AgesOfEvents: Event probabilities against calendar age

View source: R/plots.R

AgesOfEventsR Documentation

Event probabilities against calendar age

Description

Plot probability curves for events in the core, expressed against calendar age.

Usage

AgesOfEvents(
  window,
  move,
  set = get("info"),
  plot.steps = FALSE,
  BCAD = set$BCAD,
  age.lab = c(),
  yr.lab = age.lab,
  age.lim = c(),
  yr.lim = age.lim,
  prob.lab = "probability",
  prob.lim = c(),
  rotate.axes = FALSE,
  rev.age = TRUE,
  rev.yr = rev.age,
  yaxs = "i",
  bty = "l"
)

Arguments

window

Width of the window.

move

Step size with which the window moves.

set

Detailed information of the current run, stored within this session's memory as variable info.

plot.steps

Plot probability values step-wise (defaults to plot.steps=FALSE, which plots smooth curves instead).

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.

age.lab

The labels for the calendar axis (default age.lab="cal BP" or "BC/AD" if BCAD=TRUE).

yr.lab

Deprecated - use age.lab instead

age.lim

Minimum and maximum calendar age ranges, calculated automatically by default (age.lim=c()).

yr.lim

Deprecated - use age.lim instead

prob.lab

Label of the probability axis (default prob.lab="probability").

prob.lim

Limits of the probability axis (calculated automatically by default).

rotate.axes

The default of plotting age on the horizontal axis and event probability on the vertical one can be changed with rotate.axes=TRUE.

rev.age

The direction of the age axis, which can be reversed using rev.age=TRUE.

rev.yr

Deprecated - use rev.age instead

yaxs

Extension of the y-axis. Defaults to the exact ranges of the probability values. White space can be added to the vertical axis using yaxs="r".

bty

Type of box to be drawn around plots. Draw a box around the graph ("n" for none, and "l", "7", "c", "u", "]" or "o" for correspondingly shaped boxes).

Details

Probabilities of depths with 'events' in an age-modelled core can be plotted against time, taking into account chronological uncertainties (Blaauw et al. 2007). Such events could be for example core depths at which proxies indicate changes toward wetter local conditions. This can be expressed as values between 0 (no event) and 1 (event at 100% probability) for each depth.

Blaauw et al. 2010 propose to estimate probabilities of events by finding specific proxy features such as increasing curves. Probabilities are then estimated through resampling from the proxy values, where low to modest rises of proxy curves result in low event probabilities, and clear proxy rises in high probabilities. A smooth spline can be applied to adapt the balance of short-term vs long-term events. To calculate the event probabilities, produce a file with two columns (depth and corresponding proxy-derived probabilities, separated by white spaces). Do not provide headers at the file's first line, and save the file with extension "_events.txt" within the core's Bacon folder. See Cores/MSB2K/MSB2K_events.txt (or Bacon_runs/MSB2K/MSB2K_events.txt) for an example. Events are calculated as the probability that an event took place within specific time windows - or more specifically, that the Bacon age-depth model puts depths with assigned event probabilities in that time window.

does not yet deal correctly with hiatuses.

Value

The resulting probabilities are plotted and saved within the core's folder (file names ending with the window width and "_probs.txt").

Author(s)

Maarten Blaauw, J. Andres Christen

References

Blaauw, M., Christen, J.A., Mauquoy, D., van der Plicht, J., Bennett, K.D. (2007) Testing the timing of radiocarbon-dated events between proxy archives. _The Holocene_, *17*, 283-288. Blaauw, M., Wohlfarth, B., Christen, J.A., Ampel, L., Veres, D., Hughen, K.A., Preusser, F., Svensson, A. (2010) Were last glacial climate events simultaneous between Greenland and France? A quantitative comparison using non-tuned chronologies. _Journal of Quaternary Science_ *25*, 387-394.

Examples


  Bacon(run=FALSE, coredir=tempfile())
  agedepth(yr.res=50)
  AgesOfEvents(100, 10)


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