Merge branch 'main' into support-distributional

easystats · Jan 31, 2025 · a134c85 · a134c85
2 parents a99307c + d8edd37
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,28 +1,28 @@
 Type: Package
 Package: bayestestR
 Title: Understand and Describe Bayesian Models and Posterior Distributions
-Version: 0.14.0.11
+Version: 0.15.1.2
 Authors@R:
     c(person(given = "Dominique",
              family = "Makowski",
              role = c("aut", "cre"),
              email = "[email protected]",
-             comment = c(ORCID = "0000-0001-5375-9967", Twitter = "@Dom_Makowski")),
+             comment = c(ORCID = "0000-0001-5375-9967")),
       person(given = "Daniel",
              family = "Lüdecke",
              role = "aut",
              email = "[email protected]",
-             comment = c(ORCID = "0000-0002-8895-3206", Twitter = "@strengejacke")),
+             comment = c(ORCID = "0000-0002-8895-3206")),
       person(given = "Mattan S.",
              family = "Ben-Shachar",
              role = "aut",
              email = "[email protected]",
-             comment = c(ORCID = "0000-0002-4287-4801", Twitter = "@mattansb")),
+             comment = c(ORCID = "0000-0002-4287-4801")),
       person(given = "Indrajeet",
              family = "Patil",
              role = "aut",
              email = "[email protected]",
-             comment = c(ORCID = "0000-0003-1995-6531", Twitter = "@patilindrajeets")),
+             comment = c(ORCID = "0000-0003-1995-6531")),
       person(given = "Micah K.",
              family = "Wilson",
              role = "aut",
@@ -32,7 +32,7 @@ Authors@R:
              family = "Wiernik",
              role = "aut",
              email = "[email protected]",
-             comment = c(ORCID = "0000-0001-9560-6336", Twitter = "@bmwiernik")),
+             comment = c(ORCID = "0000-0001-9560-6336")),
       person(given = "Paul-Christian",
              family = "Bürkner",
              role = "rev",
@@ -66,8 +66,8 @@ Description: Provides utilities to describe posterior
 Depends:
     R (>= 3.6)
 Imports:
-    insight (>= 0.20.4),
-    datawizard (>= 0.12.3),
+    insight (>= 1.0.0),
+    datawizard (>= 1.0.0),
     graphics,
     methods,
     stats,
@@ -81,6 +81,7 @@ Suggests:
     blavaan,
     bridgesampling,
     brms,
+    collapse,
     curl,
     distributional,
     effectsize,
@@ -89,14 +90,13 @@ Suggests:
     ggdist,
     ggplot2,
     glmmTMB,
-    httr,
     httr2,
     KernSmooth,
     knitr,
     lavaan,
     lme4,
     logspline (>= 2.1.21),
-    marginaleffects (>= 0.21.0),
+    marginaleffects (>= 0.24.0),
     MASS,
     mclust,
     mediation,
@@ -113,7 +113,8 @@ Suggests:
     rstanarm,
     see (>= 0.8.5),
     testthat,
-    tweedie
+    tweedie,
+    withr
 License: GPL-3
 URL: https://easystats.github.io/bayestestR/
 BugReports: https://github.com/easystats/bayestestR/issues
@@ -128,4 +129,3 @@ Config/testthat/parallel: true
 Config/rcmdcheck/ignore-inconsequential-notes: true
 Config/Needs/website: easystats/easystatstemplate
 Config/Needs/check: stan-dev/cmdstanr
-Remotes: easystats/insight, easystats/datawizard
diff --git a/NAMESPACE b/NAMESPACE
@@ -112,7 +112,6 @@ S3method(ci,sim.merMod)
 S3method(ci,slopes)
 S3method(ci,stanfit)
 S3method(ci,stanreg)
-S3method(cwi,data.frame)
 S3method(describe_posterior,BFBayesFactor)
 S3method(describe_posterior,BGGM)
 S3method(describe_posterior,MCMCglmm)
@@ -643,7 +642,6 @@ export(contr.orthonorm)
 export(convert_bayesian_as_frequentist)
 export(convert_p_to_pd)
 export(convert_pd_to_p)
-export(cwi)
 export(density_at)
 export(describe_posterior)
 export(describe_prior)

