new methods and cleaned up docs #738

mattansb · 2025-09-02T19:28:23Z

gemini-code-assist

Summary of Changes

Hello @mattansb, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request focuses on enhancing the usability and clarity of the Bayes factor functionalities within the bayestestR package. It introduces a centralized documentation hub for Bayes factor methods and refactors the underlying S3 method dispatch to improve code organization and maintainability. The changes aim to provide a more consistent and informative experience for users working with Bayes factor objects.

Highlights

New Unified Bayes Factor Methods Documentation: A new dedicated documentation page, ?bayesfactor_methods, has been added to centralize information regarding various methods for Bayes factor objects, including interpretation, transitivity, and prior/posterior considerations.
Consolidation of S3 Methods: S3 methods for Bayes factor objects (e.g., as.numeric, as.matrix, as.logical, as.vector) have been consolidated under a new internal bayestestRBF class, streamlining method dispatch and reducing redundancy across individual Bayes factor functions.
Improved Function Documentation: Existing Bayes factor functions (bayesfactor_inclusion, bayesfactor_models, bayesfactor_parameters, bayesfactor_restricted, si) have received updated and cleaned-up documentation, with references to the new unified methods page and clearer explanations.

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Code Review

This pull request introduces a significant and beneficial refactoring by centralizing Bayes factor methods and their documentation into a new R/bayesfactor-methods.R file. This greatly improves code maintainability and consistency across the package by using a new bayestestRBF parent class. The documentation has also been cleaned up nicely. I've found a couple of minor issues to address: a small regression in functionality in the new print method and a typo in a warning message.

R/bayesfactor-methods.R

codecov · 2025-09-28T08:09:44Z

Codecov Report

❌ Patch coverage is 61.41732% with 49 lines in your changes missing coverage. Please review.
✅ Project coverage is 55.58%. Comparing base (6a8cb98) to head (585bff3).
⚠️ Report is 59 commits behind head on main.

Files with missing lines	Patch %	Lines
R/diagnostic_posterior.R	0.00%	16 Missing ⚠️
R/bayesfactor-methods.R	82.19%	13 Missing ⚠️
R/utils_bayesfactor.R	0.00%	11 Missing ⚠️
R/bayesfactor_models.R	75.00%	3 Missing ⚠️
R/print.equivalence_test.R	0.00%	2 Missing ⚠️
R/effective_sample.R	0.00%	1 Missing ⚠️
R/mcse.R	0.00%	1 Missing ⚠️
R/utils_check_collinearity.R	50.00%	1 Missing ⚠️
R/utils_clean_stan_parameters.R	50.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #738      +/-   ##
==========================================
+ Coverage   54.33%   55.58%   +1.25%     
==========================================
  Files          64       67       +3     
  Lines        6000     6196     +196     
==========================================
+ Hits         3260     3444     +184     
- Misses       2740     2752      +12

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

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strengejacke · 2025-10-16T12:31:53Z

gogogo!

github-actions · 2025-10-16T12:31:53Z

R/bayesfactor_models.R

    res <- .bayesfactor_models_stan_REG(mods, denominator, verbose)
    bf_method <- "marginal likelihoods (bridgesampling)"
-    unsupported_models <- FALSE
+    unsupported_models <- if (inherits(mods[[1]], c("stanfit", "CmdStanFit"))) TRUE else FALSE


[air] _{reported by reviewdog 🐶}

Suggested change

unsupported_models <- if (inherits(mods[[1]], c("stanfit", "CmdStanFit"))) TRUE else FALSE

unsupported_models <- if (inherits(mods[[1]], c("stanfit", "CmdStanFit"))) {

TRUE

} else {

FALSE

}

github-actions · 2025-10-16T12:31:53Z

R/bayesfactor_models.R

+    unsupported_models <- if (inherits(mods[[1]], c("stanfit", "CmdStanFit"))) TRUE else FALSE
  }

  .bf_models_output(res,


[air] _{reported by reviewdog 🐶}

Suggested change

.bf_models_output(res,

.bf_models_output(

res,

github-actions · 2025-10-16T12:31:53Z

R/bayesfactor_models.R

+      insight::format_error("Models were not computed from the same data.")
+    }
+  } else if (verbose) {
+    insight::format_alert("Unable to validate that all models were fit with the same data.")


[air] _{reported by reviewdog 🐶}

Suggested change

insight::format_alert("Unable to validate that all models were fit with the same data.")

insight::format_alert(

"Unable to validate that all models were fit with the same data."

