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calculate the duration of stratigraphic gaps using astronomical cycles

Source: R/dur_gaps.R
dur_gaps.Rd

calculate the duration of stratigraphic gaps using the duration of stable astronomical cycles

Usage

dur_gaps(
  proxies = NULL,
  retracked_period_1 = NULL,
  retracked_period_2 = NULL,
  min_max = NULL,
  n_simulations = 10,
  tracked_cycle_period = NULL,
  tracked_cycle_period_unc = NULL,
  tracked_cycle_period_unc_dist = "u",
  pts = 5,
  dj = 1/200,
  lowerPeriod = 1,
  upperPeriod = 3200,
  period_max = NULL,
  period_min = NULL,
  missing_cycle_dur = NULL,
  n_cycles_missing = 1,
  missing_cycle_unc = NULL,
  missing_cycle_unc_dist = "u",
  seed_nr = 1337,
  run_multicore = FALSE,
  n_cores = NULL
)

Arguments

proxies

Proxy records that were used to build the astrochronological age model and from which the gap duration is estimated (list of two-column matrices or data frames: depth/height in column 1, proxy value in column 2). In each simulation one proxy of the list is drawn at random. Required (Default=NULL).

retracked_period_1

Tracked cycle curve of the interval below/before the gap (three-column matrix or data frame: depth/height in column 1, period of the tracked cycle in column 2, its 1 standard deviation uncertainty in column 3, e.g. the output of retrack_wt_MC). In each simulation a curve is drawn from this normal uncertainty envelope and used to tune the proxy with curve2tune. The gap must lie between retracked_period_1 and retracked_period_2. Required (Default=NULL).

retracked_period_2

Tracked cycle curve of the interval above/after the gap, in the same format as retracked_period_1. Required (Default=NULL).

min_max

For each proxy in proxies, whether the gap duration is measured between minima ("min", peaks found with min_detect) or maxima ("max", max_detect) of the extracted cycle (list or character vector of the same length as proxies). Required (Default=NULL).

n_simulations

Number of Monte Carlo simulations, i.e. number of gap durations calculated (integer, > 0). Default=10.

tracked_cycle_period

Duration in time of the tracked cycle (numeric, e.g. in kyr; e.g. 405 for the long eccentricity cycle). The tuned records and the gap duration are in this time unit. Required (Default=NULL).

tracked_cycle_period_unc

Uncertainty of tracked_cycle_period, in the same unit (numeric, >= 0): half-width of the range for "u", standard deviation for "n" (see tracked_cycle_period_unc_dist). Required (Default=NULL).

tracked_cycle_period_unc_dist

Distribution from which the tracked cycle period is drawn in each simulation (character): "u" uniform between tracked_cycle_period -/+ tracked_cycle_period_unc or "n" normal with mean tracked_cycle_period and standard deviation tracked_cycle_period_unc. Default="u".

pts

Number of points on each side that a point must exceed (maximum) or be below (minimum) to be detected as a peak in the extracted cycle; passed to max_detect/min_detect (integer, >= 1). Larger values give more certain peaks but may miss minor ones. Default=5.

dj

Spacing between successive scales of the wavelet transform of the tuned records, in octaves (numeric, > 0), passed to analyse_wavelet. Smaller values give a finer period resolution but a longer computation time. Default=1/200.

lowerPeriod

Shortest period of the wavelet transform of the tuned records, in the time unit of tracked_cycle_period (numeric, > 0), passed to analyse_wavelet. Default=1.

upperPeriod

Longest period of the wavelet transform of the tuned records, in the time unit of tracked_cycle_period (numeric, > lowerPeriod), passed to analyse_wavelet. Default=3200.

period_max

Upper period boundary (time unit) of the cycle extracted from the tuned records with extract_signal_stable_V2 (numeric, > period_min). Required (Default=NULL).

period_min

Lower period boundary (time unit) of the cycle extracted from the tuned records with extract_signal_stable_V2 (numeric, > 0). Required (Default=NULL).

missing_cycle_dur

Duration of one missing cycle in the gap, in the time unit (numeric). If it equals tracked_cycle_period, the value drawn for the tracked cycle is also used for the missing cycle. Required (Default=NULL).

n_cycles_missing

Number of cycles of duration missing_cycle_dur that are missing in the gap (numeric, >= 0). Default=1.

missing_cycle_unc

Uncertainty of missing_cycle_dur in the time unit (numeric, >= 0): half-width for "u", standard deviation for "n". Only used when missing_cycle_dur differs from tracked_cycle_period. Required in that case (Default=NULL).

missing_cycle_unc_dist

Distribution from which the missing cycle duration is drawn (character): "u" uniform or "n" normal (see missing_cycle_unc). Default="u".

seed_nr

Seed of the random number generator (integer), set with set.seed() so that the Monte Carlo results can be reproduced. Default=1337.

run_multicore

Run the simulations in parallel on several cores (logical, TRUE or FALSE). Default=FALSE.

n_cores

Number of cores used when run_multicore=TRUE (integer or NULL). NULL picks an automatic, safe number: physical cores minus one, at most 4, and limited by the free memory; set options(waverider.n_cores = ...) to change that default. Results do not depend on the number of cores. Default=NULL.

Value

a vector with all the calculated gap durations