ymatts.r-universe.dev

[x-biosignal] PhysioExperiment 2.3.1

mail.to.matsui@gmail.com (Yusuke Matsui) — Sat, 03 Oct 2026 13:11:53 GMT

Provides the shared data model for the Physio ecosystem: the PhysioExperiment class, a 'SummarizedExperiment' extension for multi-modal physiological signal data (such as electroencephalography, electromyography, and electrocardiography), together with the containers for multiple simultaneously recorded streams, repeated sessions of one subject, and cohorts of subjects. Includes core accessors, channel and event management, provenance, and basic 'S4' methods. Domain packages apply specialized methods to these shared containers and are installed separately.

[x-biosignal] PhysioRehab 0.5.2

mail.to.matsui@gmail.com (Yusuke Matsui) — Sat, 03 Oct 2026 13:11:50 GMT

Re-centres physiological measurement around the way rehabilitation reasons about the individual: International Classification of Functioning (ICF) semantics, individualised goal-referenced outcomes (Goal Attainment Scaling), single-case change detection that fuses quantitative signals with qualitative ICF qualifiers, a hypothesis-to-evidence reasoning scaffold that keeps the clinician in the loop, and an auto-drafted, ICF-structured progress note. Adapters ingest real signals from the ecosystem (markerless gait from 'PhysioMoCap', muscle fatigue from 'PhysioEMG'); the ICF layer resolves against 'PhysioAnnotationHub'; single-case statistics come from 'PhysioAppKit'. The worked instance is stroke hemiplegic gait; the framework is condition-agnostic. A research tool with synthetic examples, not a medical device: outputs are clinician-in-the-loop measurement, documentation and reasoning support, never diagnosis.

[x-biosignal] PhysioTwin 0.1.2

mail.to.matsui@gmail.com (Yusuke Matsui) — Sat, 03 Oct 2026 13:11:50 GMT

A digital-twin engine that couples mechanistic simulation of movement and physiology with realistic sensor emulation and data assimilation, so a subject-specific model can be personalised from real measurements and then used for in-silico experiments. It ships a parameterised limb model (forward dynamics) and mechanistic physiological and network generators -- a Jansen-Rit neural-mass EEG column with an optional 1/f aperiodic background, a McSharry limit-cycle electrocardiogram, a Windkessel arterial blood-pressure model with a closed-loop baroreflex, a respiration waveform and respiratory-sinus-arrhythmia heart-rate-variability generator, and Kuramoto coupled-oscillator and Matsuoka central-pattern-generator rhythms. A forward sensor-emulation layer turns clean signals into realistic recordings (inertial-measurement-unit, optical-marker occlusion, surface-electromyography electrode and electrocardiogram lead), with richer chains for multi-channel electromyography crosstalk and amplifier characteristics, multi-lead electrocardiogram and analogue-to-digital conversion. A data-assimilation layer personalises the twin to recorded data with a family of state-space estimators (unscented, extended, particle and ensemble Kalman filters), likelihood-free Bayesian calibration (rejection and sequential Monte-Carlo approximate Bayesian computation), Markov-chain Monte- Carlo, a Gaussian-process surrogate and GP-accelerated (Bayesian-optimisation) calibration -- including personalising the closed-loop cardiovascular- respiratory twin to measured heart-rate and blood-pressure variability -- as well as particle Markov-chain Monte-Carlo and particle Gibbs (with ancestor sampling) for whole-waveform Bayesian fitting -- including a whole-record fit of the closed-loop cardiovascular model that identifies the baroreflex and respiratory gains a summary fit cannot, with either a resonant Mayer-oscillator or a broadband first-order-autoregressive low-frequency component for records without a distinct Mayer peak -- and Fisher-information optimal experimental design for choosing the most informative experimental condition. Applications include single- and population-level in-silico intervention (perturb parameters and predict the change, with effect size, responder rate and statistical power), multi-modal coupling, and labelled synthetic training-data generation with sensor domain randomisation, all backed by a simulation validity-and-verification harness (identifiability, global sensitivity and validation against real recordings). A clinical decision loop ties these together as research tooling: a personalised twin is certified by a validation gate (goodness of fit and parameter identifiability) before it may advise, candidate interventions are scored with their predictive uncertainty and ranked on multiple criteria, mechanistic predictions are reconciled with external evidence rather than overriding it, and a follow-up measurement is checked against the predicted interval. A closed-loop cardiovascular-respiratory model couples a delayed baroreflex with respiration to produce emergent Mayer waves and respiratory sinus arrhythmia, and an optional bridge holds the twin's predictions to account against a real single-case (SCED/MCID/ICF) clinical evaluation.

[x-biosignal] PhysioAppKit 0.2.1

mail.to.matsui@gmail.com (Yusuke Matsui) — Sat, 03 Oct 2026 13:11:49 GMT

A small, domain-neutral engine for single-case (N-of-1) analysis shared by physiological application layers (rehabilitation, sport, psychophysiology, and others). Provides the Nonoverlap of All Pairs (NAP) effect size, a threshold-and-band single-case analysis, a phase plot, an honest hypothesis-to-evidence verdict combiner, and a dependency-free Rasch model for turning ordinal ratings into an interval scale. Application layers supply their domain slots (ontology, threshold, goal, reasoning, report) and call this engine; the engine knows nothing about any specific domain.

