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Retrieve metabom8 provenance metadata

Source: R/utils_provenance.R
get_provenance.Rd

Extracts preprocessing provenance stored in the "m8_prep" attribute. Allows access to the full processing log, a specific step, or a specific parameter within a step.

Usage

get_provenance(x, step = NULL, param = NULL)

Arguments

x

A metabom8 object (named list with element X) or a numeric matrix containing metabom8 provenance metadata.

step

Optional. Either:

  • Numeric index of the preprocessing step

  • Character string matching the recorded step name

If NULL, the full provenance log is returned.

param

Optional character string specifying a parameter name within the selected step. If provided, only this parameter value is returned.

Value

Depending on the arguments:

  • Full provenance list (if step = NULL)

  • A single preprocessing step (if step specified)

  • A single parameter value (if param specified)

Details

Provenance metadata are recorded automatically by metabom8 preprocessing functions and stored as structured attributes on the spectral matrix. This function provides programmatic access to these records.

See also

Other provenance: add_note(), print_provenance()

Examples

data(hiit_raw)

hiit_proc <- hiit_raw |>
  calibrate(type = "tsp") |>
  excise()

# Retrieve full log
log <- get_provenance(hiit_proc)

# Retrieve specific step
get_provenance(hiit_proc, step = 2)
#> $step
#> [1] "excise1d"
#> 
#> $params
#> $params$regions
#> $params$regions$upfield_noise
#> [1] -5.217943  0.250000
#> 
#> $params$regions$water
#> [1] 4.5 5.2
#> 
#> $params$regions$urea
#> [1] 5.5 6.0
#> 
#> $params$regions$downfield_noise
#> [1]  9.70000 14.80367
#> 
#> 
#> 
#> $notes
#> [1] "Specified chemical shift regions removed using get_idx()."
#> 
#> $time
#> [1] "2026-04-23 10:41:16.582379"
#> 
#> $pkg
#> [1] "metabom8"
#> 
#> $pkg_version
#> [1] "0.99.10"
#> 

# Retrieve parameter from a named step
get_provenance(hiit_proc, step = "calibrate", param = "target")
#> $mode
#> [1] "singlet"
#> 
#> $window
#> [1] -0.2  0.2
#> 
#> $centre
#> [1] 0
#>