A Computational Tool for Astrochronology

Documentation for package ‘astrochron’ version 1.2

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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)
bicoherence	bicoherence: Calculate bispectrum and bicoherence using WOSA method as detailed in Choudhury et al. (2008).
bioturb	Bioturbate time series using diffusion model from Guinasso and Schinck (1975), as in Liu et al. (2021)

-- C --

calcPeriods	Calculate eccentricity, obliquity and precession periods in ka, given g, s 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
insoDiff	insolation difference map using Laskar et al. (2004) insolation calculations
insoMap	generate an insolation map using Laskar et al. (2004) insolation calculations
insoSeries	Laskar et al. (2004) insolation calculations
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
tanerFC	Apply Taner bandpass or lowpass filter to Fourier coefficients
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