A B C D E F G H I L M N P R S T U W X Z

astrochron-package | astrochron: A Computational Tool for Astrochronology |

anchorTime | Anchor a floating astrochronology to a radioisotopic age |

ar1 | Generate AR(1) surrogates |

ar1etp | AR(1) + ETP simulation routine |

arcsinT | Arcsine transformation of stratigraphic series |

armaGen | Generate autoregressive moving-average model |

asm | Average Spectral Misfit |

astrochron | astrochron: A Computational Tool for Astrochronology |

autoPlot | Automatically plot multiple stratigraphic series, with smoothing if desired |

bandpass | Bandpass filter stratigraphic series |

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

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

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

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

cb | Combine multiple vectors |

clipIt | Create non-linear response by clipping stratigraphic series |

confAdjust | Adjust spectrum confidence levels for multiple comparisons |

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

conv_fft | Convolution through Fast Fourier Transform |

cosTaper | Apply cosine taper to stratigraphic series |

cycles | Generate harmonic model |

deconv | Wiener Deconvolution through Fast Fourier Transform |

delPts | Interactively delete points in plot |

demean | Remove mean value from stratigraphic series |

detrend | Subtract linear trend from stratigraphic series |

diffAccum | Model differential accumulation |

divTrend | Divide by linear trend in stratigraphic series |

dpssTaper | Apply DPSS taper to stratigraphic series |

eAsm | Evolutive Average Spectral Misfit |

eAsmTrack | Track ASM null hypothesis significance level minima in eASM results |

eha | Evolutive Harmonic Analysis & Evolutive Power Spectral Analysis |

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

eTimeOptTrack | Track eTimeOpt r2 maxima |

etp | Generate eccentricity-tilt-precession models |

extract | Extract record from EHA time-frequency output or eAsm output |

flip | Flip stratigraphic series |

freq2sedrate | Convert record of local spatial frequency (from EHA) to sedimentation rate curve |

gausTaper | Apply Gaussian taper to stratigraphic series |

getColor | Query R for color information |

getData | Download file from astrochron data server |

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

hannTaper | Apply Hann taper to stratigraphic series |

headn | List column numbers for each variable |

hilbert | Hilbert transform of stratigraphic series |

idPts | Interactively identify points in plot |

imbrie | Imbrie and Imbrie (1980) ice sheet model |

impulseResponse | Impulse response function calculation |

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

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

insoSeries | Laskar et al. (2004) insolation calculations |

integratePower | Determine the total power within a given bandwidth |

iso | Isolate data from a specified stratigraphic interval |

linage | Tune stratigraphic series to an astronomical target using graphical interface |

linterp | Piecewise linear interpolation of stratigraphic series |

logT | Log transformation of stratigraphic series |

lowpass | Lowpass filter stratigraphic series |

lowspec | Robust Locally-Weighted Regression Spectral Background Estimation |

makeNoise | Generate noise surrogates from a theoretical power spectrum |

modelA | Example stratigraphic model series |

mtm | Multitaper method spectral analysis |

mtmAR | Intermediate spectrum test of Thomson et al. (2001) |

mtmML96 | Mann and Lees (1996) robust red noise MTM analysis |

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

multiTest | Adjust spectral p-values for multiple comparisons |

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

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

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 |

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

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

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

noKernel | Remove Gaussian kernel smoother from stratigraphic series |

noLow | Fit and remove Lowess smoother from stratigraphic series |

pad | Pad stratigraphic series with zeros |

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

periodogram | Simple periodogram |

pl | Set up plots |

plotEha | Create color time-frequency plots from eha results. |

plS | Set default plotting parameters for vertical stratigraphic plots |

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

prewhiteAR1 | Prewhiten stratigraphic series with AR1 filter, using 'standard' or unbiased estimate of rho |

pwrLaw | Generate power law (1/f) noise surrogates |

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

rankSeries | Create lithofacies rank series from bed thickness data |

read | Read data from file |

readMatrix | Read data matrix from file |

repl0 | Replace values < 0 with 0 |

replEps | Replace values <= 0 with smallest positive value |

resample | Resample stratigraphic series |

rmNA | Remove stratigraphic levels that contain one or more NAs |

s | Standardize variable in stratigraphic series |

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

sedrate2time | Integrate sedimentation rate curve to obtain time-space map |

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

sortNave | Remove missing entries, sort data, average duplicates |

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

stratPCA | Principal Component Analysis on Stratigraphic Series |

strats | Summary statistics for stratigraphic series |

surrogateCor | Estimate correlation coefficient and significance for serially correlated data |

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

synthStrat | Synthesize stratigraphy from forcing function |

taner | Apply Taner bandpass or lowpass filter to stratigraphic series |

tanerFC | Apply Taner bandpass or lowpass filter to Fourier coefficients |

testBackground | Evaluate power spectrum false positive rates via Monte Carlo simulation |

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

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

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

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

timeOptPlot | TimeOptPlot: Generate summary figure for TimeOpt analyses |

timeOptSim | Monte Carlo simulation for TimeOpt |

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

timeOptTemplate | TimeOpt analysis using variable sedimentation models |

timeOptTemplatePlot | TimeOptTemplatePlot: Generate summary figure for TimeOptTemplate analyses |

timeOptTemplateSim | Simulations for timeOptTemplate |

tones | Calculate all possible difference and combinations tones |

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

tracePeak | A tool to interactively trace peak trajectories on plots |

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

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

trim | Remove outliers from stratigraphic series |

trimAT | Remove outliers from stratigraphic series |

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

tune | Tune stratigraphic series |

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

writeCSV | Write CSV file |

writeT | Write tab-delimited file |

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

xplot | Generate cross-plot with kernel density estimates on axes |

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