proxy.ghost: Proxies analysed along the depths of a core can be plotted as...

View source: R/plots.R

proxy.ghostR Documentation

Proxies analysed along the depths of a core can be plotted as 'proxy-ghost' graphs against calendar time while taking into account chronological uncertainties. Here darker grey indicates more likely calendar ages for specific proxy values.

Description

Proxies analysed along the depths of a core can be plotted as 'proxy-ghost' graphs against calendar time while taking into account chronological uncertainties. Here darker grey indicates more likely calendar ages for specific proxy value.

Usage

proxy.ghost(
  proxy = 1,
  proxy.lab = NULL,
  proxy.res = 250,
  age.res = 200,
  yr.res = age.res,
  rgb.scale = c(0, 0, 0),
  rgb.res = 100,
  set = get("info"),
  cutoff = 0.001,
  dark = 1,
  darkest = 1,
  rotate.axes = FALSE,
  proxy.rev = FALSE,
  age.rev = FALSE,
  yr.rev = age.rev,
  plot.mean = FALSE,
  mean.col = "red",
  age.lim = NULL,
  yr.lim = age.lim,
  proxy.lim = NULL,
  sep = ",",
  xaxs = "i",
  yaxs = "i",
  xaxt = "s",
  yaxt = "s",
  bty = "l",
  BCAD = set$BCAD,
  age.lab = ifelse(BCAD, "BC/AD", "cal yr BP"),
  yr.lab = age.lab,
  verbose = TRUE,
  add = FALSE
)

Arguments

proxy

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

proxy.lab

Label of the proxy axis. Default names are taken from the csv file.

proxy.res

Greyscale pixels are calculated for proxy.res=250 proxy values by default, as a compromise between image quality and calculation speed. If the output looks very pixel-like (e.g., when choosing to plot only part of the record using proxy.lim), set this option to higher values.

age.res

Resolution or amount of greyscale pixels to cover the age scale of the age-model plot. Default age.res=250 as a compromise between image quality and calculation speed. If the output looks very pixel-like (e.g., when choosing to plot only part of the record using age.lim), set this option to higher values.

yr.res

Deprecated - use age.res instead

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.

set

Detailed information of the current run, stored within this session's memory as variable info.

cutoff

Point below which colours will no longer be printed. Default cutoff=0.001.

dark

By default, the darkest grey value is assigned to the most likely value within the entire core (normalised to 1; dark=1). By setting dark to, e.g., dark=.8, all values of and above 0.8 will be darkest (and values below that threshold will be lighter grey the lower their probabilities).

darkest

Darkness of the most likely value. Is black by default (darkest=1); lower values will result in lighter grey.

rotate.axes

The default is to plot the calendar horizontally, however the plot can be rotated (rotate.axes=TRUE).

proxy.rev

The proxy axis can be reversed if proxy.rev=TRUE.

age.rev

The calendar axis can be reversed using yr.rev=TRUE.

yr.rev

Deprecated - use age.rev instead

plot.mean

The mean ages of the proxy values can be added using plot.mean=TRUE.

mean.col

Colour of the weighted mean ages of the proxy values.

age.lim

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

yr.lim

Deprecated - use age.lim instead

proxy.lim

Ranges of the proxy axis, calculated automatically by default (proxy.lim=NULL).

sep

Separator between the fields of the plain text file containing the depth and proxy data.

xaxs

Extension of x-axis. By default, no white-space will be added at the axis extremes (xaxs="i"). See ?par for other options.

yaxs

Extension of y-axis. By default, no white-space will be added at the axis extremes (xaxs="i"). See ?par for other options.

xaxt

The x-axis is plotted by default, but this can be switched off using xaxt="n".

yaxt

The y-axis is plotted by default, but this can be switched off using yaxt="n".

bty

Type of box to be drawn around the plot ("n" for none, and "l" (default), "7", "c", "u", or "o" for correspondingly shaped boxes).

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

verbose

Provide feedback on what is happening (default verbose=TRUE).

add

Add to an existing graph (default add=FALSE).

Details

Place a csv file with the values of proxies against depth within your core's folder. The values should be in columns separated by commas (default sep=","), the first column containing the depths and the first line (header) containing the proxy names. The file name should start with the core's name and end with "_proxies.csv". For an example see "Bacon_coredir/MSB2K/MSB2K_proxies.csv" or "Cores/MSB2K/MSB2K_proxies.csv".

Value

A grey-scale graph of the proxy against calendar age.

Author(s)

Maarten Blaauw, J. Andres Christen

Examples


  Bacon(ask=FALSE, coredir=tempfile())
  layout(1)
  proxy.ghost()


rbacon documentation built on March 29, 2022, 5:05 p.m.