Package: astrochron 1.7

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_1.7.tar.gz
astrochron_1.7.tar.gz(r-4.7-arm64)astrochron_1.7.tar.gz(r-4.7-x86_64)astrochron_1.7.tar.gz(r-4.6-arm64)astrochron_1.7.tar.gz(r-4.6-x86_64)
astrochron_1.7.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
astrochron/json (API)

# 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

On CRAN:

Conda:

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

glibc

4.39 score 6 stars 1 packages 136 scripts 609 downloads 5 mentions 132 exports 15 dependencies

Last updated from:ff44fdf3ba. Checks:6 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK166
linux-devel-x86_64OK176
source / vignettesOK182
linux-release-arm64OK180
linux-release-x86_64OK165
wasm-releaseOK149

Exports:accumanchorTimear1ar1etparcsinTarmaGenasmautoPlotbandpassbergerPeriodsbicoherencebioturbcalcPeriodscbclipItconfAdjustconstantSedrateconv_fftcosTapercyclesdeconvdelPtsdemeandetrenddiffAccumdivTrenddpssTapereAsmeAsmTrackehaeTimeOpteTimeOptTracketpextractflipfreq2sedrategausTapergetColorgetDatagetLaskarhannTaperheadnhilberthoangPriorsidPtsimbrieimpulseResponseinsoDiffinsoMapinsoSeriesintegratePowerisolinagelinterplinterpLH13logTlowpasslowspecmakeNoisemtmmtmARmtmML96mtmPLmultiTestmwCormwinmwinGridmwMinMaxmwStatsmwStatsGridnoKernelnoLowpadpeakperiodogramplplotEhaplSprewhiteARprewhiteAR1pwrLawpwrLawFitrankSeriesreadreadMatrixrepl0replEpsresamplermNAssedRampsedrate2timeslideCorsortNavestepHeatstratPCAstratssurrogateCorsurrogatessynthStrattanertanerFCtestBackgroundtestPrecessiontestTilttimeOpttimeOptBtimeOptBMCMCtimeOptBMCMCplottimeOptBSimtimeOptMCMCtimeOptPlottimeOptSimtimeOptSimPwrLawtimeOptTemplatetimeOptTemplatePlottimeOptTemplateSimtonestraceFreqtracePeaktrackFreqtrackPeaktrimtrimATtroughtuneunbioturbwriteCSVwriteTwtMeanxplotzoomIn

Dependencies:codetoolsdoParalleldotCall64fieldsforeachIDPmisciteratorslatticemapsmultitaperpalinsolRColorBrewerRcppspamviridisLite

