Plot a grey-scale representation of a core's estimated accumulation rates against time.
accrate.age.ghost(set = get("info"), age.lim = c(), yr.lim = age.lim,
age.lab = c(), yr.lab = age.lab, age.res = 200, yr.res = age.res,
grey.res = 50, prob = 0.95, plot.range = TRUE,
range.col = grey(0.5), range.lty = 2, plot.mean = TRUE,
mean.col = "red", mean.lty = 2, acc.lim = c(), acc.lab = c(),
upper = 0.99, dark = 50, BCAD = set$BCAD, cmyr = FALSE,
rotate.axes = FALSE, rev.age = FALSE, rev.yr = rev.age,
rev.acc = FALSE, xaxs = "i", yaxs = "i", bty = "l")Detailed information of the current run, stored within this session's memory as variable info.
Minimum and maximum calendar age ranges, calculated automatically by default (age.lim=c()).
Deprecated - use age.lim instead
The labels for the calendar axis (default age.lab="cal BP" or "BC/AD" if BCAD=TRUE).
Deprecated - use age.lab instead
Resolution or amount of greyscale pixels to cover the age scale of the age-model plot. Default age.res=200.
Deprecated - use age.res instead
Resolution of greyscales. Default grey.res=50, which does not aim to poke fun at a famous novel.
Probability ranges. Defaults to prob=0.95.
If plot.range=TRUE, the confidence ranges (two-tailed; half of the probability at each side) are plotted.
Colour of the confidence ranges.
Line type of the confidence ranges.
If plot.mean=TRUE, the means are plotted.
Colour of the mean accumulation rates.
Type of the mean lines.
Axis limits for the accumulation rates.
Axis label for the accumulation rate.
Maximum accumulation rates to plot. Defaults to the upper 99%; upper=0.99.
The darkest grey value is dark=1 by default; lower values will result in lighter grey but values >1 are not advised.
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.
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.
The default is to plot the calendar age horizontally and accumulation rates vertically. Change to rotate.axes=TRUE value to rotate axes.
The direction of the age axis, which can be reversed using rev.age=TRUE.
Deprecated - use rev.age instead
The direction of the accumulation rate axis, which can be reversed (rev.acc=TRUE.
Extension of the x-axis. White space can be added to the vertical axis using xaxs="r".
Extension of the y-axis. White space can be added to the vertical axis using yaxs="r".
Type of box to be drawn around the plot ("n" for none, and "l" (default), "7", "c", "u", or "o" for correspondingly shaped boxes).
A greyscale plot of accumulation rate against calendar age.
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.
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(run=FALSE, coredir=tempfile())
agedepth(yr.res=50, d.res=50, d.by=10)
layout(1)
accrate.age.ghost()
# }
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