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,21 @@
-# bayestestR (development version)
+# bayestestR 0.15.2
+
+## Changes
+
+* `describe_posterior()` no longer re-samples a model when computing
+  indices.
+
+# bayestestR 0.15.1
+
+## Changes
+
+* Several minor changes to deal with recent changes in other packages.
+
+## Bug fixes
+
+* Fix to `emmeans` / `marginaleffects` / `data.frame(<rvar>)` methods when using multiple credible levels (#688).
+
+# bayestestR 0.15.0
 
 ## Changes
 

diff --git a/R/bayesfactor.R b/R/bayesfactor.R
@@ -2,11 +2,11 @@
 #'
 #' This function compte the Bayes factors (BFs) that are appropriate to the
 #' input. For vectors or single models, it will compute [`BFs for single
-#' parameters()`][bayesfactor_parameters], or is `hypothesis` is specified,
-#' [`BFs for restricted models()`][bayesfactor_restricted]. For multiple models,
+#' parameters`][bayesfactor_parameters], or is `hypothesis` is specified,
+#' [`BFs for restricted models`][bayesfactor_restricted]. For multiple models,
 #' it will return the BF corresponding to [`comparison between
-#' models()`][bayesfactor_models] and if a model comparison is passed, it will
-#' compute the [`inclusion BF()`][bayesfactor_inclusion].
+#' models`][bayesfactor_models] and if a model comparison is passed, it will
+#' compute the [`inclusion BF`][bayesfactor_inclusion].
 #' \cr\cr
 #' For a complete overview of these functions, read the [Bayes factor vignette](https://easystats.github.io/bayestestR/articles/bayes_factors.html).
 #'
@@ -17,19 +17,20 @@
 #' @inheritParams bayesfactor_models
 #' @inheritParams bayesfactor_inclusion
 #'
-#' @return Some type of Bayes factor, depending on the input. See [bayesfactor_parameters()], [bayesfactor_models()] or [bayesfactor_inclusion()]
+#' @return Some type of Bayes factor, depending on the input. See
+#' [`bayesfactor_parameters()`], [`bayesfactor_models()`] or [`bayesfactor_inclusion()`].
 #'
 #' @note There is also a [`plot()`-method](https://easystats.github.io/see/articles/bayestestR.html) implemented in the \href{https://easystats.github.io/see/}{\pkg{see}-package}.
 #'
 #' @examplesIf require("rstanarm") && require("logspline")
+#' \dontrun{
 #' library(bayestestR)
 #'
 #' prior <- distribution_normal(1000, mean = 0, sd = 1)
-#' posterior <- distribution_normal(1000, mean = .5, sd = .3)
+#' posterior <- distribution_normal(1000, mean = 0.5, sd = 0.3)
 #'
 #' bayesfactor(posterior, prior = prior, verbose = FALSE)
 #'
-#' \donttest{
 #' # rstanarm models
 #' # ---------------
 #' model <- suppressWarnings(rstanarm::stan_lmer(extra ~ group + (1 | ID), data = sleep))

diff --git a/R/bayesfactor_parameters.R b/R/bayesfactor_parameters.R
@@ -323,7 +323,6 @@ bayesfactor_parameters.stanreg <- function(posterior,
 }
 
 
-
 #' @rdname bayesfactor_parameters
 #' @export
 bayesfactor_parameters.brmsfit <- bayesfactor_parameters.stanreg

diff --git a/R/bci.R b/R/bci.R
@@ -27,7 +27,6 @@ bci <- function(x, ...) {
 bcai <- bci
 
 
-
 #' @rdname bci
 #' @export
 bci.numeric <- function(x, ci = 0.95, verbose = TRUE, ...) {
@@ -40,7 +39,6 @@ bci.numeric <- function(x, ci = 0.95, verbose = TRUE, ...) {
 }
 
 
-
 #' @rdname bci
 #' @inheritParams p_direction
 #' @export
@@ -66,7 +64,6 @@ bci.data.frame <- function(x, ci = 0.95, rvar_col = NULL, verbose = TRUE, ...) {
 }
 
 
-
 #' @export
 bci.draws <- function(x, ci = 0.95, verbose = TRUE, ...) {
   dat <- .compute_interval_dataframe(x = .posterior_draws_to_df(x), ci = ci, verbose = verbose, fun = "bci")
@@ -89,7 +86,6 @@ bci.MCMCglmm <- function(x, ci = 0.95, verbose = TRUE, ...) {
 }
 
 
-
 #' @export
 bci.mcmc <- function(x, ci = 0.95, verbose = TRUE, ...) {
   d <- as.data.frame(x)
@@ -99,7 +95,6 @@ bci.mcmc <- function(x, ci = 0.95, verbose = TRUE, ...) {
 }
 
