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CycloDesk

Lifecycle: alpha R-CMD-check License: GPL (>= 2)

A point-and-click workbench for cyclostratigraphy and paleoclimate time series, built on R.

CycloDesk puts the R packages WaverideR and astrochron behind menus and buttons. Open a folder with your data, pick a tool, press Run: spectra, wavelets, filters, cycle tracking, age models, tuning, TimeOpt and COCO, without writing code. Every step writes its result as a plain text file next to your data and records the equivalent R code, so anything you click can be repeated in a script.

It runs in your web browser, but on your own computer: your data never leaves your machine.

Status: alpha. CycloDesk works and is being used for real records, but menus, defaults and file names may still change. Please report anything that breaks, looks wrong or is confusing. Feedback now shapes the first stable release.

CycloDesk: tracking a cycle on the wavelet scalogram, with the extracted cycle, floating age model and tuned series below
CycloDesk: tracking a cycle on the wavelet scalogram, with the extracted cycle, floating age model and tuned series below

What it does

Menu Tools
File / Plot Working-folder browser (drives, places, drag-and-drop), text, csv, Excel and LAS files; overlay, stacked and standardised plots, zoom, data table, sampling rate, data distribution
Basic Series Astronomical solutions (La2004, La2010, La2011), insolation, ETP, signal and noise generator, example data
Math Sorting, interpolation, selecting/removing parts (draggable lines), clipping, transformations, derivative, smoothing, Bayesian change points
Time Series Detrending, pre-whitening; MTM, LOWSPEC, MESA, AMTM, SWA and other spectra; evolutive spectra; wavelets (22 mother wavelets), superlets and synchrosqueezing; coherence, cross wavelet, bispectral analysis; filtering, Hilbert amplitude, age models, tuning; TimeOpt/eTimeOpt, COCO/eCOCO; rho1, DYNOT, PDA, spectral moments
Track Track a cycle on the scalogram by clicking (snap to peaks or free), follow the ridge (HMM) or snap the whole curve to the nearest peaks, LOWESS smoothing, helper lines for other cycles, floating age model, extraction of any cycle, tuning check against the amplitude modulation
Anchor Tie a floating record to an astronomical solution, insolation or a metronome by clicking matching peaks

Heavy calculations run in a separate R process, so the window stays usable and can cancel them. The R code tab collects the code of every step; Help > Which R function does what lists the function behind each menu.

Spectral analysis Wavelet analysis
Spectral analysis with confidence levels Wavelet scalogram with average spectrum
Tuning check Anchoring
Tuning check: envelope of a cycle against the modulating cycle Anchoring a floating record to La2004

Installation

Windows, no R experience needed

  1. Install R from https://cloud.r-project.org/bin/windows/base/ (the default options are fine).
  2. Download CycloDesk-launcher.zip and unzip it somewhere permanent, for example into Documents\Apps (not in Downloads). This gives a folder CycloDesk.
  3. In that folder, double-click SETUP.bat. It installs CycloDesk, WaverideR and the other R packages it needs (a few minutes the first time) and puts a CycloDesk icon on your desktop.
  4. Double-click the icon. CycloDesk opens in your browser.

CycloDesk checks once a day, at start-up, whether a newer version of CycloDesk or WaverideR is on GitHub and installs it.

From R (Windows, macOS, Linux) 

install.packages("remotes")
remotes::install_github("stratigraphy/WaverideR")   # always the newest WaverideR
remotes::install_github("stratigraphy/CycloDesk")
CycloDesk::run_app()                                # or run_app("path/to/your/data")

Both packages are pure R; no compilers or Rtools are needed.

Getting started

The tutorial walks through a complete analysis of the IODP Site 926 grey-scale record that comes with WaverideR: spectrum, wavelet, tracking the eccentricity cycle, a floating age model, the tuning check and anchoring to La2004.

Feedback and help

Contributions are welcome; see CONTRIBUTING.md.

Citation

If CycloDesk helps your work, please cite it, together with the packages that do the calculations:

plus the papers of the methods you used (listed in each tool’s help panel). In R: citation("CycloDesk").

Acknowledgements

The menu layout and the working-folder workflow are inspired by Acycle (Li, Hinnov and Kump, 2019, Computers & Geosciences 127, 12-22, https://doi.org/10.1016/j.cageo.2019.02.011). CycloDesk contains no Acycle code; all calculations are done by WaverideR and astrochron.

Licence

GPL (>= 2). See LICENSE.md.