Package: WaverideR 0.3.2

WaverideR: Extracting Signals from Wavelet Spectra

The continuous wavelet transform enables the observation of transient/non-stationary cyclicity in time-series. The goal of cyclostratigraphic studies is to define frequency/period in the depth/time domain. By conducting the continuous wavelet transform on cyclostratigraphic data series one can observe and extract cyclic signals/signatures from signals. These results can then be visualized and interpreted enabling one to identify/interpret cyclicity in the geological record, which can be used to construct astrochronological age-models and identify and interpret cyclicity in past and present climate systems. The 'WaverideR' R package builds upon existing literature and existing codebase. The list of articles which are relevant can be grouped in four subjects; cyclostratigraphic data analysis,example data sets,the (continuous) wavelet transform and astronomical solutions. References for the cyclostratigraphic data analysis articles are: Stephen Meyers (2019) <doi:10.1016/j.earscirev.2018.11.015>. Mingsong Li, Linda Hinnov, Lee Kump (2019) <doi:10.1016/j.cageo.2019.02.011> Stephen Meyers (2012)<doi:10.1029/2012PA002307> Mingsong Li, Lee R. Kump, Linda A. Hinnov, Michael E. Mann (2018) <doi:10.1016/j.epsl.2018.08.041>. Wouters, S., Crucifix, M., Sinnesael, M., Da Silva, A.C., Zeeden, C., Zivanovic, M., Boulvain, F., Devleeschouwer, X. (2022) <doi:10.1016/j.earscirev.2021.103894>. Wouters, S., Da Silva, A.-C., Boulvain, F., and Devleeschouwer, X. (2021) <doi:10.32614/RJ-2021-039>. Huang, Norden E., Zhaohua Wu, Steven R. Long, Kenneth C. Arnold, Xianyao Chen, and Karin Blank (2009) <doi:10.1142/S1793536909000096>. Cleveland, W. S. (1979)<doi:10.1080/01621459.1979.10481038> Hurvich, C.M., Simonoff, J.S., and Tsai, C.L. (1998) <doi:10.1111/1467-9868.00125>, Golub, G., Heath, M. and Wahba, G. (1979) <doi:10.2307/1268518>. References for the example data articles are: Damien Pas, Linda Hinnov, James E. (Jed) Day, Kenneth Kodama, Matthias Sinnesael, Wei Liu (2018) <doi:10.1016/j.epsl.2018.02.010>. Steinhilber, Friedhelm, Abreu, Jacksiel, Beer, Juerg , Brunner, Irene, Christl, Marcus, Fischer, Hubertus, HeikkilA, U., Kubik, Peter, Mann, Mathias, Mccracken, K. , Miller, Heinrich, Miyahara, Hiroko, Oerter, Hans , Wilhelms, Frank. (2012 <doi:10.1073/pnas.1118965109>. Christian Zeeden, Frederik Hilgen, Thomas Westerhold, Lucas Lourens, Ursula Röhl, Torsten Bickert (2013) <doi:10.1016/j.palaeo.2012.11.009>. References for the (continuous) wavelet transform articles are: Morlet, Jean, Georges Arens, Eliane Fourgeau, and Dominique Glard (1982a) <doi:10.1190/1.1441328>. J. Morlet, G. Arens, E. Fourgeau, D. Giard (1982b) <doi:10.1190/1.1441329>. Torrence, C., and G. P. Compo (1998)<https://paos.colorado.edu/research/wavelets/bams_79_01_0061.pdf>, Gouhier TC, Grinsted A, Simko V (2021) <https://github.com/tgouhier/biwavelet>. Angi Roesch and Harald Schmidbauer (2018) <https://CRAN.R-project.org/package=WaveletComp>. Russell, Brian, and Jiajun Han (2016)<https://www.crewes.org/Documents/ResearchReports/2016/CRR201668.pdf>. Gabor, Dennis (1946) <http://genesis.eecg.toronto.edu/gabor1946.pdf>. J. Laskar, P. Robutel, F. Joutel, M. Gastineau, A.C.M. Correia, and B. Levrard, B. (2004) <doi:10.1051/0004-6361:20041335>. Laskar, J., Fienga, A., Gastineau, M., Manche, H. (2011a) <doi:10.1051/0004-6361/201116836>. References for the astronomical solutions articles are: Laskar, J., Gastineau, M., Delisle, J.-B., Farres, A., Fienga, A. (2011b <doi:10.1051/0004-6361/201117504>. J. Laskar (2019) <doi:10.1016/B978-0-12-824360-2.00004-8>. Zeebe, Richard E (2017) <doi:10.3847/1538-3881/aa8cce>. Zeebe, R. E. and Lourens, L. J. (2019) <doi:10.1016/j.epsl.2022.117595>. Richard E. Zeebe Lucas J. Lourens (2022) <doi:10.1126/science.aax0612>.

