WaverideR (version 0.4.1)

dynamic_extraction: Extract a signal in between tracked boundaries in a wavelet scalogram

Description

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 = "rainbow",
  color_brewer = "grDevices",
  plot_horizontal = TRUE,
  smooth = FALSE,
  add_mean = TRUE
)

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

Arguments

wavelet

Wavelet object created using the analyze_wavelet function.

n.levels

Number of color levels Default=100.

add_peaks

Setting which indicates whether spectral peaks should be added to the tracking plot Default=FALSE.

periodlab

label for the y-axis Default="Period (metres)".

x_lab

label for the x-axis Default="depth (metres)".

palette_name

Name of the color palette which is used for plotting. The color palettes than can be chosen depends on which the R package is specified in the color_brewer parameter. The included R packages from which palettes can be chosen from are; the 'RColorBrewer', 'grDevices', 'ColorRamps' and 'Viridis' R packages. There are many options to choose from so please read the documentation of these packages Default=rainbow. The R package 'viridis' has the color palette options: “magma”, “plasma”, “inferno”, “viridis”, “mako”, and “rocket” and “turbo” To see the color palette options of the The R pacakge 'RColorBrewer' run the RColorBrewer::brewer.pal.info() function The R package 'colorRamps' has the color palette options:"blue2green", "blue2green2red", "blue2red", "blue2yellow", "colorRamps", "cyan2yellow", "green2red", "magenta2green", "matlab.like", "matlab.like2" and "ygobb" The R package 'grDevices' has the built in palette options:"rainbow", "heat.colors", "terrain.colors","topo.colors" and "cm.colors" To see even more color palette options of the The R pacakge 'grDevices' run the grDevices::hcl.pals() function

color_brewer

Name of the R package from which the color palette is chosen from. The included R packages from which palettes can be chosen are; the RColorBrewer, grDevices, ColorRamps and Viridis R packages. There are many options to choose from so please read the documentation of these packages. "Default=grDevices

plot_horizontal

plot the wavelet horizontal or vertical eg y axis is depth or y axis power Default=TRUE

smooth

smooth the tracked period using the "loess_auto" function

add_mean

add the mean to the extracted signal

Author

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

References

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

Examples

if (FALSE) {
#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 <- analyze_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
)
}