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astrochron (version 1.2)

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

1.2

License

GPL-3

Maintainer

Stephen Meyers

Last Published

August 26th, 2023

Functions in astrochron (1.2)

Adjust spectrum confidence levels for multiple comparisons

constantSedrate

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

Wiener Deconvolution through Fast Fourier Transform

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

Subtract linear trend from stratigraphic series

Track ASM null hypothesis significance level minima in eASM results

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

Remove mean value from stratigraphic series

Generate harmonic model

Apply DPSS taper to stratigraphic series

Convolution through Fast Fourier Transform

Track eTimeOpt r2 maxima

Apply cosine taper to stratigraphic series

Evolutive Average Spectral Misfit

Download file from astrochron data server

Model differential accumulation

Divide by linear trend in stratigraphic series

Apply Gaussian taper to stratigraphic series

Evolutive Harmonic Analysis & Evolutive Power Spectral Analysis

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

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

Flip stratigraphic series

List column numbers for each variable

Query R for color information

Apply Hann taper to stratigraphic series

Tune stratigraphic series to an astronomical target using graphical interface

Interactively delete points in plot

Isolate data from a specified stratigraphic interval

Hilbert transform of stratigraphic series

Piecewise linear interpolation of stratigraphic series

Log transformation of stratigraphic series

Interactively identify points in plot

impulseResponse

Impulse response function calculation

Generate eccentricity-tilt-precession models

Mann and Lees (1996) robust red noise MTM analysis

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

Imbrie and Imbrie (1980) ice sheet model

Multitaper method spectral analysis

Laskar et al. (2004) insolation calculations

Lowpass filter stratigraphic series

Determine the total power within a given bandwidth

Extract record from EHA time-frequency output or eAsm output

Generate noise surrogates from a theoretical power spectrum

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

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

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

Robust Locally-Weighted Regression Spectral Background Estimation

Intermediate spectrum test of Thomson et al. (2001)

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

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

Adjust spectral p-values for multiple comparisons

Generate power law (1/f) noise surrogates

Remove Gaussian kernel smoother from stratigraphic series

Determine 'dynamic moving window' for stratigraphic series, adjusting for changing sample density to maintain a window of constant duration; output on evenly spaced grid

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

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

Example stratigraphic model series

Create lithofacies rank series from bed thickness data

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

Set default plotting parameters for vertical stratigraphic plots

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

Create color time-frequency plots from eha results.

Integrate sedimentation rate curve to obtain time-space map

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

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

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

Simple periodogram

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

Evaluate power spectrum false positive rates via Monte Carlo simulation

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

Pad stratigraphic series with zeros

Fit and remove Lowess smoother from stratigraphic series

Read data from file

Replace values < 0 with 0

Remove missing entries, sort data, average duplicates

Replace values <= 0 with smallest positive value

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

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

timeOptTemplate

TimeOpt analysis using variable sedimentation models

Remove outliers from stratigraphic series

Remove outliers from stratigraphic series

timeOptTemplatePlot

TimeOptTemplatePlot: Generate summary figure for TimeOptTemplate analyses

Standardize variable in stratigraphic series

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

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

Synthesize stratigraphy from forcing function

Generate cross-plot with kernel density estimates on axes

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

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

Tune stratigraphic series

A tool to interactively trace peak trajectories on plots

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

TimeOptPlot: Generate summary figure for TimeOpt analyses

Apply Taner bandpass or lowpass filter to stratigraphic series

Apply Taner bandpass or lowpass filter to Fourier coefficients

Resample stratigraphic series

Summary statistics for stratigraphic series

Estimate correlation coefficient and significance for serially correlated data

Remove stratigraphic levels that contain one or more NAs

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

Read data matrix from file

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

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

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

Monte Carlo simulation for TimeOpt

timeOptSimPwrLaw

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

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

Write tab-delimited file

timeOptTemplateSim

Simulations for timeOptTemplate

Calculate all possible difference and combinations tones

Average Spectral Misfit

Generate autoregressive moving-average model

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

Anchor a floating astrochronology to a radioisotopic age

astrochron-package

astrochron: A Computational Tool for Astrochronology

Bandpass filter stratigraphic series

Automatically plot multiple stratigraphic series, with smoothing if desired

Combine multiple vectors

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

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

Generate AR(1) surrogates

Arcsine transformation of stratigraphic series

Create non-linear response by clipping stratigraphic series

AR(1) + ETP simulation routine