[x-biosignal] synergyMixR 1.0.1

mail.to.matsui@gmail.com (Yusuke Matsui) — Sat, 03 Oct 2026 13:11:49 GMT

Provides tools for analyzing muscle synergy using various statistical methods including MPCA and MFA. Enables researchers to identify distinct subgroups within populations that exhibit different muscle synergy patterns, rather than forcing all subjects into a single global model.

[x-biosignal] PoseFixeR 0.2.1

mail.to.matsui@gmail.com (Yusuke Matsui) — Sat, 03 Oct 2026 13:11:49 GMT

Detects and corrects the anatomical, biomechanical, physical, and detection-confidence anomalies that arise in two-dimensional video-based gait analysis with OpenPose, then imputes and smooths the corrected keypoint trajectories. Implements the method of Sugiyama, Uno and Matsui (2023) .

[x-biosignal] PhysioNetPhysiology 0.3.1

mail.to.matsui@gmail.com (Yusuke Matsui) — Sat, 03 Oct 2026 13:11:49 GMT

Tools for Network Physiology: the study of dynamic interactions among diverse physiological systems (brain, heart, respiration, muscle). Implements Time Delay Stability (TDS) analysis to identify stable dynamic couplings between signals, builds organ-interaction networks whose links are significance-tested against phase-randomised surrogates, and quantifies how those networks reconfigure across physiological states (e.g. sleep stages). Designed to operate on the multimodal PhysioExperiment data model, but the core engine works on plain multivariate time series. Methods follow Bashan et al. (2012) and Bartsch et al. (2015) .

[x-biosignal] PhysioRecipes 0.7.4

mail.to.matsui@gmail.com (Yusuke Matsui) — Sat, 03 Oct 2026 13:11:48 GMT

A version-controlled database of self-contained, reproducible analysis case studies on public physiological data, built on the PhysioExperiment ecosystem. Each case states a proposition, answers a question on a public dataset and completes through to figures and a conclusion, with every reported number traced to an artifact and the whole op-DAG replayable byte-identically. The package ships the verified run bundles and a small API to browse the case metadata, open a case's bundle, and check the invariants that every case must satisfy.

[x-biosignal] PhysioPipe 0.1.1

mail.to.matsui@gmail.com (Yusuke Matsui) — Sat, 03 Oct 2026 13:11:48 GMT

A collection of reusable 'targets' target factories for the Physio ecosystem: drop-in pipelines for the standard single-modality analyses (ECG heart-rate variability, EEG band power, EMG amplitude/fatigue, EDA skin conductance) plus multi-record cohort branching and Quarto reporting. Each factory returns a list of targets so a whole reproducible '_targets.R' is a couple of lines, with incremental re-runs and byte-level provenance.

[x-biosignal] PhysioReport 0.1.2

mail.to.matsui@gmail.com (Yusuke Matsui) — Sat, 03 Oct 2026 13:11:47 GMT

Parameterized, bilingual (Japanese/English), colorblind-safe clinical reports (gait, HRV, EMG) with normative overlays and MDC/MCID-annotated change for the x-biosignal physiological signal ecosystem.

[x-biosignal] PhysioLake 0.1.3

mail.to.matsui@gmail.com (Yusuke Matsui) — Sat, 03 Oct 2026 13:11:47 GMT

Integrates the PhysioExperiment ecosystem with 'OmicsLake', a versioned, on-disk data-management engine built on 'DuckDB', 'Apache Arrow' and 'Parquet' with automatic dataset-level lineage tracking. Rather than reimplementing a data lake, PhysioLake inherits the domain-agnostic OmicsLake core (storage backend, snapshots and time-travel, cross-dataset lineage, query layer) and registers physiology-specific adapters and utilities: 'PhysioExperiment' objects are stored and retrieved with full fidelity, preserving the sampling-rate slot and the W3C-PROV provenance held in object metadata. This connects the ecosystem's per-object (micro) provenance with the lake's cross-dataset (macro) lineage.

[x-biosignal] PhysioClinStats 0.3.1

mail.to.matsui@gmail.com (Yusuke Matsui) — Sat, 03 Oct 2026 13:11:47 GMT

Statistical inference for rehabilitation studies: mixed-effects / MMRM longitudinal models, single-case (N-of-1) designs, estimands with multiple imputation, and per-estimate uncertainty. Heavy modelling backends are optional (guarded) Suggests.

[x-biosignal] PhysioClinical 0.7.0

mail.to.matsui@gmail.com (Yusuke Matsui) — Sat, 03 Oct 2026 13:11:47 GMT

Validated clinical outcome-measure scoring (FMA, Berg, ARAT, TUG, 6MWT, Barthel, Katz, Lawton-Brody IADL, ...), MDC/MCID responder classification, ICF tagging, interval (Rasch) analysis of ordinal ADL/IADL instruments, and normative deviation scoring for the x-biosignal rehabilitation ecosystem.

[x-biosignal] PhysioAnnotationHub 0.2.1