Certifying outputs and detecting drift

This vignette covers Tier 2 of the reproducr workflow in depth: certify(), check_drift(), and list_certs(). These three functions together form the baseline and drift detection system.

The problem they solve — a real scenario

Scenario — The revision drift problem

You submit a paper in March. Before submission you run the analysis and note the key results: hazard ratio 0.582 (95% CI: 0.446–0.760, p < 0.001).

In May a reviewer asks for a revision. While working on the response you upgrade your packages — including lme4, which adjusted its default optimizer tolerances between versions 1.1.29 and 1.1.30. You re-run the analysis: hazard ratio 0.591 (95% CI: 0.452–0.768).

The numbers are slightly different. No error was thrown. The code is identical. Without a record of what the March run produced, you would not know whether the change came from your revision or from the package upgrade.

[DRIFTED] hr:       0.582 → 0.591
[DRIFTED] ci_lower: 0.446 → 0.452
[DRIFTED] ci_upper: 0.760 → 0.768

With certify() and check_drift(), this is caught immediately and you can investigate before submitting to the reviewer.

More broadly, packages change hands, maintainers push silent fixes, platform-level libraries (BLAS, LAPACK) get updated by system administrators, and R itself changes RNG defaults between minor versions. Any of these can alter your numerical results without producing an error.

certify() and check_drift() detect this. The idea is simple:

After a successful analysis run, hash the key outputs and store the hashes.
Later — after any change to the environment — re-run the analysis and compare the new hashes against the stored ones.
Any mismatch is reported explicitly, by output name.

`certify()` — creating a baseline

What gets hashed

Pass a fully named list of any R objects you want to protect. Common choices:

model <- lm(mpg ~ wt + cyl, data = mtcars)

certify(
  outputs = list(
    coefs       = coef(model),
    r_squared   = summary(model)$r.squared,
    sigma       = sigma(model),
    n_obs       = nrow(mtcars),
    n_complete  = sum(complete.cases(mtcars)),
    group_means = aggregate(mpg ~ cyl, data = mtcars, FUN = mean)
  ),
  tag = "baseline-v1",
  script = "analysis.R",
  file = cert_file
)
#> reproducr: certified 6 output(s) [2026-06-20] under tag 'baseline-v1'

Choosing what to certify

Certify outputs that are:

Conclusions — the numbers that appear in your paper or report
Stable — not random session artefacts like timestamps or row ordering
Interpretable — so a drift report tells you something meaningful

Avoid certifying objects that are expected to differ across runs by design, such as proc.time() outputs or Sys.time() values.

Tags and the certification store

Every certification requires a tag — a human-readable label:

certify(
  outputs = list(coefs = coef(model)),
  tag     = "pre-peer-review",
  file    = cert_file
)
#> reproducr: certified 1 output(s) [2026-06-20] under tag 'pre-peer-review'

certify(
  outputs = list(coefs = coef(model)),
  tag     = "post-revision",
  file    = cert_file
)
#> reproducr: certified 1 output(s) [2026-06-20] under tag 'post-revision'

Passing a duplicate tag overwrites the existing record with a warning:

certify(
  outputs = list(coefs = coef(model)),
  tag     = "baseline-v1",
  file    = cert_file
)
#> Warning: Tag 'baseline-v1' already exists in '/tmp/RtmpqLnHka/file9c28142b59'.
#> Overwriting.
#> reproducr: certified 1 output(s) [2026-06-20] under tag 'baseline-v1'

`list_certs()` — inspecting the store

list_certs(file = cert_file)
#>               tag                timestamp r_version                      os
#> 1     baseline-v1 2026-06-20T17:30:57+0000     4.6.0 Linux 6.17.0-1018-azure
#> 2 pre-peer-review 2026-06-20T17:30:57+0000     4.6.0 Linux 6.17.0-1018-azure
#> 3   post-revision 2026-06-20T17:30:57+0000     4.6.0 Linux 6.17.0-1018-azure
#>   n_outputs script
#> 1         1   <NA>
#> 2         1   <NA>
#> 3         1   <NA>

