A Computational Tool for Astrochronology

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Documentation for package ‘astrochron’ version 1.1

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astrochron-package astrochron: A Computational Tool for Astrochronology

-- A --

anchorTime Anchor a floating astrochronology to a radioisotopic age
ar1 Generate AR(1) surrogates
ar1etp AR(1) + ETP simulation routine
arcsinT Arcsine transformation of stratigraphic series
armaGen Generate autoregressive moving-average model
asm Average Spectral Misfit
astrochron astrochron: A Computational Tool for Astrochronology
autoPlot Automatically plot multiple stratigraphic series, with smoothing if desired

-- B --

bandpass Bandpass filter stratigraphic series
bergerPeriods Obliquity and precession periods of Berger et al. (1992)
bioturb Bioturbate time series using diffusion model from Guinasso and Schinck (1975), as in Liu et al. (2021)

-- C --

calcPeriods Calculate eccentricity and precession periods in ka, given g and k in arcsec/yr
cb Combine multiple vectors
clipIt Create non-linear response by clipping stratigraphic series
confAdjust Adjust spectrum confidence levels for multiple comparisons
constantSedrate Apply a constant sedimentation rate model to transform a spatial series to temporal series
conv_fft Convolution through Fast Fourier Transform
cosTaper Apply cosine taper to stratigraphic series
cycles Generate harmonic model

-- D --

deconv Wiener Deconvolution through Fast Fourier Transform
delPts Interactively delete points in plot
demean Remove mean value from stratigraphic series
detrend Subtract linear trend from stratigraphic series
diffAccum Model differential accumulation
divTrend Divide by linear trend in stratigraphic series
dpssTaper Apply DPSS taper to stratigraphic series

-- E --

eAsm Evolutive Average Spectral Misfit
eAsmTrack Track ASM null hypothesis significance level minima in eASM results
eha Evolutive Harmonic Analysis & Evolutive Power Spectral Analysis
eTimeOpt eTimeOpt: Evolutive implementation of TimeOpt (Meyers, 2015; Meyers, 2019)
eTimeOptTrack Track eTimeOpt r2 maxima
etp Generate eccentricity-tilt-precession models
extract Extract record from EHA time-frequency output or eAsm output

-- F --

flip Flip stratigraphic series
freq2sedrate Convert record of local spatial frequency (from EHA) to sedimentation rate curve

-- G --

gausTaper Apply Gaussian taper to stratigraphic series
getColor Query R for color information
getData Download file from astrochron data server
getLaskar Download Laskar et al. (2004, 2011a, 2011b) astronomical solutions

-- H --

hannTaper Apply Hann taper to stratigraphic series
headn List column numbers for each variable
hilbert Hilbert transform of stratigraphic series

-- I --

idPts Interactively identify points in plot
imbrie Imbrie and Imbrie (1980) ice sheet model
impulseResponse Impulse response function calculation
integratePower Determine the total power within a given bandwidth
iso Isolate data from a specified stratigraphic interval

-- L --

linage Tune stratigraphic series to an astronomical target using graphical interface
linterp Piecewise linear interpolation of stratigraphic series
logT Log transformation of stratigraphic series
lowpass Lowpass filter stratigraphic series
lowspec Robust Locally-Weighted Regression Spectral Background Estimation

-- M --

makeNoise Generate noise surrogates from a theoretical power spectrum
modelA Example stratigraphic model series
mtm Multitaper method spectral analysis
mtmAR Intermediate spectrum test of Thomson et al. (2001)
mtmML96 Mann and Lees (1996) robust red noise MTM analysis
mtmPL Multitaper Method Spectral Analysis with Power Law (1/f) fit
multiTest Adjust spectral p-values for multiple comparisons
mwCor Calculate moving window correlation coefficient for two stratigraphic series, using a 'dynamic window'
mwin Determine 'dynamic moving window' for stratigraphic series, adjusting for changing sample density to maintain a window of constant duration
mwinGrid Determine 'dynamic moving window' for stratigraphic series, adjusting for changing sample density to maintain a window of constant duration; output on evenly spaced grid
mwMinMax 'Dynamic window' moving assessment of maxima and minima in stratigraphic series
mwStats 'Dynamic window' moving average, median and variance of stratigraphic series
mwStatsGrid 'Dynamic window' moving average, median and variance of stratigraphic series, using evenly spaced spatial/temporal grid

