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astrochron (version 1.5)

A Computational Tool for Astrochronology

Description

Routines for astrochronologic testing, astronomical time scale construction, and time series analysis . Also included are a range of statistical analysis and modeling routines that are relevant to time scale development and paleoclimate analysis.

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Install

install.packages('astrochron')

Monthly Downloads

1,095

Version

1.5

License

GPL-3

Maintainer

Stephen Meyers

Last Published

April 28th, 2025

Functions in astrochron (1.5)

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)
calcPeriods

Calculate eccentricity, obliquity and precession periods in ka, given g, s and k in arcsec/yr
conv_fft

Convolution through Fast Fourier Transform
constantSedrate

Apply a constant sedimentation rate model to transform a spatial series to temporal series
detrend

Subtract linear trend from stratigraphic series
eAsm

Evolutive Average Spectral Misfit
delPts

Interactively delete points in plot
demean

Remove mean value from stratigraphic series
eha

Evolutive Harmonic Analysis & Evolutive Power Spectral Analysis
etp

Generate eccentricity-tilt-precession models
diffAccum

Model differential accumulation
eAsmTrack

Track ASM null hypothesis significance level minima in eASM results
getData

Download file from astrochron data server
deconv

Wiener Deconvolution through Fast Fourier Transform
cycles

Generate harmonic model
getColor

Query R for color information
getLaskar

Download Laskar et al. (2004, 2011a, 2011b) astronomical solutions
extract

Extract record from EHA time-frequency output or eAsm output
headn

List column numbers for each variable
hannTaper

Apply Hann taper to stratigraphic series
hilbert

Hilbert transform of stratigraphic series
flip

Flip stratigraphic series
eTimeOpt

eTimeOpt: Evolutive implementation of TimeOpt (Meyers, 2015; Meyers, 2019)
cosTaper

Apply cosine taper to stratigraphic series
impulseResponse

Impulse response function calculation
dpssTaper

Apply DPSS taper to stratigraphic series
divTrend

Divide by linear trend in stratigraphic series
insoDiff

insolation difference map using Laskar et al. (2004) insolation calculations
insoMap

generate an insolation map using Laskar et al. (2004) insolation calculations
idPts

Interactively identify points in plot
gausTaper

Apply Gaussian taper to stratigraphic series
freq2sedrate

Convert record of local spatial frequency (from EHA) to sedimentation rate curve
imbrie

Imbrie and Imbrie (1980) ice sheet model
integratePower

Determine the total power within a given bandwidth
linterpLH13

Piecewise linear interpolation of stratigraphic series using the approach of Laepple and Huybers (2013)
eTimeOptTrack

Track eTimeOpt r2 maxima
logT

Log transformation of stratigraphic series
makeNoise

Generate noise surrogates from a theoretical power spectrum
iso

Isolate data from a specified stratigraphic interval
mwStatsGrid

'Dynamic window' moving average, median and variance of stratigraphic series, using evenly spaced spatial/temporal grid
modelA

Example stratigraphic model series
mtmPL

Multitaper Method Spectral Analysis with Power Law (1/f) fit
mwin

Determine 'dynamic moving window' for stratigraphic series, adjusting for changing sample density to maintain a window of constant duration
mtmML96

Mann and Lees (1996) robust red noise MTM analysis
linage

Tune stratigraphic series to an astronomical target using graphical interface
mwStats

'Dynamic window' moving average, median and variance of stratigraphic series
mwMinMax

'Dynamic window' moving assessment of maxima and minima in stratigraphic series
insoSeries

Laskar et al. (2004) insolation calculations
linterp

Piecewise linear interpolation of stratigraphic series
peak

Identify maxima of peaks in series, filter at desired threshold value
pl

Set up plots
mtm

Multitaper method spectral analysis
noKernel

Remove Gaussian kernel smoother from stratigraphic series
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
lowpass

Lowpass filter stratigraphic series
rankSeries

Create lithofacies rank series from bed thickness data
plotEha

Create color time-frequency plots from eha results.
mtmAR

Intermediate spectrum test of Thomson et al. (2001)
prewhiteAR

Prewhiten stratigraphic series with autoregressive filter, order selected by Akaike Information Criterion
pwrLawFit

