plot_Scatterplots: Display Scatter Plot Matrix of the Bayesian Age Results

In BayLum: Chronological Bayesian Models Integrating Optically Stimulated Luminescence and Radiocarbon Age Dating

Display Scatter Plot Matrix of the Bayesian Age Results

Description

Create a hexbin plot matrix (hexbin::hexplom) of age results returned by the Bayesian age calculation.

Usage

plot_Scatterplots(
  object,
  variables = c("A"),
  sample_names = NULL,
  sample_selection = NULL,
  n.chains = NULL,
  plot_type = "hexbin",
  plot_mode = "matrix",
  ...
)

ScatterSamples(...)

Arguments

object	coda::mcmc.list or a data.frame (required): mcmc list objects generated by rjags::jags.model in AgeS_Computation, AgeC14_Computation or Age_OSLC14. If a data.frame is provided, only the first two columns are taken and NA values are automatically removed. The function can also handle BayLum.list objects directly for certain functions
variables	character (with default): variable to be selected for the scatter plot, e.g., "A". Please note that you can only select one variable at the time
sample_names	character (optional): sample names shown in the plot matrix
sample_selection	numeric (with default): vector of samples to be plotted in the scatter matrix, e.g., c(1,2) will plot the first two samples, c(1,3) will plot samples 1 and 3 and c(1:3) will plot the first three samples
n.chains	integer (with default): allows to limit the number of chains shown, by default the results of all chains are plotted.
plot_type	character (with default): switch between different plot types, "hexbin" (the default), based on the function hexbin::hexplom and smoothScatter (the alternative) based on a highly customised plot function using the function graphics::smoothScatter
plot_mode	character (with default): switch between a matrix plot mode and a single plot mode. The plot mode single only works for plot_type = smoothScatter and creates a single plot panel for each sample. Please note that this cannot be further combined with other par settings.
...	further arguments to control the plot output, standard plot arguments supported are main, xlab, ylab, xlim, ylim, cex. For additional arguments supporting a fine tuning of the plot, see details.

Details

Additional supported plot arguments

The following table lists additional arguments supported by the function in order to fine tune the graphical output. Such arguments, can just be added in the function call. Example, for disabling the graphics::rug in the plot mode smoothScatter you can type plot_Scatterplots(..., rug = FALSE) Please note that not all arguments are supported by all plot types.

ARGUMENT	SUPPORTED BY PLOT TYPE	DESCRIPTION
colramp	hexbin and smoothScatter	Option to define an own colour ramp, by defining an own function, e.g., function(n) heat.colors(n, alpha = 1).
pscales	hexbin and smoothScatter	Controls the number of ticks shown on the plot axes, please note that the number works proportionally.
bw_smoothScatter	smoothScatter	Controls the bandwidth of the smooth scatter, cf. graphics::smoothScatter
rug	smoothScatter	enables/disables rugs
nlevels	smoothScatter	controls the number of isolines shown (cf. graphics::contour)
nrpoints	smoothScatter	defines the number of nrpoints to be plotted graphics::smoothScatter
col_contour	smoothScatter	defines the colour of the contour lines
col_nrpoints	smoothScatter	sets colour of the nrpoints in the scatter plot

Value

A scatter plot based on hexbin::hexplom

Function version

0.3.2

How to cite

Kreutzer, S., Christophe, C., Philippe, A., Guérin, G., 2023. plot_Scatterplots(): Display Scatter Plot Matrix of the Bayesian Age Results. Function version 0.3.2. In: Christophe, C., Philippe, A., Kreutzer, S., Guérin, G., Baumgarten, F.H., 2023. BayLum: Chronological Bayesian Models Integrating Optically Stimulated. R package version 0.3.1. https://CRAN.r-project.org/package=BayLum

Author(s)

Sebastian Kreutzer, Institute of Geography, Ruprecht-Karl University of Heidelberg (Germany) , based on the function 'ScatterSamples()' by Claire Christophe, Anne Philippe, Guillaume Guérin

See Also

Age_Computation, AgeS_Computation, AgeC14_Computation, and rjags packages.

Examples

data(AgeS,envir = environment())

##hexbin
plot_Scatterplots(
   object = AgeS$Sampling,
   sample_names = c("GDB5", "GDB3"),
   sample_selection = c(1,2)
 )

##scatter smooth (matrix)
plot_Scatterplots(
   object = AgeS$Sampling,
   sample_names = c("GDB5", "GDB3"),
   sample_selection = c(1,2),
   plot_type = "smoothScatter")


##scatter smooth (single)
plot_Scatterplots(
   object = AgeS$Sampling,
   sample_names = c("GDB5", "GDB3"),
   sample_selection = c(1,2),
   plot_type = "smoothScatter",
   plot_mode = "single")

BayLum documentation built on April 14, 2023, 12:24 a.m.