accrate.depth.ghost: Plot modelled accumulation rates against the depths of a...

In rbacon: Age-Depth Modelling using Bayesian Statistics

Plot modelled accumulation rates against the depths of a core.

Description

Plot grey-scale representation of modelled accumulation rates over a core's depth. Each section of the core (see Bacon's option "thick") will have modelled accumulation rates.

Usage

accrate.depth.ghost(
  set = get("info"),
  d = set$elbows,
  d.lim = c(),
  acc.lim = c(),
  d.lab = c(),
  cmyr = FALSE,
  acc.lab = c(),
  dark = 1,
  cutoff = 0.001,
  rgb.scale = c(0, 0, 0),
  rgb.res = 100,
  prob = 0.95,
  plot.range = TRUE,
  range.col = grey(0.5),
  range.lty = 2,
  plot.mean = TRUE,
  mean.col = "red",
  mean.lty = 2,
  plot.median = TRUE,
  median.col = "blue",
  median.lty = 2,
  rotate.axes = FALSE,
  rev.d = FALSE,
  rev.acc = FALSE,
  xaxs = "r",
  yaxs = "r",
  bty = "l",
  remove.laststep = TRUE
)

Arguments

set	Detailed information of the current run, stored within this session's memory as variable info.
d	The depths for which the accumulation rates are to be calculated. Default to the entire core.
d.lim	Axis limits for the depths.
acc.lim	Axis limits for the accumulation rates.
d.lab	Label for the depth axis.
cmyr	Accumulation rates can be calculated in cm/year or year/cm. By default cmyr=FALSE and accumulation rates are calculated in year per cm. Axis limits are difficult to calculate when cmyr=TRUE, so a manual adaptation of acc.lim might be a good idea.
acc.lab	Axis label for the accumulation rate.
dark	The darkest grey value is dark=1 by default; lower values will result in lighter grey but values >1 are not advised.
cutoff	Point below which colours will no longer be printed. Default cutoff=0.001.
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.
prob	Probability ranges. Defaults to prob=0.95.
plot.range	If plot.range=TRUE, the confidence ranges (two-tailed; half of the probability at each side) are plotted.
range.col	Colour of the confidence ranges.
range.lty	Line type of the confidence ranges.
plot.mean	If plot.mean=TRUE, the means are plotted.
mean.col	Colour of the mean accumulation rates.
mean.lty	Type of the mean lines.
plot.median	If plot.mean=TRUE, the medians are plotted.
median.col	Colour of the median accumulation rates.
median.lty	Type of the median lines.
rotate.axes	The default is to plot the accumulation rates horizontally and the depth vertically (rotate.axes=FALSE). Change rotate.axes value to rotate axes.
rev.d	The direction of the depth axis can be reversed from the default (rev.d=TRUE.
rev.acc	The direction of the accumulation rate axis can be reversed from the default (rev.acc=TRUE).
xaxs	Extension of x-axis. By default, add some extra white-space at both extremes (xaxs="r"). See ?par for other options.
yaxs	Extension of y-axis. By default, add no extra white-space at both extremes (yaxs="i"). See ?par for other options.
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).
remove.laststep	Add a white line to remove spurious lines at the extreme of the graph. Defaults to TRUE.

Details

This plot shows the modelled accumulation rates in grey-scales, where darker grey indicates more likely accumulation rates. Axis limits for accumulation rates are estimated automatically, however upper limits can be very variable (and thus hard to predict) if calculated in cm/yr; therefore you might want to manually adapt the axis limits after plotting with default settings (e.g., acc.lim=c(0,1)). See also accrate.age.ghost, accrate.depth and accrate.age.

Value

A grey-scale plot of accumulation rate against core depth, and (invisibly) the list of depths and their accumulation rates (ranges, medians, means).

Author(s)

Maarten Blaauw, J. Andres Christen

Examples

## Not run: 
  Bacon(run=FALSE, coredir=tempfile())
  agedepth(yr.res=50, d.res=50, d.by=10)
  layout(1)
  tmp <- accrate.depth.ghost()
  head(tmp)

## End(Not run)

rbacon documentation built on Sept. 30, 2024, 9:40 a.m.