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Record a PROV activity around an operation

Source: R/provenance.R
recordActivity.Rd

Evaluates expr (an operation that transforms x and returns a PhysioExperiment), timing it to fill the PROV startedAtTime / endedAtTime, and appends one activity to the result. The input's provenance log is carried onto the result if the operation dropped it.

Usage

recordActivity(
  x,
  activity,
  expr,
  params = list(),
  input_assay = NA_character_,
  output_assay = NA_character_,
  agent = NA_character_,
  software_version = NA_character_,
  package = NA_character_
)

Arguments

x

The input PhysioExperiment.

activity

Character scalar naming the PROV activity.

expr

An expression, evaluated lazily, that returns the modified object (e.g. filterSignals(x, low = 1)).

params

Named list of parameters to record.

input_assay, output_assay, agent, software_version, package

As in appendProvenance.

Value

The object returned by expr, with the timed activity appended.

See also

withProvenance, logStep

Examples

pe <- PhysioExperiment(
  S4Vectors::SimpleList(raw = matrix(rnorm(20), 10, 2)), samplingRate = 100)
scale2 <- function(p) { SummarizedExperiment::assay(p, "raw") <-
  SummarizedExperiment::assay(p, "raw") * 2; p }
pe <- recordActivity(pe, "rescale", scale2(pe), params = list(gain = 2))
provenance(pe)$activity
#> [1] "rescale"