Analysis Manifests and Reproducible Bayesian Workflows

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A manifest is an analysis contract about the analysis contract

A fitted model is not enough to reconstruct an analysis decision process. gp3bayes 0.2.0 therefore provides an analysis manifest that records the approved model contract, preparation/transformation record, specification, prespecified estimands, sensitivity plan, seed, backend metadata, software versions, and a fingerprint of the analysis data.

The manifest stores a fingerprint rather than duplicating the analysis data. It is provenance metadata, not a hidden data archive.

Create a manifest before fitting

simulation <- simulate_hierarchical_binary_data(
  n_participants = 10,
  trials_per_participant = 8,
  n_items = 5,
  random_slope_sd = 0,
  seed = 42
)

contract <- create_model_contract(
  "binary", "selected", "participant_id",
  item_col = "item_id",
  trial_col = "trial_id",
  condition_col = "condition"
)

prepared <- prepare_hierarchical_binary_data(
  simulation$data,
  contract,
  condition_levels = c("control", "treatment")
)

specification <- specify_binary_model(prepared, baseline = 0.35)

manifest <- create_analysis_manifest(
  specification = specification,
  estimands = "standardized_probability_contrast",
  seed = 2026,
  label = "Synthetic binary release case"
)

manifest
#> <gp3bayes_analysis_manifest>
#>   Version: 0.2
#>   Label: Synthetic binary release case
#>   Family: binary
#>   Data: 80 x 8
#>   Data hash: 09ab941d91559d015dc9fe304ebfb2e7
#>   Frozen: FALSE
analysis_manifest_table(manifest)
#>              component                            value
#> 1               family                           binary
#> 2         model_family              hierarchical_binary
#> 3            data_hash 09ab941d91559d015dc9fe304ebfb2e7
#> 4        contract_hash a004cd56a9d35cff138e36f46a836579
#> 5   specification_hash 309b774249f3f72e44c7e76d8a98f318
#> 6  transformation_hash bb87585a96dfafaf1dc60c74014e0038
#> 7                 seed                             2026
#> 8              backend                             <NA>
#> 9               frozen                            FALSE
#> 10       manifest_hash                             <NA>
validate_analysis_manifest(manifest)
#> <gp3bayes_manifest_validation>
#>   Status: pass
#>             check status                           detail
#>    manifest_class   pass       gp3bayes_analysis_manifest
#>   required_fields   pass                         complete
#>  data_fingerprint   pass 09ab941d91559d015dc9fe304ebfb2e7
#>   approved_family   pass                           binary

Freeze only when the analysis-defining fields are ready

Freezing computes a manifest hash. With file = NULL, no file is written.

frozen <- freeze_analysis_manifest(manifest)
frozen
#> <gp3bayes_analysis_manifest>
#>   Version: 0.2
#>   Label: Synthetic binary release case
#>   Family: binary
#>   Data: 80 x 8
#>   Data hash: 09ab941d91559d015dc9fe304ebfb2e7
#>   Frozen: TRUE
#>   Manifest hash: 20fba3737ca2d81bb535d8f8ccb24b7f

Writing is always explicit. Temporary files are used here so the vignette does not write into the package or working directory.

manifest_file <- tempfile(fileext = ".rds")
report_file <- tempfile(fileext = ".md")

freeze_analysis_manifest(manifest, file = manifest_file)
#> <gp3bayes_analysis_manifest>
#>   Version: 0.2
#>   Label: Synthetic binary release case
#>   Family: binary
#>   Data: 80 x 8
#>   Data hash: 09ab941d91559d015dc9fe304ebfb2e7
#>   Frozen: TRUE
#>   Manifest hash: 20fba3737ca2d81bb535d8f8ccb24b7f
restored <- read_analysis_manifest(manifest_file)
write_reproducibility_report(restored, report_file)

file.exists(manifest_file)
#> [1] TRUE
file.exists(report_file)
#> [1] TRUE

unlink(c(manifest_file, report_file))

Compare analysis provenance

A difference is reported, not judged automatically.

alternative <- create_analysis_manifest(
  specification = specification,
  estimands = "standardized_probability_contrast",
  seed = 2027,
  label = "Alternative seed"
)

comparison <- compare_analysis_manifests(manifest, alternative)
comparison
#> <gp3bayes_manifest_comparison>
#>   Identical: FALSE
#>   Changed: seed
plot(comparison)

This comparison is particularly useful during revisions, refits, or a package upgrade: it makes changes to the data fingerprint, transformations, priors, estimands, seed, backend settings, or software environment visible without pretending that every difference is scientifically consequential.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.