Prepare CRAN submission (#691)

* Prepare CRAN submission * fix vignette? * styler * fix * docs
easystats · Jan 17, 2025 · fb746e3 · fb746e3
1 parent 55f598a
commit fb746e3
Show file tree

Hide file tree

Showing 47 changed files with 51 additions and 191 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: bayestestR
 Title: Understand and Describe Bayesian Models and Posterior Distributions
-Version: 0.15.0.4
+Version: 0.15.1
 Authors@R:
     c(person(given = "Dominique",
              family = "Makowski",
@@ -67,7 +67,7 @@ Depends:
     R (>= 3.6)
 Imports:
     insight (>= 1.0.0),
-    datawizard (>= 0.13.0),
+    datawizard (>= 1.0.0),
     graphics,
     methods,
     stats,
@@ -95,7 +95,7 @@ Suggests:
     lavaan,
     lme4,
     logspline (>= 2.1.21),
-    marginaleffects (>= 0.24.0.6),
+    marginaleffects (>= 0.24.0),
     MASS,
     mclust,
     mediation,
@@ -128,4 +128,3 @@ Config/testthat/parallel: true
 Config/rcmdcheck/ignore-inconsequential-notes: true
 Config/Needs/website: easystats/easystatstemplate
 Config/Needs/check: stan-dev/cmdstanr
-Remotes: easystats/datawizard, vincentarelbundock/marginaleffects
diff --git a/NEWS.md b/NEWS.md
@@ -1,10 +1,13 @@
-# bayestestR 0.15.0.4
+# 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_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/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
@@ -95,7 +95,6 @@ p_to_pd <- function(p, direction = "two-sided", ...) {
 }
 
 
-
 #' @rdname pd_to_p
 #' @export
 convert_p_to_pd <- p_to_pd

diff --git a/R/describe_posterior.R b/R/describe_posterior.R
@@ -11,11 +11,11 @@
 #'   `"SPI"` (see [`spi()`]), or `"SI"` (see [`si()`]).
 #' @param test The indices of effect existence to compute. Character (vector) or
 #'   list with one or more of these options: `"p_direction"` (or `"pd"`),
-#'   `"rope"`, `"p_map"`, `"equivalence_test"` (or `"equitest"`),
-#'   `"bayesfactor"` (or `"bf"`) or `"all"` to compute all tests. For each
-#'   "test", the corresponding \pkg{bayestestR} function is called (e.g.
-#'   [`rope()`] or [`p_direction()`]) and its results included in the summary
-#'   output.
+#'   `"rope"`, `"p_map"`, `"p_significance"` (or `"ps"`), `"p_rope"`,
+#'   `"equivalence_test"` (or `"equitest"`), `"bayesfactor"` (or `"bf"`) or
+#'   `"all"` to compute all tests. For each "test", the corresponding
+#'   \pkg{bayestestR} function is called (e.g. [`rope()`] or [`p_direction()`])
+#'   and its results included in the summary output.
 #' @param rope_range ROPE's lower and higher bounds. Should be a vector of two
 #'   values (e.g., `c(-0.1, 0.1)`), `"default"` or a list of numeric vectors of
 #'   the same length as numbers of parameters. If `"default"`, the bounds are
@@ -528,8 +528,6 @@ describe_posterior.default <- function(posterior, ...) {
 }
 
 
-
-
 # Models based on simple data frame of posterior ---------------------
 
 
@@ -728,7 +726,6 @@ describe_posterior.draws <- function(posterior,
 describe_posterior.rvar <- describe_posterior.draws
 
 
-
 # easystats methods ------------------------
 
 
@@ -825,8 +822,6 @@ describe_posterior.get_predicted <- function(posterior,
 }
 
 
-
-
 # emmeans ---------------------------
 
 
@@ -1221,8 +1216,6 @@ describe_posterior.brmsfit <- function(posterior,
 describe_posterior.blavaan <- describe_posterior.stanfit
 
 
-
-
 # other models --------------------------------
 
 
@@ -1345,8 +1338,6 @@ describe_posterior.bamlss <- function(posterior,
 }
 
 
-
-
 # BayesFactor --------------------
 
 
@@ -1431,9 +1422,6 @@ describe_posterior.BFBayesFactor <- function(posterior,
 }
 
 
-
-
-
 # Helpers -----------------------------------------------------------------
 
 

diff --git a/R/describe_prior.R b/R/describe_prior.R
@@ -53,7 +53,6 @@ describe_prior.brmsfit <- function(model,
 # Internal ----------------------------------------------------------------
 
 
-
 #' @keywords internal
 .describe_prior <- function(model, parameters = NULL, ...) {
   priors <- insight::get_priors(model, ...)

diff --git a/R/distribution.R b/R/distribution.R
@@ -67,10 +67,6 @@ distribution_custom <- function(n, type = "norm", ..., random = FALSE) {
 }
 
