Learn R Programming

astrochron (version 1.4)

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.

Copy Link

Version

Install

install.packages('astrochron')

Monthly Downloads

751

Version

1.4

License

GPL-3

Maintainer

Last Published

September 17th, 2024

Functions in astrochron (1.4)

astrochron-package

astrochron: A Computational Tool for Astrochronology

Bandpass filter stratigraphic series

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

Subtract linear trend from stratigraphic series

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

Track ASM null hypothesis significance level minima in eASM results

Evolutive Average Spectral Misfit

Create non-linear response by clipping stratigraphic series

Combine multiple vectors

Model differential accumulation

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

Adjust spectrum confidence levels for multiple comparisons

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

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

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

Apply Gaussian taper to stratigraphic series

constantSedrate

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

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

AR(1) + ETP simulation routine

Query R for color information

Download file from astrochron data server

Generate harmonic model

Divide by linear trend in stratigraphic series

Interactively delete points in plot

Laskar et al. (2004) insolation calculations

Generate noise surrogates from a theoretical power spectrum

Example stratigraphic model series

Tune stratigraphic series to an astronomical target using graphical interface

Interactively identify points in plot

Piecewise linear interpolation of stratigraphic series

Apply Hann taper to stratigraphic series

'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

Apply DPSS taper to stratigraphic series

Remove mean value from stratigraphic series

Evolutive Harmonic Analysis & Evolutive Power Spectral Analysis

Generate eccentricity-tilt-precession models

Mann and Lees (1996) robust red noise MTM analysis

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

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

Track eTimeOpt r2 maxima

Wiener Deconvolution through Fast Fourier Transform

Fit and remove Lowess smoother from stratigraphic series

Pad stratigraphic series with zeros

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

Imbrie and Imbrie (1980) ice sheet model

List column numbers for each variable

Hilbert transform of stratigraphic series

Extract record from EHA time-frequency output or eAsm output

impulseResponse

Impulse response function calculation

Flip stratigraphic series

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

Determine the total power within a given bandwidth

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

Log transformation of stratigraphic series

Isolate data from a specified stratigraphic interval

Multitaper method spectral analysis

Create color time-frequency plots from eha results.

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

Create lithofacies rank series from bed thickness data

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

Intermediate spectrum test of Thomson et al. (2001)

Principal Component Analysis on Stratigraphic Series

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

Summary statistics for stratigraphic series

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

Lowpass filter stratigraphic series

Robust Locally-Weighted Regression Spectral Background Estimation

Adjust spectral p-values for multiple comparisons

Replace values <= 0 with smallest positive value

Replace values < 0 with 0

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

Remove missing entries, sort data, average duplicates

Apply Taner bandpass or lowpass filter to Fourier coefficients

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

Read data from file

Evaluate power spectrum false positive rates via Monte Carlo simulation

timeOptSimPwrLaw

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

Integrate sedimentation rate curve to obtain time-space map

Read data matrix from file

Remove Gaussian kernel smoother from stratigraphic series

Standardize variable in stratigraphic series

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

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

TimeOptPlot: Generate summary figure for TimeOpt analyses

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

Generate power law (1/f) noise surrogates

Set default plotting parameters for vertical stratigraphic plots

timeOptTemplate

TimeOpt analysis using variable sedimentation models

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

Synthesize stratigraphy from forcing function

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

Monte Carlo simulation for TimeOpt

timeOptTemplatePlot

TimeOptTemplatePlot: Generate summary figure for TimeOptTemplate analyses

Resample stratigraphic series

Simple periodogram

Write tab-delimited file

Calculate all possible difference and combinations tones

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

Tune stratigraphic series

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

timeOptTemplateSim

Simulations for timeOptTemplate

A tool to interactively trace peak trajectories on plots

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

Remove outliers from stratigraphic series

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

Generate cross-plot with kernel density estimates on axes

Apply Taner bandpass or lowpass filter to stratigraphic series

Remove stratigraphic levels that contain one or more NAs

Estimate correlation coefficient and significance for serially correlated data

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

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

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

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

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

Remove outliers from stratigraphic series

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

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

Average Spectral Misfit

Generate AR(1) surrogates

Automatically plot multiple stratigraphic series, with smoothing if desired

Arcsine transformation of stratigraphic series

Calculate geochemical proxy accumulation rates

Generate autoregressive moving-average model

Anchor a floating astrochronology to a radioisotopic age

Convolution through Fast Fourier Transform

Apply cosine taper to stratigraphic series