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Changelog

Source: NEWS.md

PhysioMoCap 0.7.1

The generic functional-PCA, waveform-reliability and circular-statistics implementations moved to PhysioCore (their single source of truth) and are re-exported here, so fPCA()/reconstructFPCA()/registerCurves(), waveformCMC()/waveformICC()/waveformReliability() and circularSummary()/ rayleighTest()/watsonWilliamsTest()/circularLinearCorrelation() behave exactly as before. The ggplot2 visualiser plotFPCA() stays in this package.

PhysioMoCap 0.7.0

Movement-disorder quantification: tremor, ataxia and instrumented spasticity.

  • Tremor: tremorSpectrum() (dependency-free Welch periodogram → dominant frequency, in-band power, half-power bandwidth, harmonic ratio in a 3-12 Hz band), tremorAmplitude() (band-limited RMS) and tremorMetrics() (combined, tagged rest/postural/kinetic).
  • Ataxia: pathStraightness() (trajectory straightness / index of curvature) plus limbAtaxiaIndex() and gaitAtaxiaIndex() — honest aggregators of the existing validated sub-metrics (endpointError, movementUnits, sparc/ldlj, summarizeGaitParameters CVs, swayMetrics) that standardise into a composite z only against a supplied healthy reference (no population weights/cut-offs are fabricated).
  • Instrumented spasticity (Tardieu): tardieuStretch() locates the catch (EMG reflex onset and/or velocity arrest) → R1; tardieuScore() derives R2 and the dynamic component R2-R1; reflexThreshold() regresses catch angle on stretch velocity. Reuses the EMG↔︎MoCap alignment, envelope and angular-velocity primitives already in the package.

PhysioMoCap 0.6.2

Fixes to the OpenCap -> OpenSim pipeline (from a code review of 0.6.1).

  • runOpenSimFromMarkers()/runOpenSimFromOpenCap() now default time_range to the whole trial (read from the marker file). Previously a NULL time_range left the tool templates’ <time_range>0 1</time_range> in place, silently truncating every trial to its first second.
  • tools now defaults to "ik" (matching the documentation); the previous c("ik","id","so") default made the bare call error on the ground-reaction requirement.
  • Inverse kinematics is run before the ID/SO setups are written, so their motion input is real rather than an empty placeholder; a failed IK is now reported instead of crashing the MOT reader on a 0-byte file, and reused-workdir stale outputs are no longer attributed to the run.
  • runOpenSimFromOpenCap() resolves the OpenCap session once (model and markers come from the same trial, no duplicate requests), validates session_id and a supplied external_loads_file before downloading, and records the resolved trial id.
  • .opencap_model_url handling tolerates empty/NA/non-scalar session metadata; a partial templates override keeps the bundled defaults for the other tools.

PhysioMoCap 0.6.1

OpenCap -> OpenSim -> downstream pipeline.

  • runOpenSimFromMarkers() wires a scaled model and marker .trc through OpenSim inverse kinematics and, optionally, inverse dynamics and static optimization: it writes the tool setup XMLs from the bundled PhysioOpenSim templates, runs them via run_opensim_toolchain(), and parses the outputs with readOpenSimOutputs(). ID/SO require an external_loads_file (markerless OpenCap has no ground reactions); dry_run = TRUE writes the setups without a backend.
  • runOpenSimFromOpenCap() runs that chain directly from an OpenCap session, and downloadOpenCapModel() fetches the session’s scaled .osim model (the input the local OpenSim toolchain needs, since OpenCap does the scaling).
  • New vignette opencap-opensim-pipeline documents both the cloud-kinematics route (no local OpenSim) and the local-OpenSim route, with its scope limits.

PhysioMoCap 0.5.0

Inter-joint coordination analysis.

  • continuousRelativePhase(): the phase-plane coordination measure (Hamill
    1. between two joints, with the mean absolute relative phase (MARP).
  • vectorCoding(): the angle-angle coupling angle, classified per frame into in-phase / anti-phase / proximal-phase / distal-phase coordination (Chang 2008; Needham 2014).
  • coordinationVariability(): trial-to-trial coordination variability – the deviation phase for CRP (linear SD) or the coupling-angle circular SD for vector coding – a motor-control marker.

