| add_wavelet {WaverideR} | R Documentation |
Add a wavelet plot
Description
Generates a plot of a wavelet scalogram which can be integrated into a larger composite plot
Usage
add_wavelet(
wavelet = NULL,
lowerPeriod = NULL,
upperPeriod = NULL,
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 = "s",
xaxt = "s",
depth_time_lab = "depth (m)"
)
Arguments
wavelet |
wavelet object created using the |
lowerPeriod |
Lowest period value which will be plotted |
upperPeriod |
Highest period value which will be plotted |
lower_depth_time |
lowest depth/time value which will be plotted |
upper_depth_time |
Highest depth/time value which will be plotted |
n.levels |
Number of color levels |
plot.COI |
Option to plot the cone of influence |
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. " |
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 |
plot_dir |
The direction of the proxy record which is assumed for tuning if time increases with increasing depth/time values
(e.g. bore hole data which gets older with increasing depth ) then plot_dir should be set to TRUE
if time decreases with depth/time values (eg stratospheric logs where 0m is the bottom of the section)
then plot_dir should be set to FALSE |
add_lines |
Add lines to the wavelet plot input should be matrix with first axis being depth/time the columns after that
should be period values |
add_points |
Add points to the wavelet plot input should be matrix with first axis being depth/time and columns after that
should be period values |
add_abline_h |
Add horizontal lines to the plot. Specify the lines as a vector e.g. c(2,3,5,6) |
add_abline_v |
Add vertical lines to the plot. Specify the lines as a vector e.g. c(2,3,5,6) |
plot_horizontal |
plot the wavelet horizontal or vertical eg y axis is depth or y axis power |
period_ticks |
tick mark spacing 1 is all tickmarks and higher value removes tick marks by the fraction of the tick mark spacing value, the opposite is true for value lower than 1 which will add aditional tickmarks |
periodlab |
lable for the the period column |
main |
main title |
yaxt |
turn on of off the yaxis "s" is on "n" is off |
xaxt |
turn on of off the xaxis "s" is on "n" is off |
depth_time_lab |
lable for the the depth/time column |
Value
returns a plot of a wavelet scalogram
Author(s)
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. https://pubs.geoscienceworld.org/geophysics/article/47/2/203/68601/Wave-propagation-and-sampling-theory-Part-I
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. https://pubs.geoscienceworld.org/geophysics/article/47/2/222/68604/Wave-propagation-and-sampling-theory-Part-II
Examples
#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])