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.
proxy.ghost(
proxy = 1,
proxy.lab = NULL,
proxy.res = 250,
age.res = 200,
yr.res = age.res,
grey.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
)Which proxy to use (counting from the column number in the .csv file after the depths column).
Label of the proxy axis. Default names are taken from the csv file.
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.
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.
Deprecated - use age.res instead
Grey-scale resolution of the proxy graph. Default grey.res=100.
Detailed information of the current run, stored within this session's memory as variable info.
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).
Darkness of the most likely value. Is black by default (darkest=1); lower values will result in lighter grey.
The default is to plot the calendar horizontally, however the plot can be rotated (rotate.axes=TRUE).
The proxy axis can be reversed if proxy.rev=TRUE.
The calendar axis can be reversed using yr.rev=TRUE.
Deprecated - use age.rev instead
The mean ages of the proxy values can be added using plot.mean=TRUE.
Colour of the weighted mean ages of the proxy values.
Minimum and maximum calendar age ranges, calculated automatically by default (yr.lim=NULL).
Deprecated - use age.lim instead
Ranges of the proxy axis, calculated automatically by default (proxy.lim=NULL).
Separator between the fields of the plain text file containing the depth and proxy data.
Extension of x-axis. By default, no white-space will be added at the axis extremes (xaxs="i"). See ?par for other options.
Extension of y-axis. By default, no white-space will be added at the axis extremes (xaxs="i"). See ?par for other options.
The x-axis is plotted by default, but this can be switched off using xaxt="n".
The y-axis is plotted by default, but this can be switched off using yaxt="n".
Type of box to be drawn around the plot ("n" for none, and "l" (default), "7", "c", "u", or "o" for correspondingly shaped boxes).
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.
The labels for the calendar axis (default age.lab="cal BP" or "BC/AD" if BCAD=TRUE).
Deprecated - use age.lab instead
Provide feedback on what is happening (default verbose=TRUE).
A grey-scale graph of the proxy against calendar age.
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".
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/euclid.ba/1339616472
# NOT RUN {
Bacon(ask=FALSE, coredir=tempfile())
layout(1)
proxy.ghost()
# }
Run the code above in your browser using DataCamp Workspace