Print metabom8 preprocessing pipeline

Displays the recorded preprocessing history attached to a metabom8 spectral matrix. The function reads the "m8_prep" attribute and prints each processing step in chronological order, including parameters and notes.

Usage

print_provenance(x, detail = FALSE, max_items = 8)

Arguments

x

A metabom8 object or spectral matrix with attached "m8_prep" provenance metadata.

detail

Prints full information trail, incl. timestamp / versioning

max_items

Limits individual list entries (e.g., parameter) to specified number

Value

Invisibly returns NULL. This function is called for its side effect of printing pipeline information.

Details

The input can be either:

• A metabom8-style list containing $X, or

• A matrix with metabom8 provenance attributes attached.

If no preprocessing metadata is found, a message is printed.

metabom8 records preprocessing steps as an ordered list of transformation descriptors stored in the "m8_prep" attribute. Each step typically contains:

• step: Name of the preprocessing operation

• params: Parameters used

• notes: Optional description

• time: Timestamp

• pkg: Package name and version

This function provides a compact audit trail of the processing workflow, facilitating reproducibility and provenance inspection.

See also

Other provenance: add_note(), get_provenance()

Examples

params <- list(
  runtime  = "docker",
  image    = Sys.getenv("IMAGE", "docker-image-dummy"),
  workflow = Sys.getenv("M8_WORKFLOW", "std_prof-urine"),
  agent    = paste0("snakemake/", Sys.getenv("SNAKEMAKE_VERSION", "v?")),
  run_id   = Sys.getenv("M8_RUN_ID", "m8-2605-001")
)

data(hiit_raw)
print_provenance(hiit_raw)
#> No metabom8 preprocessing metadata found.

hiit_proc <- hiit_raw |>
  calibrate(type = "tsp") |>
  excise() |>
  add_note('dilution-adaptive acquisition mode -> verify snr after normalisation',
    params)

print_provenance(hiit_proc)
#> metabom8 processing pipeline:
#> ==============================
#> [1] calibrate
#>      params:
#>         target :
#>             mode   : singlet
#>             window : [-0.2, 0.2]
#>             centre : 0
#>      notes: Chemical shift calibration applied.
#> 
#> [2] excise1d
#>      params:
#>         regions :
#>             upfield_noise   : [-5.21794, 0.25]
#>             water           : [4.5, 5.2]
#>             urea            : [5.5, 6]
#>             downfield_noise : [9.7, 14.8037]
#>      notes: Specified chemical shift regions removed using get_idx().
#> 
#> [3] user note
#>      params:
#>         runtime  : docker
#>         image    : docker-image-dummy
#>         workflow : std_prof-urine
#>         agent    : snakemake/v?
#>         run_id   : m8-2605-001
#>      notes: dilution-adaptive acquisition mode -> verify snr after normalisation
#>