Estimate power law (1/f) fit to power spectrum
replEps

Replace values <= 0 with smallest positive value
prewhiteAR1

Prewhiten stratigraphic series with AR1 filter, using 'standard' or unbiased estimate of rho
pwrLaw

Generate power law (1/f) noise surrogates
repl0

Replace values < 0 with 0
sortNave

Remove missing entries, sort data, average duplicates
plS

Set default plotting parameters for vertical stratigraphic plots
stepHeat

Ar/Ar Geochronology: Generate an Ar/Ar age spectrum and calculate step-heating plateau age.
stratPCA

Principal Component Analysis on Stratigraphic Series
sedrate2time

Integrate sedimentation rate curve to obtain time-space map
lowspec

Robust Locally-Weighted Regression Spectral Background Estimation
multiTest

Adjust spectral p-values for multiple comparisons
mwCor

Calculate moving window correlation coefficient for two stratigraphic series, using a 'dynamic window'
slideCor

Identify optimal spatial/temporal shift to maximize correlation between two stratigraphic/time series.
periodogram

Simple periodogram
s

Standardize variable in stratigraphic series
read

Read data from file
sedRamp

Apply 'ramping' sedimentation rate model to convert time to stratigraphy
strats

Summary statistics for stratigraphic series
noLow

Fit and remove Lowess smoother from stratigraphic series
readMatrix

Read data matrix from file
pad

Pad stratigraphic series with zeros
resample

Resample stratigraphic series
timeOptPlot

TimeOptPlot: Generate summary figure for TimeOpt analyses
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).
tanerFC

Apply Taner bandpass or lowpass filter to Fourier coefficients
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
surrogates

Generate phase-randomized surrogate series as in Ebisuzaki (1997)
surrogateCor

Estimate correlation coefficient and significance for serially correlated data
taner

Apply Taner bandpass or lowpass filter to stratigraphic series
rmNA

Remove stratigraphic levels that contain one or more NAs
synthStrat

Synthesize stratigraphy from forcing function
timeOptTemplate

TimeOpt analysis using variable sedimentation models
timeOptTemplateSim

Simulations for timeOptTemplate
timeOptSim

Monte Carlo simulation for TimeOpt
timeOptSimPwrLaw

Monte Carlo simulation for TimeOpt, using power law (1/f) noise
trim

Remove outliers from stratigraphic series
testBackground

Evaluate power spectrum false positive rates via Monte Carlo simulation
trackPeak

A tool to interactively select points to track peak trajectories on plots
timeOptTemplatePlot

TimeOptTemplatePlot: Generate summary figure for TimeOptTemplate analyses
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
zoomIn

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

Tune stratigraphic series
wtMean

Ar/Ar Geochronology: calculate weighted mean age, age uncertainty, and other associated statistics/plots (with interactive graphics for data culling).
unbioturb

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

Calculate all possible difference and combinations tones
writeT

Write tab-delimited file
xplot

Generate cross-plot with kernel density estimates on axes
traceFreq

Frequency-domain minimal tuning: Use interactive graphical interface to trace frequency drift
writeCSV

Write CSV file
trimAT

Remove outliers from stratigraphic series
trough

Identify minima of troughs in series, filter at desired threshold value
anchorTime

Anchor a floating astrochronology to a radioisotopic age
arcsinT

Arcsine transformation of stratigraphic series
ar1etp

AR(1) + ETP simulation routine
bandpass

Bandpass filter stratigraphic series
astrochron-package

astrochron: A Computational Tool for Astrochronology
armaGen

Generate autoregressive moving-average model
asm

Average Spectral Misfit
accum

Calculate geochemical proxy accumulation rates
autoPlot

Automatically plot multiple stratigraphic series, with smoothing if desired
ar1

Generate AR(1) surrogates
clipIt

Create non-linear response by clipping stratigraphic series
cb

Combine multiple vectors
confAdjust

Adjust spectrum confidence levels for multiple comparisons
bicoherence

bicoherence: Calculate bispectrum and bicoherence using WOSA method as detailed in Choudhury et al. (2008).