)

github-actions · 2025-10-16T12:31:53Z

R/bayesfactor_models.R

  attr(res, "unsupported_models") <- unsupported_models
  attr(res, "model_names") <- model_names
-  class(res) <- c("bayesfactor_models", "see_bayesfactor_models", class(res))
+  class(res) <- c("bayestestRBF", "bayesfactor_models", "see_bayesfactor_models", class(res))


[air] _{reported by reviewdog 🐶}

Suggested change

class(res) <- c("bayestestRBF", "bayesfactor_models", "see_bayesfactor_models", class(res))

class(res) <- c(

"bayestestRBF",

"bayesfactor_models",

"see_bayesfactor_models",

class(res)

)

github-actions · 2025-10-16T12:31:53Z

R/diagnostic_posterior.R

+diagnostic_posterior.CmdStanFit <- function(posterior,
+                                            diagnostic = "all",
+                                            ...) {


[air] _{reported by reviewdog 🐶}

Suggested change

diagnostic_posterior.CmdStanFit <- function(posterior,

diagnostic = "all",

...) {

diagnostic_posterior.CmdStanFit <- function(posterior, diagnostic = "all", ...) {

github-actions · 2025-10-16T12:31:54Z

R/diagnostic_posterior.R

+
+  draws <- posterior$draws(format = "draws_df")
+
+  out <- posterior::summarize_draws(draws,


[air] _{reported by reviewdog 🐶}

Suggested change

out <- posterior::summarize_draws(draws,

out <- posterior::summarize_draws(

draws,

github-actions · 2025-10-16T12:31:54Z

R/utils_bayesfactor.R

+.clean_priors_and_posteriors.stanfit <- function(posterior, prior,
+                                                 verbose = TRUE,
+                                                 ...) {


[air] _{reported by reviewdog 🐶}

Suggested change

.clean_priors_and_posteriors.stanfit <- function(posterior, prior,

verbose = TRUE,

...) {

.clean_priors_and_posteriors.stanfit <- function(posterior, prior, verbose = TRUE, ...) {

github-actions · 2025-10-16T12:31:54Z

R/utils_check_collinearity.R

 .check_multicollinearity <- function(model,
                                     method = "equivalence_test",
                                     threshold = 0.7, ...) {


[air] _{reported by reviewdog 🐶}

Suggested change

.check_multicollinearity <- function(model,

method = "equivalence_test",

threshold = 0.7, ...) {

.check_multicollinearity <- function(

model,

method = "equivalence_test",

threshold = 0.7,

...

) {

github-actions · 2025-10-16T12:31:55Z

tests/testthat/test-bayesfactor_models.R

  expect_equal(update(BFM2, subset = c(1, 2))$log_BF, c(1, 57.3, 54.52), tolerance = 0.1)

  # update reference
  expect_equal(update(BFM2, reference = 1)$log_BF,


[air] _{reported by reviewdog 🐶}

Suggested change

expect_equal(update(BFM2, reference = 1)$log_BF,

expect_equal(

update(BFM2, reference = 1)$log_BF,

github-actions · 2025-10-16T12:31:55Z

tests/testthat/test-bayesfactor_models.R

  expect_equal(bfinc_matched$p_posterior, c(1, 0.875, 0.125, 0.009, 0.002), tolerance = 0.1)
  expect_equal(bfinc_matched$log_BF, c(NaN, 58.904, -3.045, -3.573, -1.493), tolerance = 0.1)


[air] _{reported by reviewdog 🐶}

Suggested change

expect_equal(bfinc_matched$p_posterior, c(1, 0.875, 0.125, 0.009, 0.002), tolerance = 0.1)

expect_equal(bfinc_matched$log_BF, c(NaN, 58.904, -3.045, -3.573, -1.493), tolerance = 0.1)

expect_equal(

bfinc_matched$p_posterior,

c(1, 0.875, 0.125, 0.009, 0.002),

tolerance = 0.1

)

expect_equal(

bfinc_matched$log_BF,

c(NaN, 58.904, -3.045, -3.573, -1.493),

tolerance = 0.1

)

github-actions · 2025-10-16T12:31:59Z

R/bayesfactor_parameters.R

[air] _{reported by reviewdog 🐶}

bayestestR/R/bayesfactor_parameters.R

Lines 182 to 187 in e6b1407

bayesfactor_parameters <- function(posterior,

prior = NULL,

direction = "two-sided",

null = 0,

...,

verbose = TRUE) {

github-actions · 2025-10-16T12:32:00Z

R/bayesfactor_parameters.R

[air] _{reported by reviewdog 🐶}

bayestestR/R/bayesfactor_parameters.R

Lines 329 to 334 in e6b1407

bayesfactor_parameters.blavaan <- function(posterior,

prior = NULL,

direction = "two-sided",

null = 0,

...,

verbose = TRUE) {

github-actions · 2025-10-16T12:32:01Z

R/bayesfactor_restricted.R

[air] _{reported by reviewdog 🐶}

bayestestR/R/bayesfactor_restricted.R

Lines 176 to 180 in e6b1407

bayesfactor_restricted.blavaan <- function(posterior, hypothesis, prior = NULL,

verbose = TRUE, ...) {

samps <- .clean_priors_and_posteriors(posterior, prior,

verbose = verbose

)

