Package: astrochron 1.4

Stephen Meyers

astrochron: A Computational Tool for Astrochronology

Routines for astrochronologic testing, astronomical time scale construction, and time series analysis <doi:10.1016/j.earscirev.2018.11.015>. Also included are a range of statistical analysis and modeling routines that are relevant to time scale development and paleoclimate analysis.

Authors:Stephen Meyers [aut, cre], Alberto Malinverno [ctb], Linda Hinnov [ctb], Christian Zeeden [ctb], Huaran Liu [ctb], Vincent Moron [ctb], Michel Crucifix [ctb]

astrochron_1.4.tar.gz
astrochron_1.4.tar.gz(r-4.5-noble)astrochron_1.4.tar.gz(r-4.4-noble)
astrochron_1.4.tgz(r-4.4-emscripten)astrochron_1.4.tgz(r-4.3-emscripten)
astrochron.pdf |astrochron.html✨
astrochron/json (API)
NEWS

# Install 'astrochron' in R:

install.packages('astrochron', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

modelA - Example stratigraphic model series

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

fortran

3.96 score 6 stars 153 scripts 652 downloads 5 mentions 127 exports 14 dependencies

Last updated 3 months agofrom:5a07dee10c. Checks:OK: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 17 2024
R-4.5-linux-x86_64	OK	Dec 17 2024

Exports:accum anchorTime ar1 ar1etp arcsinT armaGen asm autoPlot bandpass bergerPeriods bicoherence bioturb calcPeriods cb clipIt confAdjust constantSedrate conv_fft cosTaper cycles deconv delPts demean detrend diffAccum divTrend dpssTaper eAsm eAsmTrack eha eTimeOpt eTimeOptTrack etp extract flip freq2sedrate gausTaper getColor getData getLaskar hannTaper headn hilbert idPts imbrie impulseResponse insoDiff insoMap insoSeries integratePower iso linage linterp linterpLH13 logT lowpass lowspec makeNoise mtm mtmAR mtmML96 mtmPL multiTest mwCor mwin mwinGrid mwMinMax mwStats mwStatsGrid noKernel noLow pad peak periodogram pl plotEha plS prewhiteAR prewhiteAR1 pwrLaw pwrLawFit rankSeries read readMatrix repl0 replEps resample rmNA s sedRamp sedrate2time slideCor sortNave stepHeat stratPCA strats surrogateCor surrogates synthStrat taner tanerFC testBackground testPrecession testTilt timeOpt timeOptMCMC timeOptPlot timeOptSim timeOptSimPwrLaw timeOptTemplate timeOptTemplatePlot timeOptTemplateSim tones traceFreq tracePeak trackFreq trackPeak trim trimAT trough tune unbioturb writeCSV writeT wtMean xplot zoomIn

Dependencies:codetools doParallel dotCall64 fields foreach IDPmisc iterators lattice maps multitaper palinsol Rcpp spam viridisLite

