proxy.ghost | R 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 value.
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
)
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 |
age.res |
Resolution or amount of greyscale pixels to cover the age scale of the age-model plot. Default |
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.res |
Resolution of the colour spectrum depicting the age-depth model. Default |
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 |
dark |
By default, the darkest grey value is assigned to the most likely value within the entire core (normalised to 1; |
darkest |
Darkness of the most likely value. Is black by default ( |
rotate.axes |
The default is to plot the calendar horizontally, however the plot can be rotated ( |
proxy.rev |
The proxy axis can be reversed if |
age.rev |
The calendar axis can be reversed using |
yr.rev |
Deprecated - use age.rev instead |
plot.mean |
The mean ages of the proxy values can be added using |
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 |
Deprecated - use age.lim instead |
proxy.lim |
Ranges of the proxy axis, calculated automatically by default ( |
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 ( |
yaxs |
Extension of y-axis. By default, no white-space will be added at the axis extremes ( |
xaxt |
The x-axis is plotted by default, but this can be switched off using |
yaxt |
The y-axis is plotted by default, but this can be switched off using |
bty |
Type of box to be drawn around the plot ( |
BCAD |
The calendar scale of graphs and age output-files is in |
age.lab |
The labels for the calendar axis (default |
yr.lab |
Deprecated - use age.lab instead |
verbose |
Provide feedback on what is happening (default |
add |
Add to an existing graph (default |
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"
.
A grey-scale graph of the proxy against calendar age.
Maarten Blaauw, J. Andres Christen
Bacon(ask=FALSE, coredir=tempfile())
layout(1)
proxy.ghost()
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