flux.age.ghost: Plot flux rates for proxies.

In rbacon: Age-Depth Modelling using Bayesian Statistics

Plot flux rates for proxies.

Description

Plot grey-scale representation of estimated flux rates for proxies against calendar age.

Usage

flux.age.ghost(
  proxy = 1,
  age.lim = c(),
  yr.lim = age.lim,
  age.res = 200,
  yr.res = age.res,
  set = get("info"),
  flux = c(),
  plot.range = TRUE,
  prob = 0.8,
  range.col = grey(0.5),
  range.lty = 2,
  plot.mean = TRUE,
  mean.col = "red",
  mean.lty = 2,
  plot.median = TRUE,
  median.col = "blue",
  median.lty = 2,
  flux.lim = c(),
  flux.lab = expression("flux (g cm"^-1 * " yr"^-1 * ")"),
  upper = 0.95,
  rgb.scale = c(0, 0, 0),
  rgb.res = 100,
  dark = set$dark,
  cutoff = 0.001,
  BCAD = set$BCAD,
  age.lab = c(),
  yr.lab = age.lab,
  rotate.axes = FALSE,
  rev.flux = FALSE,
  rev.age = FALSE,
  rev.yr = rev.age
)

Arguments

proxy	Which proxy to use (counting from the column number in the .csv file after the depths column).
age.lim	Minimum and maximum calendar age ranges, calculated automatically by default (age.lim=c()).
yr.lim	Deprecated - use age.lim instead
age.res	Resolution or amount of greyscale pixels to cover the age scale of the plot. Default age.res=200.
yr.res	Deprecated - use age.res instead
set	Detailed information of the current run, stored within this session's memory as variable info.
flux	Define a flux variable within the R session (consisting of depths and their proxy concentrations in two columns) and provide the name of this variable, e.g.: flux.age.ghost(flux=flux1). If left empty (flux=c()), a flux file is expected (see proxy).
plot.range	Plot curves that indicate a probability range, at resolution of yr.res.
prob	Probability range, defaults to prob=0.8 (10 % at each side).
range.col	Red seems nice.
range.lty	Line type of the confidence ranges.
plot.mean	Plot the mean fluxes.
mean.col	Red seems nice.
mean.lty	Line type of the means.
plot.median	Plot the median fluxes.
median.col	Blue seems nice.
median.lty	Line type of the medians.
flux.lim	Limits of the flux axes.
flux.lab	Axis labels. Defaults to flux.lab="flux".
upper	Maximum flux rates to plot. Defaults to the upper 99%; upper=0.99.
rgb.scale	The function to produce a coloured representation of all age-models. Needs 3 values for the intensity of red, green and blue. Defaults to grey-scales: rgb.scale=c(0,0,0), but could also be, say, scales of red (rgb.scale=c(1,0,0)).
rgb.res	Resolution of the colour spectrum depicting the age-depth model. Default rgb.res=100.
dark	The darkest grey value is dark=1 by default; lower values will result in lighter grey but values >1 are not allowed.
cutoff	Point below which colours will no longer be printed. Default cutoff=0.001.
BCAD	The calendar scale of graphs and age output-files is in cal BP by default, but can be changed to BC/AD using BCAD=TRUE.
age.lab	The labels for the calendar axis (default age.lab="cal BP" or "BC/AD" if BCAD=TRUE).
yr.lab	Deprecated - use age.lab instead
rotate.axes	The default of plotting calendar year on the horizontal axis and fluxes on the vertical one can be changed with rotate.axes=TRUE.
rev.flux	The flux axis can be reversed with rev.flux=TRUE.
rev.age	The direction of the age axis can be reversed using rev.age=TRUE.
rev.yr	Deprecated - use rev.age instead

Details

To plot flux rates (e.g. pollen grains/cm2/yr) as greyscales, provide a plain text file with headers and the data in columns separated by commas, ending in '_flux.csv' and saved in your core's folder. The first column should contain the depths, and the next columns should contain the proxy concentration values (leaving missing values empty). Then type for example flux.age.ghost(1) to plot the flux values for the first proxy in the .csv file. Instead of using a _flux.csv file, a flux variable can also be defined within the R session (consisting of depths and their proxy concentrations in two columns). Then provide the name of this variable, e.g.: flux.age.ghost(flux=flux1). See Bacon_runs/MSB2K/MSB2K_flux.csv for an example.

Value

A plot of flux rates.

Author(s)

Maarten Blaauw, J. Andres Christen

Examples

## Not run: 
  Bacon(run=FALSE, coredir=tempfile())
  agedepth(yr.res=50)
  flux.age.ghost(1)

## End(Not run)

rbacon documentation built on Sept. 30, 2024, 9:40 a.m.