Help page	Topics
astrochron: A Computational Tool for Astrochronology	astrochron-package astrochron
Calculate geochemical proxy accumulation rates	accum
Anchor a floating astrochronology to a radioisotopic age	anchorTime
Generate AR(1) surrogates	ar1
AR(1) + ETP simulation routine	ar1etp
Arcsine transformation of stratigraphic series	arcsinT
Generate autoregressive moving-average model	armaGen
Average Spectral Misfit	asm
Automatically plot multiple stratigraphic series, with smoothing if desired	autoPlot
Bandpass filter stratigraphic series	bandpass
Obliquity and precession periods of Berger et al. (1992)	bergerPeriods
bicoherence: Calculate bispectrum and bicoherence using WOSA method as detailed in Choudhury et al. (2008).	bicoherence
Bioturbate time series using diffusion model from Guinasso and Schinck (1975), as in Liu et al. (2021)	bioturb
Calculate eccentricity, obliquity and precession periods in ka, given g, s and k in arcsec/yr	calcPeriods
Combine multiple vectors	cb
Create non-linear response by clipping stratigraphic series	clipIt
Adjust spectrum confidence levels for multiple comparisons	confAdjust
Apply a constant sedimentation rate model to transform a spatial series to temporal series	constantSedrate
Convolution through Fast Fourier Transform	conv_fft
Apply cosine taper to stratigraphic series	cosTaper
Generate harmonic model	cycles
Wiener Deconvolution through Fast Fourier Transform	deconv
Interactively delete points in plot	delPts
Remove mean value from stratigraphic series	demean
Subtract linear trend from stratigraphic series	detrend
Model differential accumulation	diffAccum
Divide by linear trend in stratigraphic series	divTrend
Apply DPSS taper to stratigraphic series	dpssTaper
Evolutive Average Spectral Misfit	eAsm
Track ASM null hypothesis significance level minima in eASM results	eAsmTrack
Evolutive Harmonic Analysis & Evolutive Power Spectral Analysis	eha
eTimeOpt: Evolutive implementation of TimeOpt (Meyers, 2015; Meyers, 2019)	eTimeOpt
Track eTimeOpt r2 maxima	eTimeOptTrack
Generate eccentricity-tilt-precession models	etp
Extract record from EHA time-frequency output or eAsm output	extract
Flip stratigraphic series	flip
Convert record of local spatial frequency (from EHA) to sedimentation rate curve	freq2sedrate
Apply Gaussian taper to stratigraphic series	gausTaper
Query R for color information	getColor
Download file from astrochron data server	getData
Download Laskar et al. (2004, 2011a, 2011b) astronomical solutions	getLaskar
Apply Hann taper to stratigraphic series	hannTaper
List column numbers for each variable	headn
Hilbert transform of stratigraphic series	hilbert
Interactively identify points in plot	idPts
Imbrie and Imbrie (1980) ice sheet model	imbrie
Impulse response function calculation	impulseResponse
insolation difference map using Laskar et al. (2004) insolation calculations	insoDiff
generate an insolation map using Laskar et al. (2004) insolation calculations	insoMap
Laskar et al. (2004) insolation calculations	insoSeries
Determine the total power within a given bandwidth	integratePower
Isolate data from a specified stratigraphic interval	iso
Tune stratigraphic series to an astronomical target using graphical interface	linage
Piecewise linear interpolation of stratigraphic series	linterp
Piecewise linear interpolation of stratigraphic series using the approach of Laepple and Huybers (2013)	linterpLH13
Log transformation of stratigraphic series	logT
Lowpass filter stratigraphic series	lowpass
Robust Locally-Weighted Regression Spectral Background Estimation	lowspec
Generate noise surrogates from a theoretical power spectrum	makeNoise
Example stratigraphic model series	modelA
Multitaper method spectral analysis	mtm
Intermediate spectrum test of Thomson et al. (2001)	mtmAR
Mann and Lees (1996) robust red noise MTM analysis	mtmML96
Multitaper Method Spectral Analysis with Power Law (1/f) fit	mtmPL
Adjust spectral p-values for multiple comparisons	multiTest
Calculate moving window correlation coefficient for two stratigraphic series, using a 'dynamic window'	mwCor
Determine 'dynamic moving window' for stratigraphic series, adjusting for changing sample density to maintain a window of constant duration	mwin
Determine 'dynamic moving window' for stratigraphic series, adjusting for changing sample density to maintain a window of constant duration; output on evenly spaced grid	mwinGrid
'Dynamic window' moving assessment of maxima and minima in stratigraphic series	mwMinMax
