Package index • PhysioMoCap

All functions

Event(): Create an Event definition
Phase(): Create a Phase definition
SkeletonModel(): Create a SkeletonModel object
TaskSchema(): Create a Task Schema
adlReachTask(): Assess an upper-limb ADL reach from its speed profile
alignEMGtoMoCap(): Align EMG to motion-capture sampling grid
analyzeForcePlate(): Run complete force-plate analysis
analyzeForcePlatePE(): Analyze force-plate signals from a PhysioExperiment object
approximateEntropy(): Approximate entropy (Pincus)
assessMoCapReadiness(): Assess readiness of a MoCap dataset for downstream analysis
batchNormalize(): Batch normalize multiple trials
batch_analyze_opensim(): Batch analyze OpenSim session data
benchmarkAgreement(): Compute agreement metrics against a reference signal table
benchmarkManifestTemplate(): Create a benchmark manifest template
butterworthFilter(): Apply a Butterworth filter to numeric data
calculateCOM(): Calculate whole-body center of mass from marker positions
calculateCOP(): Calculate center of pressure (COP) from force-plate data
calculateGaitParameters(): Calculate gait temporal-spatial parameters
calculateJointAngles(): Calculate joint angles from marker positions
calculateSegmentCOM(): Calculate per-segment centers of mass
calculateStepSymmetry(): Calculate step symmetry from gait parameters
calibrateIMU(): Calibrate IMU from static data
classifyGaitPatterns(): Classify gait pathology patterns from a bundle of gait variables
combineTrials(): Combine multiple trials with segmented phases
computeAcceleration(): Compute acceleration from position or velocity data
computeImpulse(): Compute vertical impulse from GRF
computeJerk(): Compute jerk from position data
computeJointPower(): Compute joint power from moment and angular velocity
computeLoadingRate(): Compute vertical loading rate from GRF
computeRMSEnvelope(): Compute moving RMS envelope of EMG
computeSpeed(): Compute scalar speed from velocity
computeVelocity(): Compute velocity from position data
continuousRelativePhase(): Continuous relative phase between two joints
contractionWork(): Angular work and impulse for strength-test repetitions
coordinationVariability(): Inter-joint coordination variability across cycles
copFromPressure(): Derive center of pressure from a pressure movie
correctSwaps(): Correct Marker Label Swaps
createBenchmarkExample(): Create a synthetic benchmark dataset bundle
create_schema_from_opensim(): Create a TaskSchema from OpenSim model for gait analysis
defaultBenchmarkThresholds(): Get default benchmark thresholds
define_skeleton(): Create a pre-defined skeleton model
demoMoCapData(): Create a beginner-friendly demo dataset
detectCircumduction(): Detect circumduction (excessive lateral swing trajectory)
detectEvents(): Detect events in movement data
detectEventsZeni(): Detect gait events with the Zeni coordinate method
detectForcePlateContacts(): Detect contact windows for one or more force plates
detectGaps(): Detect gaps (contiguous NA runs) in assay data
detectPushOffDeficit(): Detect push-off deficit (reduced ankle A2 power / plantarflexor output)
detectStanceZUPT(): Detect foot-IMU stance phases for zero-velocity updates
detectStiffKnee(): Detect stiff-knee gait (reduced / delayed peak swing knee flexion)
detectSwaps(): Detect Marker Label Swaps
detectTrendelenburg(): Detect Trendelenburg sign (excessive contralateral pelvic drop)
differentiate(): Differentiate a numeric vector or matrix
dimensionlessJerk(): Dimensionless jerk of a speed profile
dmpFit(): Fit a Dynamic Movement Primitive to a demonstration
dmpGenerate(): Generate a trajectory from a Dynamic Movement Primitive
downloadOpenCapModel(): Download the OpenSim Model for an OpenCap Session
dtwAverage(): DTW Barycenter Averaging (DBA)
dtwClustering(): DTW-based clustering
dtwDistance(): Dynamic Time Warping (DTW) for Biomechanics
dtwDistanceMatrix(): Compute DTW distance matrix
dtwWarp(): Warp a waveform using DTW alignment
endpointError(): Reaching endpoint accuracy and precision
estimateOrientation(): Estimate orientation from IMU sensors using sensor fusion
