rbacon (version 2.3.3)

flux.age.ghost: 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, yr.lim = c(), yr.res = 200, 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,
  flux.lim = c(), flux.lab = "flux", upper = 0.95, dark = set$dark,
  BCAD = set$BCAD, yr.lab = c(), rotate.axes = FALSE, rev.flux = FALSE,
  rev.yr = FALSE)

Arguments

proxy

Which proxy to use (counting from the column number in the .csv file after the depths column).

yr.lim

Minimum and maximum calendar age ranges, calculated automatically by default (yr.lim=c()).

yr.res

Resolution or amount of greyscale pixels to cover the age scale of the plot. Default yr.res=200.

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.

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.

dark

The darkest grey value is dark=1 by default; lower values will result in lighter grey but values >1 are not allowed.

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.

yr.lab

The labels for the calendar axis (default yr.lab="cal BP" or "BC/AD" if BCAD=TRUE).

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.yr

The direction of the age axis can be reversed using rev.yr=TRUE.

Value

A plot of flux rates.

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.

References

Blaauw, M. and Christen, J.A., Flexible paleoclimate age-depth models using an autoregressive gamma process. Bayesian Anal. 6 (2011), no. 3, 457--474. https://projecteuclid.org/download/pdf_1/euclid.ba/1339616472

See Also

http://www.chrono.qub.ac.uk/blaauw/manualBacon_2.3.pdf

Examples

# NOT RUN {
  Bacon(run=FALSE, coredir=tempfile())
  agedepth(yr.res=50)
  flux.age.ghost(1)
# }