accum                   Calculate geochemical proxy accumulation rates
alodfromk               Compute Earth-Moon distance and length of day
                        from precession frequency
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-package      astrochron: A Computational Tool for
                        Astrochronology
autoPlot                Automatically plot multiple stratigraphic
                        series, with smoothing if desired
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)
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
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
eAsm                    Evolutive Average Spectral Misfit
eAsmTrack               Track ASM null hypothesis significance level
                        minima in eASM results
eTimeOpt                eTimeOpt: Evolutive implementation of TimeOpt
                        (Meyers, 2015; Meyers, 2019)
eTimeOptTrack           Track eTimeOpt r2 maxima
eha                     Evolutive Harmonic Analysis & Evolutive Power
                        Spectral Analysis
etp                     Generate eccentricity-tilt-precession models
extract                 Extract record from EHA time-frequency output
                        or eAsm output
flip                    Flip stratigraphic series
freq2sedrate            Convert record of local spatial frequency (from
                        EHA) to sedimentation rate curve
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
hannTaper               Apply Hann taper to stratigraphic series
headn                   List column numbers for each variable
hilbert                 Hilbert transform of stratigraphic series
hoangPriors             Priors for the fundamental frequencies of the
                        Solar System, using the formulas in Table 2 of
                        Hoang et al. (2021)
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
linage                  Tune stratigraphic series to an astronomical
                        target using graphical interface
linterp                 Piecewise linear interpolation of stratigraphic
                        series
linterpLH13             Piecewise linear interpolation of stratigraphic
                        series using the approach of Laepple and
                        Huybers (2013)
logT                    Log transformation of stratigraphic series
lowpass                 Lowpass filter stratigraphic series
lowspec                 Robust Locally-Weighted Regression Spectral
                        Background Estimation
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'
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
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
noKernel                Remove Gaussian kernel smoother from
                        stratigraphic series
noLow                   Fit and remove Lowess smoother from
                        stratigraphic series
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
plS                     Set default plotting parameters for vertical
                        stratigraphic plots
plotEha                 Create color time-frequency plots from eha
                        results.
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
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                       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.
stratPCA                Principal Component Analysis on Stratigraphic
                        Series
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
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).
timeOpt                 TimeOpt: Evaluation of eccentricity-related
                        amplitude modulation and bundling in
                        paleoclimate data
timeOptB                TimeOptB: A Bayesian implementation of TimeOpt
                        that calculates posterior PDFs for precession
                        frequency and sedimentation rate
timeOptBMCMC            TimeOptBMCMC: A Bayesian implementation of
                        TimeOpt that calculates posterior PDFs for
                        precession frequency, sedimentation rate, and
                        Solar System g- and s-frequencies, using
                        adaptive MCMC
timeOptBMCMCplot        TimeOptBMCMCplot: Generate summary figures and
                        statistics for TimeOptBMCMC results
timeOptBSim             TimeOptBSim: Significance testing via Monte
                        Carlo simulation for TimeOptB
timeOptMCMC             TimeOptMCMC: A Bayesian implementation of
                        TimeOpt that evaluates eccentricity-related
                        amplitude modulation and bundling in
                        paleoclimate data, 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
unbioturb               Bioturbation removal function following the
                        approach of Liu et al (2021)
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).
xplot                   Generate cross-plot with kernel density
                        estimates on axes
zoomIn                  Dynamically explore cross-plot, zoom-in into
                        specified region