estimateSegmentInertia(): Estimate segment inertial properties for lower-limb inverse dynamics
eulerToQuaternion(): Convert Euler angles to quaternion
extractPhase(): Extract a single phase from segmented data
extractWaveformFeatures(): Dimensionality Reduction for Biomechanics
fillGaps(): Fill gaps in motion capture data
fillGapsLinear(): Linear interpolation for a single vector
fillGapsSpline(): Spline interpolation for a single vector
filterGRF(): Low-pass filter ground reaction force data
filterSignals(): Filter signals in a PhysioExperiment object
floquetMultipliers(): Floquet multipliers (orbital stability of a cyclic movement)
footImuGait(): Foot-IMU spatiotemporal gait parameters
forwardDynamics(): Forward dynamics: integrate the equations of motion
forwardKinematics2D(): Forward kinematics of a planar chain
gaitAtaxiaIndex(): Gait-ataxia composite from gait-variability sub-metrics
gaitDeviationIndex(): Gait Deviation Index (Schwartz & Rozumalski 2008)
gaitPatternLibrary(): Registry of supported gait pathology patterns
gaitProfileScore(): Gait Profile Score (overall RMS deviation from the norm)
gaitVariableScore(): Gait Variable Score (per-variable RMS deviation from the norm)
gdiBasis(): Build a Gait Deviation Index feature basis from a normative reference
getEvent(): Get an event by name from a TaskSchema
getEventNames(): Get event names from a TaskSchema
getPhase(): Get a phase by name from a TaskSchema
getPhaseColors(): Get phase colors from a TaskSchema
getPhaseData(): Get data for all phases as a list of matrices
getPhaseNames(): Get phase names from a TaskSchema
getSchema(): Get a pre-built schema by name
get_bone_connections(): Get bone connections from a skeleton
get_limb_pairs(): Get left/right limb pairs for symmetry analysis
get_segment_lengths(): Compute segment lengths from a PhysioExperiment and skeleton
goalEquivalentManifold(): Goal-Equivalent Manifold (GEM) decomposition for a scalar goal
groodSuntayAngles(): Signed Grood-Suntay / ISB joint angles from segment frames
hamstringQuadRatio(): Conventional and functional hamstring-to-quadriceps ratios
harmonicRatio(): Harmonic ratio of a trunk-acceleration signal
hasValidPhases(): Check if all phases are valid
instrumented10mWT(): Instrumented 10-metre walk test (10mWT)
instrumentedTUG(): Instrumented Timed Up-and-Go (iTUG)
integrateEMGMoCap(): Integrate EMG and MoCap signals onto a common timeline
inverseDynamics2D(): Compute 2D lower-limb joint moments with inverse dynamics
inverseDynamics3D(): Compute 3D lower-limb joint moments with inverse dynamics
inverseDynamicsRNE(): Recursive Newton-Euler inverse dynamics for the lower limb
inverseKinematicsMarkers(): Model-based inverse kinematics from markers (planar)
jointCoordinateSystem(): Build embedded anatomical segment coordinate systems from marker clusters
jointWork(): Integrate joint power into concentric and eccentric work
kalmanOrientation(): Kalman orientation filter (tilt + gyro-bias)
labelPowerBursts(): Label joint power bursts with Winter nomenclature
ldlj(): Log Dimensionless Jerk (LDLJ) movement smoothness
limbAtaxiaIndex(): Limb-ataxia composite from reaching sub-metrics
limitsOfStability(): Limits of Stability (LOS) reaction time, excursion and directional control
listSchemas(): Get list of all pre-built schemas
localDynamicStability(): Local dynamic stability (short- and long-term divergence)
mCTSIB(): Modified Clinical Test of Sensory Interaction on Balance (mCTSIB)
mahonyAHRS(): Mahony AHRS orientation filter
manualEvents(): Manually specify event times
maxLyapunovExponent(): Largest Lyapunov exponent (Rosenstein)
movementAnalysisProfile(): Movement Analysis Profile (GVS per variable plus the GPS)
movementSmoothness(): Movement-smoothness battery (SPARC + LDLJ)
movementTime(): Reaching movement time
movementUnits(): Count reaching movement units
movingAverage(): Simple moving average filter
nhptDexterity(): Instrumented Nine-Hole-Peg dexterity from a hand-speed profile
normalizeEMG(): Normalize EMG by MVC or peak
normalizeMovement(): Normalize movement data
normalizedTimeAxis(): Time axis for normalized data