 
-
 #' @export
 bci.bamlss <- function(x,
                        ci = 0.95,
@@ -114,7 +109,6 @@ bci.bamlss <- function(x,
 }
 
 
-
 #' @export
 bci.bcplm <- function(x, ci = 0.95, verbose = TRUE, ...) {
   d <- insight::get_parameters(x)
@@ -137,7 +131,6 @@ bci.mcmc.list <- bci.bcplm
 bci.BGGM <- bci.bcplm
 
 
-
 #' @rdname bci
 #' @export
 bci.sim.merMod <- function(x,
@@ -161,7 +154,6 @@ bci.sim.merMod <- function(x,
 }
 
 
-
 #' @rdname bci
 #' @export
 bci.sim <- function(x, ci = 0.95, parameters = NULL, verbose = TRUE, ...) {
@@ -178,7 +170,6 @@ bci.sim <- function(x, ci = 0.95, parameters = NULL, verbose = TRUE, ...) {
 }
 
 
-
 #' @rdname bci
 #' @export
 bci.emmGrid <- function(x, ci = 0.95, verbose = TRUE, ...) {
@@ -249,7 +240,6 @@ bci.stanfit <- bci.stanreg
 bci.blavaan <- bci.stanreg
 
 
-
 #' @rdname bci
 #' @export
 bci.brmsfit <- function(x, ci = 0.95, effects = c("fixed", "random", "all"),
@@ -279,7 +269,6 @@ bci.brmsfit <- function(x, ci = 0.95, effects = c("fixed", "random", "all"),
 }
 
 
-
 #' @rdname bci
 #' @export
 bci.BFBayesFactor <- function(x, ci = 0.95, verbose = TRUE, ...) {

diff --git a/R/bic_to_bf.R b/R/bic_to_bf.R
@@ -27,8 +27,8 @@ bic_to_bf <- function(bic, denominator, log = FALSE) {
   delta <- (denominator - bic) / 2
 
   if (log) {
-    return(delta)
+    delta
   } else {
-    return(exp(delta))
+    exp(delta)
   }
 }
diff --git a/R/check_prior.R b/R/check_prior.R
@@ -50,9 +50,6 @@ check_prior <- function(model, method = "gelman", simulate_priors = TRUE, ...) {
 }
 
 
-
-
-
 #' @export
 check_prior.brmsfit <- function(model,
                                 method = "gelman",

diff --git a/R/contr.equalprior.R b/R/contr.equalprior.R
@@ -184,7 +184,6 @@ contr.equalprior_deviations <- function(n, contrasts = TRUE, sparse = FALSE) {
 }
 
 
-
 # OLD ------------------------------
 
 #' @export

diff --git a/R/convert_pd_to_p.R b/R/convert_pd_to_p.R
@@ -19,11 +19,11 @@
 #'
 #' When `direction = "two-sided"`
 #'
-#' \deqn{p = 2 \times (1 - p_d)}{p = 2 * (1 - pd)}
+#' \ifelse{html}{\out{p = 2 * (1 - p<sub>d</sub>)}}{\eqn{p = 2 \times (1 - p_d)}}
 #'
 #' When `direction = "one-sided"`
 #'
-#' \deqn{p = 1 - p_d}{p = 1 - pd}
+#' \ifelse{html}{\out{p = 1 - p<sub>d</sub>}}{\eqn{p = 1 - p_d}}
 #'
 #' Note that this conversion is only valid when the lowest possible values of pd
 #' is 0.5 - i.e., when the posterior represents continuous parameter space (see
@@ -95,7 +95,6 @@ p_to_pd <- function(p, direction = "two-sided", ...) {
 }
 
 
-
 #' @rdname pd_to_p
 #' @export
 convert_p_to_pd <- p_to_pd
-Original file line number
+Diff line change
@@ Expand Up / @@ -323,7 +323,6 @@ bayesfactor_parameters.stanreg <- function(posterior, @@
     }
     #' @rdname bayesfactor_parameters
     #' @export
     bayesfactor_parameters.brmsfit <- bayesfactor_parameters.stanreg
@@ Expand Down @@
Original file line number	Diff line number	Diff line change
Expand Up		@@ -184,7 +184,6 @@ contr.equalprior_deviations <- function(n, contrasts = TRUE, sparse = FALSE) {
		}



		# OLD ------------------------------

		#' @export
Expand Down