rbacon: proxy.ghost – R documentation

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proxy.ghost

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

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"),
  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.
`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

Age-Depth Modelling using Bayesian Statistics

v2.5.5

GPL (>= 2)

Authors

Maarten Blaauw [aut, cre], J. Andres Christen [aut, ctb, cph], Marco A. Aquino Lopez [aut], Judith Esquivel Vazquez [ctb], Oscar M. Gonzalez V. [ctb], Ted Belding [cph], James Theiler [cph], Brian Gough [cph], Charles Karney [cph]

Initial release

2021-05-04