'Dynamic window' moving average, median and variance of stratigraphic series	mwStats
'Dynamic window' moving average, median and variance of stratigraphic series, using evenly spaced spatial/temporal grid	mwStatsGrid
Remove Gaussian kernel smoother from stratigraphic series	noKernel
Fit and remove Lowess smoother from stratigraphic series	noLow
Pad stratigraphic series with zeros	pad
Identify maxima of peaks in series, filter at desired threshold value	peak
Simple periodogram	periodogram
Set up plots	pl
Create color time-frequency plots from eha results.	plotEha
Set default plotting parameters for vertical stratigraphic plots	plS
Prewhiten stratigraphic series with autoregressive filter, order selected by Akaike Information Criterion	prewhiteAR
Prewhiten stratigraphic series with AR1 filter, using 'standard' or unbiased estimate of rho	prewhiteAR1
Generate power law (1/f) noise surrogates	pwrLaw
Estimate power law (1/f) fit to power spectrum	pwrLawFit
Create lithofacies rank series from bed thickness data	rankSeries
Read data from file	read
Read data matrix from file	readMatrix
Replace values < 0 with 0	repl0
Replace values <= 0 with smallest positive value	replEps
Resample stratigraphic series	resample
Remove stratigraphic levels that contain one or more NAs	rmNA
Standardize variable in stratigraphic series	s
Apply 'ramping' sedimentation rate model to convert time to stratigraphy	sedRamp
Integrate sedimentation rate curve to obtain time-space map	sedrate2time
Identify optimal spatial/temporal shift to maximize correlation between two stratigraphic/time series.	slideCor
Remove missing entries, sort data, average duplicates	sortNave
Ar/Ar Geochronology: Generate an Ar/Ar age spectrum and calculate step-heating plateau age.	stepHeat
Principal Component Analysis on Stratigraphic Series	stratPCA
Summary statistics for stratigraphic series	strats
Estimate correlation coefficient and significance for serially correlated data	surrogateCor
Generate phase-randomized surrogate series as in Ebisuzaki (1997)	surrogates
Synthesize stratigraphy from forcing function	synthStrat
Apply Taner bandpass or lowpass filter to stratigraphic series	taner
Apply Taner bandpass or lowpass filter to Fourier coefficients	tanerFC
Evaluate power spectrum false positive rates via Monte Carlo simulation	testBackground
Astrochronologic testing via the precession amplitude modulation approach of Zeeden et al. (2015).	testPrecession
Astrochronologic testing via the obliquity amplitude modulation approach of Zeeden et al. (2019 submitted).	testTilt
TimeOpt: Evaluation of eccentricity-related amplitude modulation and bundling in paleoclimate data	timeOpt
TimeOptMCMC: Evaluation of eccentricity-related amplitude modulation and bundling in paleoclimate data ("TimeOpt"), with uncertainties via Markov-Chain Monte Carlo	timeOptMCMC
TimeOptPlot: Generate summary figure for TimeOpt analyses	timeOptPlot
Monte Carlo simulation for TimeOpt	timeOptSim
Monte Carlo simulation for TimeOpt, using power law (1/f) noise	timeOptSimPwrLaw
TimeOpt analysis using variable sedimentation models	timeOptTemplate
TimeOptTemplatePlot: Generate summary figure for TimeOptTemplate analyses	timeOptTemplatePlot
Simulations for timeOptTemplate	timeOptTemplateSim
Calculate all possible difference and combinations tones	tones
Frequency-domain minimal tuning: Use interactive graphical interface to trace frequency drift	traceFreq
A tool to interactively trace peak trajectories on plots	tracePeak
Frequency-domain minimal tuning: Use interactive graphical interface and sorting to track frequency drift	trackFreq
A tool to interactively select points to track peak trajectories on plots	trackPeak
Remove outliers from stratigraphic series	trim
Remove outliers from stratigraphic series	trimAT
Identify minima of troughs in series, filter at desired threshold value	trough
Tune stratigraphic series	tune
Bioturbation removal function following the approach of Liu et al (2021)	unbioturb
Write CSV file	writeCSV
Write tab-delimited file	writeT
Ar/Ar Geochronology: calculate weighted mean age, age uncertainty, and other associated statistics/plots (with interactive graphics for data culling).	wtMean
Generate cross-plot with kernel density estimates on axes	xplot
Dynamically explore cross-plot, zoom-in into specified region	zoomIn

Package: astrochron 1.4

astrochron: A Computational Tool for Astrochronology

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