`check_drift()` — comparing against a baseline

Basic usage

model2 <- lm(mpg ~ wt + cyl, data = mtcars)

result <- check_drift(
  outputs = list(
    coefs       = coef(model2),
    r_squared   = summary(model2)$r.squared,
    sigma       = sigma(model2),
    n_obs       = nrow(mtcars),
    n_complete  = sum(complete.cases(mtcars)),
    group_means = aggregate(mpg ~ cyl, data = mtcars, FUN = mean)
  ),
  against = "baseline-v1",
  file = cert_file
)
#> -- reproducr drift check vs 'baseline-v1' --
#>   Verdict  : ALL OUTPUTS MATCH
#>   OK       : 1
#>   Drifted  : 0
#>   Missing  : 0
#>   New      : 5

The four statuses

certify(
  outputs = list(
    stays_same  = 42L,
    will_change = coef(lm(mpg ~ wt, data = mtcars)),
    will_vanish = "this output disappears next run"
  ),
  tag = "four-statuses",
  file = cert_file
)
#> reproducr: certified 3 output(s) [2026-06-20] under tag 'four-statuses'

demo_result <- check_drift(
  outputs = list(
    stays_same  = 42L,
    will_change = coef(lm(mpg ~ hp, data = mtcars)),
    brand_new   = "this output is new"
  ),
  against = "four-statuses",
  file = cert_file
)
#> -- reproducr drift check vs 'four-statuses' --
#>   Verdict  : DRIFT DETECTED
#>   OK       : 1
#>   Drifted  : 1
#>   Missing  : 1
#>   New      : 1
#>   Drifted outputs:
#>     - will_change

print(demo_result)
#> 
#> -- reproducr drift report --
#> 
#> [OK]      stays_same
#> [DRIFT]   will_change
#>             Hash mismatch (numeric tolerance check requires stored values).
#> [NEW]     brand_new
#>             Not present in the baseline certification.
#> [MISSING] will_vanish
#>             Present in baseline but not supplied to check_drift().

Status	Meaning
`ok`	Hash matches the baseline exactly
`drifted`	Hash differs — output has changed
`missing`	Present in baseline, not supplied to `check_drift()`
`new`	Supplied to `check_drift()`, not in baseline

Using `"latest"`

certify(outputs = list(x = 1L), tag = "run-1", file = cert_file)
#> reproducr: certified 1 output(s) [2026-06-20] under tag 'run-1'
certify(outputs = list(x = 1L), tag = "run-2", file = cert_file)
#> reproducr: certified 1 output(s) [2026-06-20] under tag 'run-2'
certify(outputs = list(x = 1L), tag = "run-3", file = cert_file)
#> reproducr: certified 1 output(s) [2026-06-20] under tag 'run-3'

check_drift(outputs = list(x = 1L), against = "latest", file = cert_file)
#> reproducr: comparing against latest tag: 'run-3'
#> -- reproducr drift check vs 'run-3' --
#>   Verdict  : ALL OUTPUTS MATCH
#>   OK       : 1
#>   Drifted  : 0
#>   Missing  : 0
#>   New      : 0

Using drift results programmatically

result <- check_drift(outputs = current_outputs, against = "latest")

n_drifted <- sum(result$status == "drifted")
if (n_drifted > 0L) {
  drifted_names <- result$output[result$status == "drifted"]
  stop(sprintf(
    "%d output(s) have drifted since last certification: %s",
    n_drifted,
    paste(drifted_names, collapse = ", ")
  ))
}

Recommended workflow

At submission

certify(
  outputs = list(
    primary_coef = coef(model)[2],
    primary_pval = summary(model)$coefficients[2, 4],
    n            = nrow(data),
    effect_size  = compute_d(model)
  ),
  tag    = "submitted-2026-01-15",
  script = "main_analysis.R"
)

After reviewer comments

check_drift(
  outputs = list(
    primary_coef = coef(model)[2],
    primary_pval = summary(model)$coefficients[2, 4],
    n            = nrow(data),
    effect_size  = compute_d(model)
  ),
  against = "submitted-2026-01-15"
)

Version control

Commit .reproducr.rds to your Git repository. This gives you a permanent, auditable history of what every run produced, and lets you compare against any past milestone.

Add to .gitattributes to prevent noisy diffs:

.reproducr.rds binary