github-actions · 2025-10-16T12:32:01Z

R/si.R

[air] _{reported by reviewdog 🐶}

bayestestR/R/si.R

Lines 117 to 122 in e6b1407

si.stanreg <- function(posterior, prior = NULL,

BF = 1, verbose = TRUE,

effects = "fixed",

component = "location",

parameters = NULL,

...) {

github-actions · 2025-10-16T12:32:02Z

R/si.R

[air] _{reported by reviewdog 🐶}

bayestestR/R/si.R

Lines 125 to 127 in e6b1407

samps <- .clean_priors_and_posteriors(posterior, prior,

effects = effects, component = component,

parameters = parameters, verbose = verbose

github-actions · 2025-10-16T12:32:03Z

R/spi.R

[air] _{reported by reviewdog 🐶}

bayestestR/R/spi.R

Lines 191 to 197 in e6b1407

spi.stanreg <- function(x,

ci = 0.95,

effects = "fixed",

component = "location",

parameters = NULL,

verbose = TRUE,

...) {

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

github-actions · 2025-10-17T10:36:37Z

R/bayesfactor-methods.R

+  )
+
+  # caption and footer
+  caption <- switch(attr(orig_x, "bf_fun"),


[air] _{reported by reviewdog 🐶}

Suggested change

caption <- switch(attr(orig_x, "bf_fun"),

caption <- switch(

attr(orig_x, "bf_fun"),

github-actions · 2025-10-17T10:36:37Z

R/bayesfactor-methods.R

+#' @export
+as.numeric.bayestestRBF <- function(x, log = FALSE, ...) {
+  out <- x[["log_BF"]]
+  if (!log) out <- exp(out)


[air] _{reported by reviewdog 🐶}

Suggested change

if (!log) out <- exp(out)

if (!log) {

out <- exp(out)

}

mattansb · 2025-10-17T10:37:51Z

I think it'll be better to run AIR after merging this with main to avoid any issues.

strengejacke · 2025-10-17T13:19:14Z

Yes, I think you can ignore the formatting warnings for now.

new methods and cleaned up docs

684ec03

gemini-code-assist bot reviewed Sep 2, 2025

View reviewed changes

mattansb marked this pull request as draft September 2, 2025 19:28

gemini-code-assist bot reviewed Sep 2, 2025

View reviewed changes

R/bayesfactor-methods.R Show resolved Hide resolved

mattansb added 16 commits September 2, 2025 22:38

doc ...

899b2e7

styler

6e03063

make as.vector generic

df62b91

drop as.vector method

3fe649a

bew bfs for stan models

4c0513f

diagnostics

a656488

CI methods

149f8b3

density and point est

f8fccfa

spi and si

05f1479

fix arg name

b8d8a8f

roxygen

3fa18d5

pd etc.

6d00d58

describe_posterior

e03b2d5

equivalence_test

3bdbf11

bf_models

4603676

styler

585bff3

Merge branch 'main' into bf-docs-and-methods

e6b1407

github-actions bot reviewed Oct 16, 2025

View reviewed changes

mattansb and others added 2 commits October 17, 2025 13:35

Update R/bayesfactor-methods.R

90f6a65

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

Update R/bayesfactor-methods.R

ed52e07

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

github-actions bot reviewed Oct 17, 2025

View reviewed changes

-    unsupported_models <- if (inherits(mods[[1]], c("stanfit", "CmdStanFit"))) TRUE else FALSE
+    unsupported_models <- if (inherits(mods[[1]], c("stanfit", "CmdStanFit"))) {
+      TRUE
+    } else {
+      FALSE
+    }


		draws <- posterior$draws(format = "draws_df")

		out <- posterior::summarize_draws(draws,

	out <- posterior::summarize_draws(draws,
	out <- posterior::summarize_draws(
	draws,

	expect_equal(update(BFM2, reference = 1)$log_BF,
	expect_equal(
	update(BFM2, reference = 1)$log_BF,

		expect_equal(bfinc_matched$p_posterior, c(1, 0.875, 0.125, 0.009, 0.002), tolerance = 0.1)
		expect_equal(bfinc_matched$log_BF, c(NaN, 58.904, -3.045, -3.573, -1.493), tolerance = 0.1)

	bayesfactor_parameters <- function(posterior,
	prior = NULL,
	direction = "two-sided",
	null = 0,
	...,
	verbose = TRUE) {

	bayesfactor_parameters.blavaan <- function(posterior,
	prior = NULL,
	direction = "two-sided",
	null = 0,
	...,
	verbose = TRUE) {

	bayesfactor_restricted.blavaan <- function(posterior, hypothesis, prior = NULL,
	verbose = TRUE, ...) {
	samps <- .clean_priors_and_posteriors(posterior, prior,
	verbose = verbose
	)

	si.stanreg <- function(posterior, prior = NULL,
	BF = 1, verbose = TRUE,
	effects = "fixed",
	component = "location",
	parameters = NULL,
	...) {

	samps <- .clean_priors_and_posteriors(posterior, prior,
	effects = effects, component = component,
	parameters = parameters, verbose = verbose

	spi.stanreg <- function(x,
	ci = 0.95,
	effects = "fixed",
	component = "location",
	parameters = NULL,
	verbose = TRUE,
	...) {

	caption <- switch(attr(orig_x, "bf_fun"),
	caption <- switch(
	attr(orig_x, "bf_fun"),

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mattansb commented Sep 2, 2025 •

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