Authors:Michiel Arts [aut, cre]

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NEWS

# Install 'WaverideR' in R:
install.packages('WaverideR', repos = c('https://stratigraphy.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/stratigraphy/waverider/issues

Datasets:

On CRAN:

cyclostratigraphygeologystratigraphy

3.48 score 3 stars 146 downloads 44 exports 147 dependencies

Last updated 1 years agofrom:a9c39cbb56. Checks:OK: 1 ERROR: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 27 2024
R-4.5-winERRORAug 28 2024
R-4.5-linuxERRORAug 28 2024
R-4.4-winERRORAug 28 2024
R-4.4-macERRORAug 28 2024
R-4.3-winERRORAug 28 2024
R-4.3-macERRORAug 28 2024

Exports:add_waveletadd_wavelet_avganalyze_waveletanchor2timeastro_anchorcompleted_seriescurve2sedratecurve2timecurve2time_unccurve2time_unc_anchorcurve2tunedelpts_tracked_period_wtdur_gapsdynamic_extractionextract_amplitudeextract_powerextract_power_stableextract_signalextract_signal_stableextract_signal_stable_V2extract_signal_standard_deviationflmwgeo_colgeo_locgeo_midHilbert_transformlithlog_discloess_automax_detectmin_detectminimal_tuningmodel_red_noise_wtpercentile_from_red_noiseplot_astro_anchorplot_avg_waveletplot_sed_modelplot_waveletplot_win_fftretrack_wt_MCsedrate2tunesum_power_sedratetrack_period_waveletwavelet_uncertaintywin_fft

Dependencies:askpassastrochronbackportsbase64encbiwaveletbootbslibcachemcellrangercheckmateclassclicliprclustercodetoolscolorednoisecolorRampscolorspacecommonmarkcpp11crayoncredentialscurldata.tableDecomposeRdescDescToolsdiagramdigestdoParalleldoSNOWdotCall64dplyre1071evaluateExactexpmfANCOVAfansifarverfastmapfieldsfontawesomeforeachforeignFormulafsgenericsgertggplot2ghgitcredsgldgluegridExtragtablehexbinhighrHmischmshtmlTablehtmltoolshtmlwidgetshttpuvhttrhttr2IDPmisciniisobanditeratorsjquerylibjsonliteknitrlabelinglaterlatticelifecyclelmommagickmagrittrmapsMASSMatrixmatrixStatsmemoisemgcvmimemultitapermunsellmvtnormnlmennetopensslpalinsolpillarpkgconfigplyrprettyunitsprogresspromisesproxypurrrR6rappdirsRColorBrewerRcppRcppArmadilloreadxlrematchreshapereshape2rlangrlistrmarkdownrootSolverpartrprojrootrstudioapisassscalesshapeshinysnowsourcetoolsspamStratigrapheRstringistringrsystibbletictoctidyselecttinytextruncnormusethisutf8vctrsviridisviridisLiteWaveletCompwhiskerwithrxfunXMLxtableyamlzip

