WaverideR (version 0.4.1)

add_wavelet_avg: Add a plot of a the average spectral power of a continous wavelet transform

Description

Generates a plot of a the average spectral power of a continous wavelet transform which can be added to a larger composite plot

Usage

add_wavelet_avg(
  wavelet = NULL,
  plot_horizontal = TRUE,
  add_abline_h = NULL,
  add_abline_v = NULL,
  lowerPeriod = NULL,
  upperPeriod = NULL
)

Value

returns a plot of a the average spectral power of a continuous wavelet transform

Arguments

wavelet

wavelet object created using the analyze_wavelet function.

plot_horizontal

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

add_abline_h

Add horizontal lines to the plot. Specify the lines as a vector e.g. c(2,3,5,6) Default=NULL

add_abline_v

Add vertical lines to the plot. Specify the lines as a vector e.g. c(2,3,5,6) Default=NULL

lowerPeriod

Lowest period value which will be plotted

upperPeriod

Highest period value which will be plotted

Author

Code based on the "analyze.wavelet" and "wt.image" functions of the 'WaveletComp' R package and "wt" function of the 'biwavelet' R package which are based on the wavelet MATLAB code written by Christopher Torrence and Gibert P. Compo (1998). The MTM analysis is from the astrochron R package of Meyers et al., (2012)

References

Angi Roesch and Harald Schmidbauer (2018). WaveletComp: Computational Wavelet Analysis. R package version 1.1. https://CRAN.R-project.org/package=WaveletComp

Gouhier TC, Grinsted A, Simko V (2021). R package biwavelet: Conduct Univariate and Bivariate Wavelet Analyses. (Version 0.20.21), https://github.com/tgouhier/biwavelet

Torrence, C., and G. P. Compo. 1998. A Practical Guide to Wavelet Analysis. Bulletin of the American Meteorological Society 79:61-78. https://paos.colorado.edu/research/wavelets/bams_79_01_0061.pdf

Morlet, Jean, Georges Arens, Eliane Fourgeau, and Dominique Glard. "Wave propagation and sampling theory—Part I: Complex signal and scattering in multilayered media. " Geophysics 47, no. 2 (1982): 203-221.

J. Morlet, G. Arens, E. Fourgeau, D. Giard; Wave propagation and sampling theory; Part II, Sampling theory and complex waves. Geophysics 1982 47 (2): 222–236.

Examples

# \donttest{
#generate a plot for the magnetic susceptibility data set of Pas et al., (2018)

plot.new()
layout.matrix <- matrix(c(rep(0, 2), 1, 0,0,seq(2, 6, by = 1)),
                       nrow = 2,
                      ncol = 5 ,
                       byrow = TRUE)
graphics::layout(mat = layout.matrix,
                heights = c(0.25, 1),
                # Heights of the two rows
                widths = c(rep(c(1, 2, 4,2,2), 2)))

par(mar = c(0, 0.5, 1, 0.5))


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

add_wavelet_avg(
 wavelet = mag_wt,
 plot_horizontal = TRUE,
 add_abline_h = NULL,
 add_abline_v = NULL,
 lowerPeriod = 0.15,
 upperPeriod = 80
)


par(mar = c(4, 4, 0, 0.5))


plot(
 x = c(0, 1),
 y = c(max(mag[, 1]), min(mag[, 1])),
 col = "white",
 xlab = "",
 ylab = "Time (Ma)",
 xaxt = "n",
 xaxs = "i",
 yaxs = "i",
 ylim = rev(c(max(mag[, 1]), min(mag[, 1])))
)            # Draw empty plot


polygon(
 x = c(0, 1, 1, 0),
 y = c(max(mag[, 1]), max(mag[, 1]), min(mag[, 1]), min(mag[, 1])),
 col = geo_col("Famennian")
)

text(
 0.5,
 (max(mag[, 1]) - min(mag[, 1])) / 2,
 "Fammenian",
 cex = 1,
 col = "black",
 srt = 90
)
par(mar = c(4, 0.5, 0, 0.5))


plot(
 mag[, 2],
 mag[, 1],
 type = "l",
 ylim = rev(c(max(mag[, 1]), min(mag[, 1]))),
 yaxs = "i",
 yaxt = "n",
 xlab = "Mag. suc.",
 ylab = ""
)

add_wavelet(
 wavelet = mag_wt,
 lowerPeriod = 0.15,
 upperPeriod = 80,
 lower_depth_time = NULL,
 upper_depth_time = NULL,
 n.levels = 100,
 plot.COI = TRUE,
 color_brewer = "grDevices",
 palette_name = "rainbow",
 plot_dir = FALSE,
 add_lines = NULL,
 add_points = NULL,
 add_abline_h = NULL,
 add_abline_v = NULL,
 plot_horizontal = TRUE,
 period_ticks = 1,
 periodlab = "period (m)",
 main = NULL,
 yaxt = "n",
 xaxt = "s",
 depth_time_lab = ""
)

lines(log2(mag_track_solution[,2]),mag_track_solution[,1],lwd=4,lty=4)

mag_405 <- extract_signal(
 tracked_cycle_curve = mag_track_solution,
 wavelet = mag_wt,
 period_up = 1.2,
 period_down = 0.8,
 add_mean = TRUE,
 tracked_cycle_period = 405,
 extract_cycle = 405,
 tune = FALSE,
 plot_residual = FALSE
)

plot(mag_405[,2],mag_405[,1],type="l",
    yaxt="n", yaxs = "i",
    xlab="405-kyr ecc")


mag_110 <- extract_signal(
 tracked_cycle_curve = mag_track_solution,
 wavelet = mag_wt,
 period_up = 1.25,
 period_down = 0.75,
 add_mean = TRUE,
 tracked_cycle_period = 405,
 extract_cycle = 110,
 tune = FALSE,
 plot_residual = FALSE
)

mag_110_hil <- Hilbert_transform(mag_110,demean=FALSE)

plot(mag_110[,2],mag_110[,1],type="l",
    yaxt="n", yaxs = "i",
    xlab="110-kyr ecc")

lines(mag_110_hil[,2],mag_110_hil[,1])
# }