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Register a PhysioExperiment in the database

Source: R/db-schema.R
registerExperiment.Rd

Stores experiment metadata and optionally signal data in the database.

Usage

registerExperiment(
  con,
  x,
  experiment_id = NULL,
  subject_id = NULL,
  session_id = NULL,
  task = NULL,
  store_signals = FALSE,
  chunk_size = 10000L,
  parquet_dir = NULL
)

Arguments

con

A DuckDB connection.

x

A PhysioExperiment object.

experiment_id

Unique identifier for the experiment.

subject_id

Subject identifier.

session_id

Session identifier.

task

Task name.

store_signals

If TRUE, stores signal data in chunks.

chunk_size

Number of samples per chunk for signal storage.

parquet_dir

Optional directory for a Parquet backend. When supplied, the experiment is written with writeParquet() and its default assay is registered as a DuckDB view named <experiment_id>_signals via registerParquetAssay(), enabling out-of-core queries over the Parquet file without loading signals into R.

Value

The experiment_id.

References

Raasveldt M, Muehleisen H (2019). "DuckDB: an embeddable analytical database." Proceedings of the 2019 International Conference on Management of Data (SIGMOD). doi:10.1145/3299869.3320212

See also

loadExperiment, queryExperiments, deleteExperiment, initPhysioSchema

Examples

# DuckDB is an optional dependency; guard the example so it only runs
# when the package is installed.
if (requireNamespace("duckdb", quietly = TRUE)) {
  tf <- tempfile(fileext = ".duckdb")
  con <- connectDatabase(tf)
  initPhysioSchema(con)
  # Build a small deterministic PhysioExperiment
  pe <- PhysioExperiment(
    assays = list(raw = matrix(0, nrow = 100, ncol = 3)),
    colData = S4Vectors::DataFrame(label = c("Fp1", "Fp2", "Cz")),
    samplingRate = 256
  )
  exp_id <- registerExperiment(con, pe,
    experiment_id = "demo1", subject_id = "sub01", task = "rest")
  disconnectDatabase(con)
  unlink(tf)
}
#> duckdb keeps downloaded extensions and secrets in a temporary directory:
#> ℹ /tmp/Rtmpa6DD5K/duckdb
#> This is removed when the R session ends.
#> • Extensions are re-downloaded each session.
#> • Secrets are lost.
#> ℹ Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
#> ℹ Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
#> ℹ See ?duckdb_storage for details and alternatives.