pathStraightness(): Movement-path straightness
peakPressure(): Calculate a peak plantar-pressure map
peakTorque(): Peak torque from isometric or isokinetic dynamometry
peakVelocity(): Peak reaching velocity
phaseDurations(): Get phase durations
phaseRatios(): Calculate phase ratios
phaseTiming(): Get phase timing information
pipelineACLrts(): ACL return-to-sport pipeline (limb symmetry index)
pipelineAmputee(): Amputee prosthetic-side work-asymmetry pipeline
pipelineCPgait(): Cerebral-palsy gait pipeline (GDI + pathology flags)
pipelinePDfog(): Parkinson's freezing-of-gait pipeline (freeze index)
pipelineStrokePropulsion(): Stroke paretic-propulsion pipeline
planarLimbModel(): Planar two-segment limb model (equations of motion)
plotBlandAltman(): Bland-Altman agreement plot
plotCorrelationMatrix(): Plot correlation matrix heatmap
plotCycle(): Plot normalized movement cycle
plotDTW(): Plot DTW alignment
plotEffectSizeForest(): Plot effect size forest plot
plotFPCA(): Plot fPCA results
plotGaitCycle(): Plot gait cycle normalized waveforms
plotGroupComparison(): Plot group comparison with task context
plotMAP(): Plot a Movement Analysis Profile
plotMultiPanel(): Plot multi-panel movement data
plotPCAScatter(): Plot PCA scatter
plotPCAVariance(): Plot PCA variance explained
plotPhaseDurations(): Plot phase duration comparison
plotPhasePortrait(): Plot phase portrait
plotPressureMap(): Plot a plantar-pressure map
plotSkeleton(): Plot a 2D stick-figure skeleton
plotSkeleton3D(): Plot a skeleton frame in pseudo-3D
plotSkeletonOverlay(): Plot overlaid skeleton frames
plotSkeletonSequence(): Plot a sequence of skeleton frames
plotSpaghetti(): Plot spaghetti plot (all subjects with mean)
plotSymmetry(): Plot symmetry comparison (left vs right)
plotTUG(): Plot an instrumented TUG timeline
plotTrajectory(): Plot movement trajectory (2D)
plotUMAP(): Plot UMAP embedding
plotWaveformComparison(): Plot waveform comparison across groups
poseFix(): Detect and correct pose-estimation anomalies
poseLengthCorrect(): Standardise segment lengths (camera-distance correction)
predictiveSimulation(): Predictive simulation: minimal-effort optimal control
pressureAsymmetry(): Compare left and right plantar pressure
pressureMovie(): Construct a plantar-pressure movie
pressureTimeIntegral(): Calculate the plantar pressure-time integral
print(<ASFSkeleton>): Print method for ASFSkeleton objects
print(<SkeletonModel>): Print a SkeletonModel object
print(<benchmark_agreement>): Print benchmark agreement summary
print(<benchmark_manifest_validation>): Print benchmark manifest validation result
print(<benchmark_suite>): Print benchmark suite summary
print(<detected_events>): Print method for detected events
print(<dtw_clustering>): Print DTW clustering result
print(<dtw_result>): Print DTW result
print(<forceplate_analysis>): Print a forceplate analysis summary
print(<forceplate_analysis_multi>): Print a multi-plate forceplate analysis summary
print(<gait_parameters>): Print gait parameters
print(<mocap_quickstart>): Print a quick-start summary
print(<mocap_readiness>): Print a MoCap readiness report
print(<multi_trial_phases>): Print method for multi-trial phases
print(<segmented_phases>): Print method for segmented phases
print(<waveform_pca>): Print waveform PCA result
print(<waveform_umap>): Print waveform UMAP result
processEMG(): Process EMG for biomechanics workflows
projectTo2D(): Project 3D coordinates to a 2D plane
promCondition(): Condition a ProMP on a via-point
promFit(): Fit a Probabilistic Movement Primitive to demonstrations
quaternionToEuler(): Convert quaternion to Euler angles
quickStartMoCap(): Run a one-command beginner workflow
rateOfForceDevelopment(): Rate of force development
reachingKinematics(): Reaching kinematics report for a PhysioExperiment
readAMC(): Read AMC Motion Capture File (.amc)
readASF(): Read ASF Skeleton Definition File (.asf)
readBVH(): Read BVH Skeleton Animation File (.bvh)
readC3D(): Read C3D Motion Capture File
readDeepLabCut(): Read DeepLabCut output
readGaitRec(): Read GaitRec Dataset
readMOT(): Read OpenSim Motion File (.mot)
