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astrochron (version 1.1)

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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Version

Install

install.packages('astrochron')

Monthly Downloads

799

Version

1.1

License

GPL-3

Maintainer

Stephen Meyers

Last Published

October 5th, 2021

Functions in astrochron (1.1)

ar1

Generate AR(1) surrogates
ar1etp

AR(1) + ETP simulation routine
asm

Average Spectral Misfit
astrochron-package

astrochron: A Computational Tool for Astrochronology
autoPlot

Automatically plot multiple stratigraphic series, with smoothing if desired
arcsinT

Arcsine transformation of stratigraphic series
armaGen

Generate autoregressive moving-average model
bandpass

Bandpass filter stratigraphic series
anchorTime

Anchor a floating astrochronology to a radioisotopic age
bergerPeriods

Obliquity and precession periods of Berger et al. (1992)
confAdjust

Adjust spectrum confidence levels for multiple comparisons
calcPeriods

Calculate eccentricity and precession periods in ka, given g and k in arcsec/yr
bioturb

Bioturbate time series using diffusion model from Guinasso and Schinck (1975), as in Liu et al. (2021)
constantSedrate

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

Model differential accumulation
detrend

Subtract linear trend from stratigraphic series
cosTaper

Apply cosine taper to stratigraphic series
conv_fft

Convolution through Fast Fourier Transform
eha

Evolutive Harmonic Analysis & Evolutive Power Spectral Analysis
etp

Generate eccentricity-tilt-precession models
cycles

Generate harmonic model
eTimeOpt

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

Create non-linear response by clipping stratigraphic series
demean

Remove mean value from stratigraphic series
delPts

Interactively delete points in plot
cb

Combine multiple vectors
eTimeOptTrack

Track eTimeOpt r2 maxima
hannTaper

Apply Hann taper to stratigraphic series
imbrie

Imbrie and Imbrie (1980) ice sheet model
getLaskar

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

Interactively identify points in plot
extract

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

Flip stratigraphic series
deconv

Wiener Deconvolution through Fast Fourier Transform
divTrend

Divide by linear trend in stratigraphic series
eAsm

Evolutive Average Spectral Misfit
dpssTaper

Apply DPSS taper to stratigraphic series
logT

Log transformation of stratigraphic series
linterp

Piecewise linear interpolation of stratigraphic series
linage

Tune stratigraphic series to an astronomical target using graphical interface
mwCor

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

Apply Gaussian taper to stratigraphic series
multiTest

Adjust spectral p-values for multiple comparisons
iso

Isolate data from a specified stratigraphic interval
freq2sedrate

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

List column numbers for each variable
hilbert

Hilbert transform of stratigraphic series
eAsmTrack

Track ASM null hypothesis significance level minima in eASM results
getData

Download file from astrochron data server
getColor

Query R for color information
impulseResponse

Impulse response function calculation
noLow

Fit and remove Lowess smoother from stratigraphic series
pad

Pad stratigraphic series with zeros
lowpass

Lowpass filter stratigraphic series
mtmML96

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

Determine the total power within a given bandwidth
repl0

Replace values < 0 with 0
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
lowspec

Robust Locally-Weighted Regression Spectral Background Estimation
replEps

Replace values <= 0 with smallest positive value
mtmPL

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

Multitaper method spectral analysis
timeOptPlot

TimeOptPlot: Generate summary figure for TimeOpt analyses
sedRamp

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

Standardize variable in stratigraphic series
rankSeries

Create lithofacies rank series from bed thickness data
mwin

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

Remove Gaussian kernel smoother from stratigraphic series
mwStatsGrid

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

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

TimeOptMCMC: Evaluation of eccentricity-related amplitude modulation and bundling in paleoclimate data ("TimeOpt"), with uncertainties via Markov-Chain Monte Carlo
timeOpt

TimeOpt: Evaluation of eccentricity-related amplitude modulation and bundling in paleoclimate data
peak

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

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

Create color time-frequency plots from eha results.
makeNoise

Generate noise surrogates from a theoretical power spectrum
xplot

Generate cross-plot with kernel density estimates on axes
timeOptSim

Monte Carlo simulation for TimeOpt
mwMinMax

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

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

TimeOptTemplatePlot: Generate summary figure for TimeOptTemplate analyses
periodogram

Simple periodogram
timeOptTemplateSim

Simulations for timeOptTemplate
prewhiteAR

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

Astrochronologic testing via the obliquity amplitude modulation approach of Zeeden et al. (2019 submitted).
stepHeat

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

Frequency-domain minimal tuning: Use interactive graphical interface and sorting to track frequency drift
tracePeak

A tool to interactively trace peak trajectories on plots
sortNave

Remove missing entries, sort data, average duplicates
testPrecession

Astrochronologic testing via the precession amplitude modulation approach of Zeeden et al. (2015).
taner

Apply Taner bandpass or lowpass filter to stratigraphic series
readMatrix

Read data matrix from file
read

Read data from file
testBackground

Evaluate power spectrum false positive rates via Monte Carlo simulation
trough

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

Remove outliers from stratigraphic series
modelA

Example stratigraphic model series
prewhiteAR1

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

Tune stratigraphic series
unbioturb

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

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

Generate power law (1/f) noise surrogates
pl

Set up plots
plS

Set default plotting parameters for vertical stratigraphic plots
sedrate2time

Integrate sedimentation rate curve to obtain time-space map
slideCor

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

Summary statistics for stratigraphic series
surrogateCor

Estimate correlation coefficient and significance for serially correlated data
rmNA

Remove stratigraphic levels that contain one or more NAs
resample

Resample stratigraphic series
surrogates

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

Calculate all possible difference and combinations tones
synthStrat

Synthesize stratigraphy from forcing function
timeOptSimPwrLaw

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

Write CSV file
zoomIn

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

Write tab-delimited file
timeOptTemplate

TimeOpt analysis using variable sedimentation models
traceFreq

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

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

Remove outliers from stratigraphic series