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

View source: R/accrate.R

accrate.depth.ghostR Documentation

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,
  bty = "l"
)

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).

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).

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.

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)
  accrate.depth.ghost()

## End(Not run)

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