# A Computational Tool for Astrochronology

## Documentation for package ‘astrochron’ version 1.2

- DESCRIPTION file.
- Package NEWS.

## Help Pages

A B C D E F G H I L M N P R S T U W X Z

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)
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