Package: PhysioNIRS 0.6.1

Yusuke Matsui

PhysioNIRS: Governed Near-Infrared Spectroscopy Data and SNIRF Input/Output

Provides strict input, output, measurement identity, probe geometry, optical-density, modified Beer-Lambert, motion-correction, and short-separation nuisance, signal-quality, channel-pruning, and live neurofeedback contracts for continuous-wave functional near-infrared spectroscopy data stored in 'PhysioExperiment' objects. Shared Near Infrared Spectroscopy Format ('SNIRF') files are read and written through structured 'HDF5' APIs while preserving time bases, measurement order, probe coordinates, metadata tags, stimulus tables, and processing provenance.

Authors:Yusuke Matsui [aut, cre]

PhysioNIRS_0.6.1.tar.gz
PhysioNIRS_0.6.1.zip(r-4.7-any)PhysioNIRS_0.6.1.zip(r-4.6-any)PhysioNIRS_0.6.1.zip(r-4.5-any)
PhysioNIRS_0.6.1.tgz(r-4.6-any)PhysioNIRS_0.6.1.tgz(r-4.5-any)
PhysioNIRS_0.6.1.tar.gz(r-4.7-any)PhysioNIRS_0.6.1.tar.gz(r-4.6-any)
PhysioNIRS_0.6.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
PhysioNIRS/json (API)

# Install 'PhysioNIRS' in R:

install.packages('PhysioNIRS', repos = c('https://x-biosignal.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/x-biosignal/physionirs/issues

Pkgdown/docs site:https://x-biosignal.github.io

On CRAN:

2.70 score 27 exports 35 dependencies

Last updated from:f9c150833b. Checks:7 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel	ERROR	272
source / vignettes	OK	225
linux-release	ERROR	263
macos-release	ERROR	220
macos-oldrel	ERROR	222
windows-devel	ERROR	235
windows-release	ERROR	237
windows-oldrel	ERROR	168
wasm-release	OK	100

Exports:dpf extinctionCoefficients identifyShortChannels intensityToOD mbll measurementList motionArtifactDetect nirsActivationContrast nirsActivationGLM nirsNeurofeedback nirsNeurofeedbackScope nirsNeurofeedbackStart nirsNeurofeedbackState nirsNeurofeedbackStep nirsNeurofeedbackStop physiologyBandpass pruneChannels readSNIRF scalpCouplingIndex shortSeparationDesign shortSeparationRegress signalQualityIndex sourceDetectorDistances splineMotionCorrect tddr waveletMotionCorrect writeSNIRF

Dependencies:abind Biobase BiocGenerics biocmake cli DelayedArray digest dir.expiry filelock generics GenomicRanges IRanges jsonlite lattice lifecycle MASS Matrix MatrixGenerics matrixStats PhysioExperiment PhysioPreprocess PhysioStream Rcpp rhdf5 rhdf5filters Rhdf5lib rlang S4Arrays S4Vectors Seqinfo signal SparseArray SummarizedExperiment xml2 XVector

A continuous-wave fNIRS pipeline with synthetic data

Rendered fromnirs-pipeline.Rmdusingknitr::rmarkdown

Last update: 2026-10-03
Started: 2026-10-03

Help page	Topics
PhysioNIRS: governed NIRS data and SNIRF input/output	PhysioNIRS-package PhysioNIRS
Estimate a differential pathlength factor	dpf
Get governed haemoglobin extinction coefficients	extinctionCoefficients
Identify short source-detector channels	identifyShortChannels
Convert continuous-wave fNIRS intensity to optical density	intensityToOD
Convert optical density to haemoglobin concentration change	mbll
Return the governed SNIRF measurement list	measurementList
Detect fNIRS motion artifacts by channel	motionArtifactDetect
Contrast of an fNIRS activation GLM	nirsActivationContrast
First-level fNIRS cortical-activation GLM	nirsActivationGLM
Construct a governed live fNIRS neurofeedback controller	nirsNeurofeedback
Control and inspect live NIRS neurofeedback	nirsNeurofeedback-lifecycle nirsNeurofeedbackScope nirsNeurofeedbackStart nirsNeurofeedbackState nirsNeurofeedbackStep nirsNeurofeedbackStop
Extract an explicit fNIRS physiology frequency band	physiologyBandpass
Display a governed NIRS quality result	print.nirs_quality
Display a governed NIRS neurofeedback runtime	print.NIRSNeurofeedback
Mark or drop channels using governed NIRS quality results	pruneChannels
Read a Shared Near Infrared Spectroscopy Format file	readSNIRF
Calculate the governed fNIRS scalp-coupling index	scalpCouplingIndex
Construct a governed short-separation nuisance design	shortSeparationDesign
Regress governed short-separation nuisance signals	shortSeparationRegress
Calculate governed fNIRS signal quality	signalQualityIndex
Calculate source-detector distances for each SNIRF measurement	sourceDetectorDistances
Correct detected fNIRS motion intervals with cubic smoothing splines	splineMotionCorrect
Repair fNIRS motion artifacts with TDDR	tddr
Correct fNIRS motion with a shift-invariant db2 wavelet transform	waveletMotionCorrect
Write a Shared Near Infrared Spectroscopy Format file	writeSNIRF

Package: PhysioNIRS 0.6.1

PhysioNIRS: Governed Near-Infrared Spectroscopy Data and SNIRF Input/Output

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Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)