accrate.age.ghost: Plot a core's accumulation rates against calendar time.

In rbacon: Age-Depth Modelling using Bayesian Statistics

Plot a core's accumulation rates against calendar time.

Description

Plot a grey-scale representation of a core's estimated accumulation rates against time.

Usage

accrate.age.ghost(
  set = get("info"),
  age.lim = c(),
  age.lab = c(),
  kcal = FALSE,
  age.res = 400,
  acc.res = 200,
  cutoff = 0.001,
  dark = 1,
  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,
  acc.lim = c(),
  acc.lab = c(),
  BCAD = set$BCAD,
  cmyr = FALSE,
  rotate.axes = FALSE,
  rev.age = FALSE,
  rev.acc = FALSE,
  xaxs = "i",
  yaxs = "i",
  bty = "l"
)

Arguments

set	Detailed information of the current run, stored within this session's memory as variable info.
age.lim	Minimum and maximum calendar age ranges, calculated automatically by default (age.lim=c()).
age.lab	The labels for the calendar axis (default age.lab="cal BP" or "BC/AD" if BCAD=TRUE).
kcal	Use kcal BP. Default is kcal=FALSE.
age.res	Resolution or amount of greyscale pixels to cover the age scale of the plot. Default age.res=400.
acc.res	Resolution or amount of greyscale pixels to cover the accumulation rate scale plot. Default age.res=400.
cutoff	Point below which colours will no longer be printed. Default cutoff=0.001.
dark	The darkest grey value is dark=1 by default; lower values will result in lighter grey but values >1 are not advised.
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.
acc.lim	Axis limits for the accumulation rates.
acc.lab	Axis label for the accumulation rate.
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.
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.
rotate.axes	The default is to plot the calendar age horizontally and accumulation rates vertically. Change to rotate.axes=TRUE value to rotate axes.
rev.age	The direction of the age axis, which can be reversed using rev.age=TRUE.
rev.acc	The direction of the accumulation rate axis, which can be reversed (rev.acc=TRUE.
xaxs	Extension of the x-axis. White space can be added to the vertical axis using xaxs="r".
yaxs	Extension of the y-axis. White space can be added to the vertical axis using yaxs="r".
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

Calculating accumulation rates against calendar age will take some time to calculate, and might show unexpected rates around the core's maximum ages (only a few of all age-model iterations will reach such ages and they will tend to have modelled accumulation rates for the lower depths much lower than the other iterations). 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.depth.ghost, accrate.depth and accrate.age. The grey-scale reconstruction around the oldest ages of any reconstruction often indicates very low accumulation rates. This is due to only some MCMC iterations reaching those old ages, and these iterations will have modelled very slow accumulation rates. Currently does not deal well with hiatuses, so do not interpret accumulation rates close to depths with inferred hiatuses.

Value

A greyscale plot of accumulation rate against calendar age, and (invisibly) the list of ages and their accumulation rates (ranges, medians, means).

Author(s)

Maarten Blaauw, J. Andres Christen

Examples

## Not run: 
  Bacon(run=FALSE, coredir=tempfile())
  agedepth(age.res=20, d.res=20, d.by=10)
  layout(1)
  tmp <- accrate.age.ghost(age.res=200, acc.res=100)
  head(tmp)

## End(Not run)

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