-- N --

noKernel Remove Gaussian kernel smoother from stratigraphic series
noLow Fit and remove Lowess smoother from stratigraphic series

-- P --

pad Pad stratigraphic series with zeros
peak Identify maxima of peaks in series, filter at desired threshold value
periodogram Simple periodogram
pl Set up plots
plotEha Create color time-frequency plots from eha results.
plS Set default plotting parameters for vertical stratigraphic plots
prewhiteAR Prewhiten stratigraphic series with autoregressive filter, order selected by Akaike Information Criterion
prewhiteAR1 Prewhiten stratigraphic series with AR1 filter, using 'standard' or unbiased estimate of rho
pwrLaw Generate power law (1/f) noise surrogates
pwrLawFit Estimate power law (1/f) fit to power spectrum

-- R --

rankSeries Create lithofacies rank series from bed thickness data
read Read data from file
readMatrix Read data matrix from file
repl0 Replace values < 0 with 0
replEps Replace values <= 0 with smallest positive value
resample Resample stratigraphic series
rmNA Remove stratigraphic levels that contain one or more NAs

-- S --

s Standardize variable in stratigraphic series
sedRamp Apply 'ramping' sedimentation rate model to convert time to stratigraphy
sedrate2time Integrate sedimentation rate curve to obtain time-space map
slideCor Identify optimal spatial/temporal shift to maximize correlation between two stratigraphic/time series.
sortNave Remove missing entries, sort data, average duplicates
stepHeat Ar/Ar Geochronology: Generate an Ar/Ar age spectrum and calculate step-heating plateau age.
strats Summary statistics for stratigraphic series
surrogateCor Estimate correlation coefficient and significance for serially correlated data
surrogates Generate phase-randomized surrogate series as in Ebisuzaki (1997)
synthStrat Synthesize stratigraphy from forcing function

-- T --

taner Apply Taner bandpass or lowpass filter to stratigraphic series
testBackground Evaluate power spectrum false positive rates via Monte Carlo simulation
testPrecession Astrochronologic testing via the precession amplitude modulation approach of Zeeden et al. (2015).
testTilt Astrochronologic testing via the obliquity amplitude modulation approach of Zeeden et al. (2019 submitted).
timeOpt TimeOpt: Evaluation of eccentricity-related amplitude modulation and bundling in paleoclimate data
timeOptMCMC TimeOptMCMC: Evaluation of eccentricity-related amplitude modulation and bundling in paleoclimate data ("TimeOpt"), with uncertainties via Markov-Chain Monte Carlo
timeOptPlot TimeOptPlot: Generate summary figure for TimeOpt analyses
timeOptSim Monte Carlo simulation for TimeOpt
timeOptSimPwrLaw Monte Carlo simulation for TimeOpt, using power law (1/f) noise
timeOptTemplate TimeOpt analysis using variable sedimentation models
timeOptTemplatePlot TimeOptTemplatePlot: Generate summary figure for TimeOptTemplate analyses
timeOptTemplateSim Simulations for timeOptTemplate
tones Calculate all possible difference and combinations tones
traceFreq Frequency-domain minimal tuning: Use interactive graphical interface to trace frequency drift
tracePeak A tool to interactively trace peak trajectories on plots
trackFreq Frequency-domain minimal tuning: Use interactive graphical interface and sorting to track frequency drift
trackPeak A tool to interactively select points to track peak trajectories on plots
trim Remove outliers from stratigraphic series
trimAT Remove outliers from stratigraphic series
trough Identify minima of troughs in series, filter at desired threshold value
tune Tune stratigraphic series

-- U --

unbioturb Bioturbation removal function following the approach of Liu et al (2021)

-- W --

writeCSV Write CSV file
writeT Write tab-delimited file
wtMean Ar/Ar Geochronology: calculate weighted mean age, age uncertainty, and other associated statistics/plots (with interactive graphics for data culling).

-- X --

xplot Generate cross-plot with kernel density estimates on axes

-- Z --

zoomIn Dynamically explore cross-plot, zoom-in into specified region