circadia-bio/Rtractor: v0.1.0

📉 Multiscale family

• Added multiscale_entropy() — multiscale entropy (MSE; Costa, Goldberger & Peng 2002), the first function in the previously-empty multiscale family. Direct C++ port of the counting core in PhysioNet's reference mse.c (Costa), validated to reproduce the compiled reference binary's output exactly (to its own displayed precision) on synthetic test data, both at the sample-entropy level and for the full multiscale sweep.
• Added sample_entropy() — sample entropy (SampEn; Richman & Moorman 2000), filling a previously-planned gap in the entropy family and serving as the building block multiscale_entropy() applies at each coarse-grained scale.

🎲 Simulate family

• Added pmodel() — multifractal binomial cascade generator (Meneveau & Sreenivasan 1987), with optional Fourier-domain fractional integration (Davis et al. 1997). Clean-room R reimplementation of pmodel.m (Victor Venema). Validated against two RNG-independent structural properties: exact constant output at p=0.5, and exact mass conservation at every cascade level for any p.

🧭 Ported from mrpheus

• Added perm_entropy(), petrosian_fd(), hjorth_parameters(), and num_zerocross() — four nonlinear/complexity features centralised from Lucas França's own mrpheus package (its AASM staging feature pipeline, itself a validated R/C++ port of the YASA/antropy Python feature set). Re-validated directly against antropy 0.2.2 during this port: exact match for perm_entropy (normalized value), petrosian_fd, and num_zerocross. hjorth_parameters agrees closely but not exactly by design — it uses Bessel-corrected (ddof=1) variance, matching mrpheus's/R's convention, rather than antropy's population-variance (ddof=0) convention; the difference shrinks as signal length grows. Rtractor's existing higuchi_fd() was cross-checked against mrpheus/antropy's version and found to agree exactly for realistic epoch lengths.

🌿 Fractal family

• Added dfa() — Detrended Fluctuation Analysis. Direct C++ port of PhysioNet's reference dfa.c (Mietus, Peng & Moody), validated to reproduce the compiled reference binary's output exactly on synthetic test data. Package license changed to GPL (>= 2) as a result (see inst/COPYRIGHTS).
• Added higuchi_fd() — Higuchi Fractal Dimension. Clean-room C++ reimplementation from Higuchi (1988), validated against a MATLAB reference implementation on synthetic test data (max abs. difference ~1e-11).
• Added mfdma() — multifractal detrending moving average (Gu & Zhou 2010). Clean-room C++ reimplementation from the published algorithm, segment-fluctuation core validated against a Python transliteration of the reference MATLAB implementation on synthetic test data (exact match to displayed precision).
• Added chhabra_jensen() — multifractal spectrum via the Chhabra-Jensen box-counting method (1989). Clean-room C++ reimplementation, moments core validated against a Python transliteration of the reference implementation (exact match to displayed precision).

🔁 RQA family

• Added recurrence_microstate_entropy() — recurrence microstates maximum-entropy threshold search (Corso et al. 2018; Prado et al. 2018). Direct C++ port of the deterministic core of Max_Entropy() from circadia-bio/maxEntropy (Entropy.jl, MIT licensed), the script used in Ferre et al. (2024, PLOS ONE). Random pair sampling moved to R for set.seed()-reproducibility; core loop validated against a Python transliteration of the original (exact match on synthetic test data).

🚀 Initial scaffold

• Repository initialised: package skeleton (DESCRIPTION, .Rprofile, R/, src/, tests/testthat/) with no exported functions yet.
• Added Rtractor colour palette (rtractor_palette(), rtractor_palettes()), discrete/continuous ggplot2 scales (scale_colour_rtractor(), scale_fill_rtractor(), scale_colour_rtractor_c(), scale_fill_rtractor_c()), and theme_rtractor().
• Planned function families stubbed as file headers only (no implementations yet, pending reference code inventory): entropy, fractal, lyapunov, multiscale, rqa, embed.

🎨 Visual identity

• Hex sticker logo (man/figures/logo.svg), matching the Circadia Lab ecosystem's visual conventions: a dense woven strange-attractor motif (a nod to "Rtractor" = R + attractor) on a dotted-paper background, with the Rtractor colour palette carried through the border and wordmark. Wordmark baked as vector outlines rather than live text, so it renders correctly regardless of font availability in whatever tool processes the SVG (favicon generators, etc.).
• pkgdown site live at https://rtractor.circadia-lab.uk, with the full favicon set generated via pkgdown::build_favicons().

📚 Documentation

• vignette("getting-started") — tour of every implemented family.
• vignette("multifractal-methods") — mfdma() vs chhabra_jensen(), validated against known pmodel() ground truth rather than just checking both run without error.
• vignette("entropy-and-complexity") — perm_entropy()/ sample_entropy()/multiscale_entropy(), including the classic Costa et al. white-noise-vs-correlated-signal multiscale entropy demonstration.