Readme and manuals

Help Manual

Help pageTopics
astrochron: A Computational Tool for Astrochronologyastrochron-package astrochron
Calculate geochemical proxy accumulation ratesaccum
Anchor a floating astrochronology to a radioisotopic ageanchorTime
Generate AR(1) surrogatesar1
AR(1) + ETP simulation routinear1etp
Arcsine transformation of stratigraphic seriesarcsinT
Generate autoregressive moving-average modelarmaGen
Average Spectral Misfitasm
Automatically plot multiple stratigraphic series, with smoothing if desiredautoPlot
Bandpass filter stratigraphic seriesbandpass
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/yrcalcPeriods
Combine multiple vectorscb
Create non-linear response by clipping stratigraphic seriesclipIt
Adjust spectrum confidence levels for multiple comparisonsconfAdjust
Apply a constant sedimentation rate model to transform a spatial series to temporal seriesconstantSedrate
Convolution through Fast Fourier Transformconv_fft
Apply cosine taper to stratigraphic seriescosTaper
Generate harmonic modelcycles
Wiener Deconvolution through Fast Fourier Transformdeconv
Interactively delete points in plotdelPts
Remove mean value from stratigraphic seriesdemean
Subtract linear trend from stratigraphic seriesdetrend
Model differential accumulationdiffAccum
Divide by linear trend in stratigraphic seriesdivTrend
Apply DPSS taper to stratigraphic seriesdpssTaper
Evolutive Average Spectral MisfiteAsm
Track ASM null hypothesis significance level minima in eASM resultseAsmTrack
Evolutive Harmonic Analysis & Evolutive Power Spectral Analysiseha
eTimeOpt: Evolutive implementation of TimeOpt (Meyers, 2015; Meyers, 2019)eTimeOpt
Track eTimeOpt r2 maximaeTimeOptTrack
Generate eccentricity-tilt-precession modelsetp
Extract record from EHA time-frequency output or eAsm outputextract
Flip stratigraphic seriesflip
Convert record of local spatial frequency (from EHA) to sedimentation rate curvefreq2sedrate
Apply Gaussian taper to stratigraphic seriesgausTaper
Query R for color informationgetColor
Download file from astrochron data servergetData
Download Laskar et al. (2004, 2011a, 2011b) astronomical solutionsgetLaskar
Apply Hann taper to stratigraphic serieshannTaper
List column numbers for each variableheadn
Hilbert transform of stratigraphic serieshilbert
Priors for the fundamental frequencies of the Solar System, using the formulas in Table 2 of Hoang et al. (2021)hoangPriors
Interactively identify points in plotidPts
Imbrie and Imbrie (1980) ice sheet modelimbrie
Impulse response function calculationimpulseResponse
insolation difference map using Laskar et al. (2004) insolation calculationsinsoDiff
generate an insolation map using Laskar et al. (2004) insolation calculationsinsoMap
Laskar et al. (2004) insolation calculationsinsoSeries
Determine the total power within a given bandwidthintegratePower
Isolate data from a specified stratigraphic intervaliso
Tune stratigraphic series to an astronomical target using graphical interfacelinage
Piecewise linear interpolation of stratigraphic serieslinterp
Piecewise linear interpolation of stratigraphic series using the approach of Laepple and Huybers (2013)linterpLH13
Log transformation of stratigraphic serieslogT
Lowpass filter stratigraphic serieslowpass
Robust Locally-Weighted Regression Spectral Background Estimationlowspec
Generate noise surrogates from a theoretical power spectrummakeNoise
Example stratigraphic model seriesmodelA
Multitaper method spectral analysismtm
Intermediate spectrum test of Thomson et al. (2001)mtmAR
Mann and Lees (1996) robust red noise MTM analysismtmML96
Multitaper Method Spectral Analysis with Power Law (1/f) fitmtmPL
Adjust spectral p-values for multiple comparisonsmultiTest
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 durationmwin
Determine 'dynamic moving window' for stratigraphic series, adjusting for changing sample density to maintain a window of constant duration; output on evenly spaced gridmwinGrid
'Dynamic window' moving assessment of maxima and minima in stratigraphic seriesmwMinMax
'Dynamic window' moving average, median and variance of stratigraphic seriesmwStats
'Dynamic window' moving average, median and variance of stratigraphic series, using evenly spaced spatial/temporal gridmwStatsGrid
Remove Gaussian kernel smoother from stratigraphic seriesnoKernel
Fit and remove Lowess smoother from stratigraphic seriesnoLow
Pad stratigraphic series with zerospad
Identify maxima of peaks in series, filter at desired threshold valuepeak
Simple periodogramperiodogram
Set up plotspl
Create color time-frequency plots from eha results.plotEha
Set default plotting parameters for vertical stratigraphic plotsplS
Prewhiten stratigraphic series with autoregressive filter, order selected by Akaike Information CriterionprewhiteAR
Prewhiten stratigraphic series with AR1 filter, using 'standard' or unbiased estimate of rhoprewhiteAR1
Generate power law (1/f) noise surrogatespwrLaw
Estimate power law (1/f) fit to power spectrumpwrLawFit
Create lithofacies rank series from bed thickness datarankSeries
Read data from fileread
Read data matrix from filereadMatrix
Replace values < 0 with 0repl0
Replace values <= 0 with smallest positive valuereplEps
Resample stratigraphic seriesresample
Remove stratigraphic levels that contain one or more NAsrmNA
Standardize variable in stratigraphic seriess
Apply 'ramping' sedimentation rate model to convert time to stratigraphysedRamp
Integrate sedimentation rate curve to obtain time-space mapsedrate2time
Identify optimal spatial/temporal shift to maximize correlation between two stratigraphic/time series.slideCor
Remove missing entries, sort data, average duplicatessortNave
Ar/Ar Geochronology: Generate an Ar/Ar age spectrum and calculate step-heating plateau age.stepHeat
Principal Component Analysis on Stratigraphic SeriesstratPCA
Summary statistics for stratigraphic seriesstrats
Estimate correlation coefficient and significance for serially correlated datasurrogateCor
Generate phase-randomized surrogate series as in Ebisuzaki (1997)surrogates
Synthesize stratigraphy from forcing functionsynthStrat
Apply Taner bandpass or lowpass filter to stratigraphic seriestaner
Apply Taner bandpass or lowpass filter to Fourier coefficientstanerFC
Evaluate power spectrum false positive rates via Monte Carlo simulationtestBackground
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).testTilt
TimeOpt: Evaluation of eccentricity-related amplitude modulation and bundling in paleoclimate datatimeOpt
TimeOptB: A Bayesian implementation of TimeOpt that calculates posterior PDFs for precession frequency and sedimentation ratetimeOptB
TimeOptBMCMC: A Bayesian implementation of TimeOpt that calculates posterior PDFs for precession frequency, sedimentation rate, and Solar System g- and s-frequencies, using adaptive MCMCtimeOptBMCMC
TimeOptBMCMCplot: Generate summary figures and statistics for TimeOptBMCMC resultstimeOptBMCMCplot
TimeOptBSim: Significance testing via Monte Carlo simulation for TimeOptBtimeOptBSim
TimeOptMCMC: A Bayesian implementation of TimeOpt that evaluates eccentricity-related amplitude modulation and bundling in paleoclimate data, with uncertainties via Markov-Chain Monte CarlotimeOptMCMC
TimeOptPlot: Generate summary figure for TimeOpt analysestimeOptPlot
Monte Carlo simulation for TimeOpttimeOptSim
Monte Carlo simulation for TimeOpt, using power law (1/f) noisetimeOptSimPwrLaw
TimeOpt analysis using variable sedimentation modelstimeOptTemplate
TimeOptTemplatePlot: Generate summary figure for TimeOptTemplate analysestimeOptTemplatePlot
Simulations for timeOptTemplatetimeOptTemplateSim
Calculate all possible difference and combinations tonestones
Frequency-domain minimal tuning: Use interactive graphical interface to trace frequency drifttraceFreq
A tool to interactively trace peak trajectories on plotstracePeak
Frequency-domain minimal tuning: Use interactive graphical interface and sorting to track frequency drifttrackFreq
A tool to interactively select points to track peak trajectories on plotstrackPeak
Remove outliers from stratigraphic seriestrim
Remove outliers from stratigraphic seriestrimAT
Identify minima of troughs in series, filter at desired threshold valuetrough
Tune stratigraphic seriestune
Bioturbation removal function following the approach of Liu et al (2021)unbioturb
Write CSV filewriteCSV
Write tab-delimited filewriteT
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 axesxplot
Dynamically explore cross-plot, zoom-in into specified regionzoomIn