PhysioMoCap 0.4.0

Upper-limb ADL task assessment.

  • adlReachTask(): assess an ADL arm transport (drinking / feeding / dressing / grooming / reaching) from its hand-speed profile – movement time, peak velocity, submovement count and SPARC/LDLJ smoothness – labelled with the ICF code it realises (d560 / d550 / d540 / d520 / d445).
  • nhptDexterity(): instrumented Nine-Hole-Peg dexterity (ICF d440) from a hand-speed profile – transport count, rate, inter-transport consistency and smoothness – the sensor complement to the timed NHPT score.

PhysioMoCap 0.3.3

  • poseLengthCorrect() — segment-length standardisation (camera-distance correction): rescales each limb segment along the bone direction to a stable reference length, chained proximal to distal. Also available as poseFix(..., length_correct = TRUE). Generalised form of the length correction in PoseFixeR (Sugiyama, Uno & Matsui 2023).

PhysioMoCap 0.3.2

  • New vignette “Markerless pose to gait: OpenPose -> poseFix -> analysis” — the end-to-end pose pipeline from ingestion through poseFix() cleaning to joint angles and a gait metric.

PhysioMoCap 0.3.1

  • poseFix() gains left/right leg-swap correction (deswap = TRUE): leg-label swaps that pose estimators make as the legs cross during gait are corrected by restoring trajectory continuity, before the anomaly steps. The number of corrections is reported in metadata()$poseFix$leg_swaps.

PhysioMoCap 0.3.0

  • poseFix() — pose-estimation anomaly detection and correction, connecting markerless pose input (readOpenPose() / readMediaPipe() / readDeepLabCut()) to the downstream joint-angle / gait / kinematics analysis. Flags keypoints on four criteria (low detector confidence, implausible segment lengths, frame-to-frame jumps, out-of-range joint angles), then interpolates and smooths them. Generalised, name-based, self-referential reimplementation of the method in PoseFixeR (Sugiyama, Uno & Matsui 2023, PLOS Comput Biol 19:e1009989).

PhysioMoCap 0.2.2

  • Made the OpenSim MOT/TRC read/write round-trip tests portable to macOS: they now assert numerical equality (expect_equal) of the recovered data rather than bit-identity (expect_identical). Writing numeric data through a decimal ASCII file (17 significant digits) recovers values exactly on a correctly- rounded libc (glibc) but to ~1 ULP on macOS’s printf/strtod, so a bit- identical round-trip is not a portable guarantee; the data is still preserved to full double precision. No writer/reader behaviour changed.

PhysioMoCap 0.2.1

Validation

  • Bundled an independent OpenSim inverse-dynamics reference (inst/extdata/gait2392_id_reference.rds) so the inverseDynamicsRNE() cross-tool test now runs instead of skipping. The fixture is derived from the OpenSim gait2392 subject01_walk1 trial (opensim-models, Apache-2.0) with OpenSim 4.6’s InverseDynamicsTool; the recursive Newton-Euler solver reproduces the OpenSim hip/knee/ankle moments at r > 0.99 and < 8% peak error. Generation is documented in data-raw/gait2392_id_reference*.

PhysioMoCap 0.2.0

New Features

  • Added Venus3D CSV reader (readVenus3D()) for OptiTrack -> Motive -> Venus3D pipeline exports with automatic header metadata parsing.
  • Added marker tracking module for resolving frame-by-frame label reassignment:
    • trackMarkers() — Hungarian algorithm (via clue) or greedy assignment for establishing consistent marker identities across frames.
    • detectSwaps() — velocity-spike-based swap detection with cross-over validation.
    • correctSwaps() — automatic swap repair based on detection results.
  • readMoCapAuto() now auto-detects Venus3D CSV files (by #Venus3D header).
  • Added clue to Suggests for optimal assignment in marker tracking.

PhysioMoCap 0.1.0

Major Improvements