 
-
-
-
-
 #' @rdname distribution
 #' @inheritParams stats::rbeta
 #' @export
@@ -99,7 +95,6 @@ distribution_binomial <- function(n, size = 1, prob = 0.5, random = FALSE, ...)
 distribution_binom <- distribution_binomial
 
 
-
 #' @rdname distribution
 #' @inheritParams stats::rcauchy
 #' @export
@@ -127,7 +122,6 @@ distribution_chisquared <- function(n, df, ncp = 0, random = FALSE, ...) {
 distribution_chisq <- distribution_chisquared
 
 
-
 #' @rdname distribution
 #' @inheritParams stats::rgamma
 #' @param shape Shape parameter.
@@ -267,7 +261,6 @@ distribution_uniform <- function(n, min = 0, max = 1, random = FALSE, ...) {
 }
 
 
-
 #' @rdname distribution
 #' @inheritParams stats::rnorm
 #' @export

diff --git a/R/equivalence_test.R b/R/equivalence_test.R
@@ -147,7 +147,6 @@ equivalence_test.numeric <- function(x, range = "default", ci = 0.95, verbose =
 }
 
 
-
 #' @rdname equivalence_test
 #' @inheritParams p_direction
 #' @export
@@ -256,8 +255,6 @@ equivalence_test.BFBayesFactor <- function(x, range = "default", ci = 0.95, verb
 }
 
 
-
-
 #' @keywords internal
 .equivalence_test_models <- function(x,
                                      range = "default",
@@ -354,7 +351,6 @@ equivalence_test.brmsfit <- function(x,
 }
 
 
-
 #' @export
 equivalence_test.sim.merMod <- function(x,
                                         range = "default",
@@ -433,7 +429,6 @@ equivalence_test.mcmc.list <- equivalence_test.bcplm
 equivalence_test.bayesQR <- equivalence_test.bcplm
 
 
-
 #' @export
 equivalence_test.bamlss <- function(x,
                                     range = "default",

diff --git a/R/estimate_density.R b/R/estimate_density.R
@@ -161,7 +161,6 @@ estimate_density.default <- function(x, ...) {
 }
 
 
-
 # Methods -----------------------------------------------------------------
 
 #' @export
@@ -589,7 +588,6 @@ estimate_density.bamlss <- function(x,
 }
 
 
-
 #' Coerce to a Data Frame
 #'
 #' @inheritParams base::as.data.frame
@@ -644,8 +642,6 @@ as.data.frame.density <- function(x, ...) {
 }
 
 
-
-
 #' Density Probability at a Given Value
 #'
 #' Compute the density value at a given point of a distribution (i.e.,

diff --git a/R/eti.R b/R/eti.R
@@ -64,7 +64,6 @@ eti.numeric <- function(x, ci = 0.95, verbose = TRUE, ...) {
 }
 
 
-
 #' @export
 #' @rdname eti
 #' @inheritParams p_direction
@@ -91,7 +90,6 @@ eti.data.frame <- function(x, ci = 0.95, rvar_col = NULL, verbose = TRUE, ...) {
 }
 
 
-
 #' @export
 eti.draws <- function(x, ci = 0.95, verbose = TRUE, ...) {
   dat <- .compute_interval_dataframe(x = .posterior_draws_to_df(x), ci = ci, verbose = verbose, fun = "eti")
@@ -103,7 +101,6 @@ eti.draws <- function(x, ci = 0.95, verbose = TRUE, ...) {
 eti.rvar <- eti.draws
 
 
-
 #' @export
 eti.MCMCglmm <- function(x, ci = 0.95, verbose = TRUE, ...) {
   nF <- x$Fixed$nfl
@@ -114,7 +111,6 @@ eti.MCMCglmm <- function(x, ci = 0.95, verbose = TRUE, ...) {
 }
 
 
-
 #' @export
 eti.mcmc <- function(x, ci = 0.95, verbose = TRUE, ...) {
   d <- as.data.frame(x)
@@ -124,7 +120,6 @@ eti.mcmc <- function(x, ci = 0.95, verbose = TRUE, ...) {
 }
 
 
-
 #' @export
 eti.bamlss <- function(x, ci = 0.95, component = c("all", "conditional", "location"), verbose = TRUE, ...) {
   component <- match.arg(component)
@@ -135,7 +130,6 @@ eti.bamlss <- function(x, ci = 0.95, component = c("all", "conditional", "locati
 }
 
 
-
 #' @export
 eti.bcplm <- function(x, ci = 0.95, verbose = TRUE, ...) {
   d <- insight::get_parameters(x)
@@ -248,7 +242,6 @@ eti.stanfit <- eti.stanreg
 eti.blavaan <- eti.stanreg
 
 
-
 #' @rdname eti
 #' @export
 eti.brmsfit <- function(x, ci = 0.95, effects = c("fixed", "random", "all"),
-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