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Plot sedimentation modelling results

Source: R/plot_sed_model.R
plot_sed_model.Rd

The plot_sed_model function is used plot/re-plot the results from the flmw and sum_power_sedrate functions

Usage

plot_sed_model(
  model_results = NULL,
  plot_res = 1,
  x_lab = "depth (m)",
  y_lab = "sed rate cm/kyr",
  keep_editable = FALSE,
  palette_name = "viridis",
  color_brewer = "viridis",
  colour_brewer = NULL
)

Arguments

model_results

Sedimentation-rate modelling result to plot: the list returned by flmw or by sum_power_sedrate (a list of depth x sedimentation-rate matrices plus depth and y_axis). Required (Default=NULL gives an error).

plot_res

Which matrix of model_results is plotted (integer index of the list element, or its name). For flmw with method = "classic":

  • 1: slope coefficient, 2: r squared, 3: number of components, 4: difference to origin;

  • 5: slope coefficient percentile, 6: r squared percentile, 7: number of components percentile, 8: difference to origin percentile;

  • 11 (or "score_mat"): the combined score.

For flmw with method = "weighted" or "template": 1 (the score matrix). For sum_power_sedrate: 1, sum of the maximum spectral power; 2, number of components (cycles). Default=1.

x_lab

Label of the depth axis (character). Default="depth (m)".

y_lab

Label of the sedimentation-rate axis (character). Default="sed rate cm/kyr".

keep_editable

Keep the plot layout and graphical parameters (par) after plotting, so that extra elements can be added to the image (logical). With FALSE the previous par settings are restored on exit. Default=FALSE.

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".

colour_brewer

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

Value

Returns a plot of sedimentation rates vs depth and a value which was generated using the flmw or sum_power_sedrate functions

Examples

# \donttest{
#estimate sedimentation rate for the the magnetic susceptibility record
# of the Sullivan core of Pas et al., (2018).

mag_wt <- analyse_wavelet(data = mag[1:200, ],
dj = 1/10,
lowerPeriod = 0.1,
upperPeriod = 32,
verbose = FALSE,
omega_nr = 10)

#increase n_simulations to better define the red noise spectral power curve
mag_wt_red_noise <- model_red_noise_wt(wavelet=mag_wt,
n_simulations = 3, # increase for a better constrained result
run_multicore=FALSE,
verbose=FALSE)

sedrates <- sum_power_sedrate(red_noise=mag_wt_red_noise,
wavelet=mag_wt,
percentile=0.75,
sedrate_low = 0.5,
sedrate_high = 4,
spacing = 1,
cycles = c(2376,1600,1180,696,406,110),
x_lab="depth",
y_lab="sedrate",
run_multicore=FALSE,
genplot = FALSE,
palette_name = "rainbow",
color_brewer= "grDevices",
verbose=FALSE)

plot_sed_model(model_results=sedrates,
plot_res=1,
x_lab = "depth (m)",
y_lab = "sed rate cm/kyr",
keep_editable=FALSE,
palette_name = "rainbow",
color_brewer= "grDevices")

# }