NEWS

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dynR 0.1.2

New functions

• dyn_transitions(): first-order Markov transition probabilities between brain states. Takes a long-format timepoint-level data frame, computes source → target transitions within each group (subject × session), and returns a nested tibble of per-transition probabilities ready for grouped_perm_glmm(). Ported from clusters_markov() in the neonatal_dfc analysis pipeline (França et al., Nat Commun). remIntra = TRUE strips self-transitions before normalising.

Dependencies

• Added dplyr, tidyr, and rlang to Imports (required by dyn_transitions()).

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dynR 0.1.1

Bug fixes

• bandpass_filter(): replaced gsignal::filtfilt() (zero initial conditions) with a scipy-compatible implementation that achieves bit-perfect parity with scipy.signal.filtfilt and scipy.signal.sosfiltfilt (max |diff| < 4e-12). The old implementation produced edge transients of up to ~0.24 signal units on real fMRI data due to zero initial state; this propagated into hilbert_phases() and dyn_phase_lock(), causing LEiDA eigenvectors to diverge from the Python dynfc reference pipeline.

  The fix introduces three internal helpers:

  • .lfilter_zi(): steady-state initial conditions via companion-matrix solve (equivalent to scipy.signal.lfilter_zi).
  • .lfilter(): Direct Form II Transposed IIR filter with explicit initial state (equivalent to scipy.signal.lfilter).
  • .odd_ext(): odd-reflection signal extension matching scipy.signal._arraytools.odd_ext exactly — right extension uses x[N-2 : N-n-2 : -1], padlen = 3 × max(length(b), length(a)).

  With these corrections, per-timepoint correlations between R and Python LEiDA eigenvectors are identically 1.0 across all sessions.

Tests

• Added tests/testthat/test-bandpass_filter.R with six tests adapted from the scipy.signal.filtfilt documentation examples: output-length preservation, DC blocking, in-band sine-wave recovery, stopband attenuation (>40 dB), zero-phase property, and machine-precision agreement with scipy.signal.filtfilt on fMRI parameters (guarded by skip_if_not_installed("reticulate")).
• Added reticulate to Suggests for the scipy cross-validation test.

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dynR 0.1.0

• Initial scaffold.
• Ported core dynamic functional connectivity functions from the Python dynfc package.
• Implements: bandpass_filter(), hilbert_phases(), corr_slide(), cofluct(), corr_corr(), dyn_phase_lock(), get_leida(), kuramoto(), shannon_entropy(), do_euclid().