readMediaPipe(): Read MediaPipe landmark output
readMoCapAuto(): Read motion-capture files with automatic format detection
readMoCapCSV(): Read Motion Capture CSV Data
readOpenCap(): Read Data from OpenCap Cloud Platform
readOpenPose(): Read OpenPose JSON output
readOpenSimOutputs(): Read OpenSim Output Files
readPressureFrame(): Read a plantar-pressure ASCII export
readSTO(): Read OpenSim Storage File (.sto)
readTRC(): Read OpenSim TRC File (.trc)
readVenus3D(): Read Venus3D CSV Data
rectifyEMG(): Rectify EMG signals
recurrenceQuantification(): Recurrence quantification analysis (RQA)
reflexThreshold(): Velocity-dependent reflex threshold
regionalLoading(): Summarize plantar loading by anatomical region
removeGravity(): Remove gravity from accelerometer data
reportGaps(): Report summary statistics for detected gaps
resampleSignal(): Resample signal assays to a new sampling rate
resampleVector(): Resample a single numeric vector
runBenchmarkSuite(): Run a benchmark suite from a manifest
runCMC(): Run Computed Muscle Control (CMC) via OpenSim
runOpenSimFromMarkers(): Run the local OpenSim toolchain from a model and marker file
runOpenSimFromOpenCap(): Run the local OpenSim toolchain directly from an OpenCap session
runRRA(): Run Residual Reduction Algorithm (RRA) via OpenSim
runStaticOptimization(): Run static optimization (OpenSim, or a pure-R fallback)
run_opensim_toolchain(): Run OpenSim CLI Toolchain via PhysioOpenSim
sampleEntropy(): Sample entropy (Richman & Moorman)
savgolFilter(): Savitzky-Golay filter for smoothing and differentiation
scaleBodyModel(): Scale a body model from marker-measured segment lengths
scalePlanarModel(): Scale a planar chain model from a static pose
scaleSegmentModel(): Scale a de Leva segment inertia model to a subject
schema_balance: Pre-built Balance Schema
schema_cutting: Pre-built Cutting/Change of Direction Schema
schema_cycling: Pre-built Cycling Schema
schema_gait: Pre-built Gait Cycle Schema
schema_jump: Pre-built Jump Schema
schema_running: Pre-built Running Schema
schema_throw: Pre-built Throwing Schema
segmentParameters(): Get body segment inertial parameters (BSIP)
segmentPhases(): Segment data into phases
sensoryOrganizationTest(): Sensory Organization Test (SOT) equilibrium and sensory-ratio scoring
sparc(): Spectral Arc Length (SPARC) movement smoothness
stabilogramDiffusion(): Stabilogram diffusion analysis (Collins & De Luca 1993)
staticOptimizationR(): Pure-R static optimization of muscle activations
strapdownIntegrate(): ZUPT-aided strapdown integration of world-frame acceleration
summarizeGaitParameters(): Summarise gait parameters
swayMetrics(): Posturographic center-of-pressure sway metrics (Prieto 1996)
symmetryIndex(): Compute bilateral symmetry index
synchronizeSignals(): Synchronize multiple PhysioExperiment objects
tardieuScore(): Tardieu score: R1, R2 and the dynamic component
tardieuStretch(): Detect the spastic catch on a single passive stretch
timeDelayEmbed(): Time-delay phase-space embedding
timeToPeakTorque(): Time to peak torque
timeToPeakVelocity(): Time to peak reaching velocity
toleranceNoiseCovariation(): Tolerance-Noise-Covariation (TNC) decomposition of result error
trackMarkers(): Track Markers Across Frames
tremorAmplitude(): Band-limited tremor amplitude (RMS)
tremorMetrics(): Tremor metrics (frequency + amplitude, with a task tag)
tremorSpectrum(): Tremor power spectrum and dominant frequency
trunkCompensation(): Trunk compensation during reaching
uncontrolledManifold(): Uncontrolled Manifold (UCM) analysis of motor variability
validateBenchmarkManifest(): Validate a benchmark manifest
validateSchema(): Validate a TaskSchema
vectorAngle(): Angle between two 3D vectors
vectorCoding(): Vector coding (coupling angle) between two joints
waveformPCA(): PCA for waveform data
waveformTSNE(): t-SNE embedding for waveform data
waveformUMAP(): UMAP embedding for waveform data
writeBenchmarkManifest(): Write a benchmark manifest template to CSV
writeC3D(): Write a C3D Motion Capture File
writeMOT(): Write an OpenSim Motion File (.mot)
writeTRC(): Write an OpenSim TRC File (.trc)