Readme and manuals

Help Manual

Help pageTopics
Add a wavelet plotadd_wavelet
Add a plot of a the average spectral power of a continous wavelet transformadd_wavelet_avg
Age model of Zeeden et al., (2013) for the (154-174m) interval of the IODP 926 grey scale recordage_model_zeeden
Conduct the continuous wavelet transform on a time series/signalanalyze_wavelet
XRF records of the Bisciaro Fmanchor_points_Bisciaro_al
Example anchor points for the grey scale data set of Zeeden et al., (2013)anchor_points_grey
Convert a proxy record to the time domain using anchor pointsanchor2time
Anchor proxy record to an astronomical solutionastro_anchor
An ETP astronomical solutionastrosignal_example
Period of the short kyr ecc cycle in the Al record of the Bisciaro FmBisciaro_al_wt_track
Period of the short kyr ecc cycle in the Ca record of the Bisciaro FmBisciaro_ca_wt_track
Period of the short kyr ecc cycle in the Mg record of the Bisciaro FmBisciaro_Mg_wt_track
Period of the short kyr ecc cycle in the Mn record of the Bisciaro FmBisciaro_Mn_wt_track
Period of the short kyr ecc cycle in the si/Al record of the Bisciaro FmBisciaro_sial_wt_track
XRF records of the Bisciaro FmBisciaro_XRF
Complete the tracking of cycle in a wavelet spectracompleted_series
Convert a tracked tracked to a sedimentation rate curvecurve2sedrate
Convert the tracked curve to a depth time spacecurve2time
Convert the re-tracked curve results to a depth time space with uncertaintycurve2time_unc
Convert the re-tracked curve results to a depth time space with uncertaintycurve2time_unc_anchor
Convert data from the depth to the time domaincurve2tune
Remove tracking points which were tracked in a wavelet spectradelpts_tracked_period_wt
An example depth rank seriesdepth_rank_example
calculate the duration of stratigraphic gaps using astronomical cyclesdur_gaps
Extract a signal in between tracked boundaries in a wavelet scalogramdynamic_extraction
Extract amplitude from a signalextract_amplitude
Extract power from a wavelet spectraextract_power
Extract power from a wavelet spectra by using a constant period/durationextract_power_stable
Extract signal from a wavelet spectra using a traced period curveextract_signal
Extract a signal/cycle from a wavelet spectra using a set period and boundariesextract_signal_stable
Extract signal from a wavelet spectrum using a upper and lower period boundaryextract_signal_stable_V2
Extract a signal using standard deviationextract_signal_standard_deviation
Fit linear models to spectral peaks extracted from the wavelet spectra to astronomical cycles multiplied by sedimentation rate xflmw
Generate standard color codes for the Geological Time Scalegeo_col
Generates ages for the boundaries of a geochronological subdivisiongeo_loc
Generate the mean age of a geological subdivisiongeo_mid
Grey scale record IODP 926 of Zeeden et al., (2013)grey
Tracking points of the precession (22 kyr cycle) IODP 926 grey scale (154-174m) record of Zeeden et al., (2013)grey_track
Information of the Geological timescale 2020GTS_info
Perform a Hilbert transform on a signalHilbert_transform
Discriticizes lithologslithlog_disc
Perform an automatically loess based smoothing of a time seriesloess_auto
Magnetic susceptibility data of the Sullivan core of Pas et al., (2018)mag
Period of the 405 kyr ecc cycle in the magnetic susceptibility record of the Sullivan coremag_track_solution
Detect and filter out all maxima in a signalmax_detect
Detect and filter out all minima in a signalmin_detect
Create an age model using minimal tuningminimal_tuning
Models average spectral power based curves based on a red-noise signal generated using the characteristics of an input signal.model_red_noise_wt
Calculate average spectral power from red noise curves for a given percentilepercentile_from_red_noise
Plot proxy record anchored to an astronomical solutionplot_astro_anchor
Plot the average spectral power of a wavelet spectraplot_avg_wavelet
Plot sedimentation modelling resultsplot_sed_model
Plots a wavelet power spectraplot_wavelet
Plot windowed fft based spectral analysis resultsplot_win_fft
Re-track cycles using a Monte-Carlo simulationretrack_wt_MC
Use a sedimentation curve to convert data to the time domainsedrate2tune
Calculate sum of maximum spectral power for sedimentation rates for a wavelet spectrasum_power_sedrate
Track the period of a cycle in a wavelet spectratrack_period_wavelet
Total solar irradiation data (0-9400ka) of steinhilber et al., (2012)TSI
Calculate the uncertainty associated with the wavelet analysis based on the Gabor uncertainty principlewavelet_uncertainty
Extracting Signals from Wavelet SpectraWaverideR
Example data sets for the 'WaverideR' packageWaverideR_Datasets
Windowed fft based spectral analysiswin_fft