of the Sullivan core of Pas et al., (2018)

mag_wt <- analyse_wavelet(
 data = mag,
 dj = 1 / 100,
 lowerPeriod = 0.1,
 upperPeriod = 254,
 verbose = FALSE,
 omega_nr = 10
)

mag_ext <- dynamic_extraction(
 wavelet = mag_wt,
 n.levels = 100,
 add_peaks = FALSE,
 periodlab = "Period (metres)",
 x_lab = "depth (metres)",
 palette_name = "rainbow",
 color_brewer = "grDevices",
 plot_horizontal = TRUE,
 smooth = TRUE,
 add_mean = TRUE
)
} # }