PhysioEcosystem

One entry point for the Physio ecosystem.

Attaching PhysioEcosystem loads and re-exports the public API of the foundation and the core analysis packages — PhysioExperiment (the shared data model), PhysioIO, PhysioPreprocess and PhysioAnalysis — and provides the GUI and REST launchers (launchGUI(), startAPIServer(), checkGUIDependencies()).

This package took over the umbrella role that PhysioExperiment used to play. Code that called library(PhysioExperiment) to obtain the whole stack should call library(PhysioEcosystem) instead; library(PhysioExperiment) now attaches the data model only.

Installation

The containers build on Bioconductor, so its repositories have to be on the list as well — without them the install stops at SummarizedExperiment.

install.packages("BiocManager", repos = "https://cloud.r-project.org")
install.packages("PhysioEcosystem",
  repos = c("https://x-biosignal.r-universe.dev", BiocManager::repositories()))

Quick start

library(PhysioEcosystem)

pe <- PhysioExperiment(
  assays = list(raw = matrix(rnorm(1000), 500, 2)),
  samplingRate = 250
)
samplingRate(pe)

Domain packages — EEG, ECG, EMG, EDA, MoCap, cross-modal, MSK-Net, OpenSim, clinical — are installed separately from the same r-universe.

License

MIT. Author and maintainer: Yusuke Matsui (Nagoya University).