Merge branch 'main' into use-new-dlogspline

easystats · Feb 7, 2024 · 418b31c · 418b31c
2 parents da69f9e + d29b70c
commit 418b31c
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: bayestestR
 Title: Understand and Describe Bayesian Models and Posterior Distributions
-Version: 0.13.1.7
+Version: 0.13.1.9
 Authors@R:
     c(person(given = "Dominique",
              family = "Makowski",
@@ -66,8 +66,8 @@ Description: Provides utilities to describe posterior
 Depends:
     R (>= 3.6)
 Imports:
-    insight (>= 0.19.5),
-    datawizard (>= 0.9.0),
+    insight (>= 0.19.8),
+    datawizard (>= 0.9.1),
     graphics,
     methods,
     stats,

diff --git a/R/bayesfactor_parameters.R b/R/bayesfactor_parameters.R
@@ -297,9 +297,8 @@ bayesfactor_parameters.stanreg <- function(posterior,
   component <- match.arg(component)
 
   samps <- .clean_priors_and_posteriors(posterior, prior,
-    verbose = verbose,
     effects = effects, component = component,
-    parameters = parameters
+    parameters = parameters, verbose = verbose
   )
 
   # Get BFs

diff --git a/R/rope.R b/R/rope.R
@@ -328,10 +328,10 @@ rope.mcmc.list <- rope.bcplm
 
 
   rope <- data.frame(
-    "CI" = ci,
-    "ROPE_low" = range[1],
-    "ROPE_high" = range[2],
-    "ROPE_Percentage" = rope_percentage
+    CI = ci,
+    ROPE_low = range[1],
+    ROPE_high = range[2],
+    ROPE_Percentage = rope_percentage
   )
 
   attr(rope, "HDI_area") <- c(ci_bounds$CI_low, ci_bounds$CI_high)
@@ -493,7 +493,9 @@ rope.sim.merMod <- function(x,
     tmp <- getropedata$tmp
     HDI_area <- getropedata$HDI_area
 
-    if (!insight::is_empty_object(tmp)) {
+    if (insight::is_empty_object(tmp)) {
+      tmp <- NULL
+    } else {
       tmp <- .clean_up_tmp_stanreg(
         tmp,
         group = .x,
@@ -504,8 +506,6 @@ rope.sim.merMod <- function(x,
       if (!insight::is_empty_object(HDI_area)) {
         attr(tmp, "HDI_area") <- HDI_area
       }
-    } else {
-      tmp <- NULL
     }
 
     tmp
@@ -552,7 +552,9 @@ rope.sim <- function(x, range = "default", ci = 0.95, ci_method = "ETI", paramet
   dat <- getropedata$tmp
   HDI_area <- getropedata$HDI_area
 
-  if (!insight::is_empty_object(dat)) {
+  if (insight::is_empty_object(dat)) {
+    dat <- NULL
+  } else {
     dat <- .clean_up_tmp_stanreg(
       dat,
       group = "fixed",
@@ -563,8 +565,6 @@ rope.sim <- function(x, range = "default", ci = 0.95, ci_method = "ETI", paramet
     if (!insight::is_empty_object(HDI_area)) {
       attr(dat, "HDI_area") <- HDI_area
     }
-  } else {
-    dat <- NULL
   }
 
   attr(dat, "object_name") <- insight::safe_deparse_symbol(substitute(x))

diff --git a/R/rope_range.R b/R/rope_range.R
@@ -83,10 +83,10 @@ rope_range.default <- function(x, verbose = TRUE, ...) {
     ret <- Map(
       function(i, j, ...) .rope_range(x, i, j), information, response, response_transform, verbose
     )
-    return(ret)
   } else {
-    .rope_range(x, information, response, response_transform, verbose)
+    ret <- .rope_range(x, information, response, response_transform, verbose)
   }
+  ret
 }
 
 
@@ -114,44 +114,42 @@ rope_range.mlm <- function(x, verbose = TRUE, ...) {
 
 .rope_range <- function(x, information = NULL, response = NULL, response_transform = NULL, verbose = TRUE) {
   negligible_value <- tryCatch(
-    {
-      if (!is.null(response_transform) && grepl("log", response_transform, fixed = TRUE)) {
-        # for log-transform, we assume that a 1% change represents the ROPE adequately
-        # see https://github.com/easystats/bayestestR/issues/487
-        0.01
-      } else if (information$is_linear && information$link_function == "log") {
-        # for log-transform, we assume that a 1% change represents the ROPE adequately
-        # see https://github.com/easystats/bayestestR/issues/487
-        0.01
-      } else if (information$family == "lognormal") {
-        # for log-transform, we assume that a 1% change represents the ROPE adequately
-        # see https://github.com/easystats/bayestestR/issues/487
-        0.01
-      } else if (!is.null(response) && information$link_function == "identity") {
-        # Linear Models
-        0.1 * stats::sd(response, na.rm = TRUE)
-        # 0.1 * stats::sigma(x) # https://github.com/easystats/bayestestR/issues/364
-      } else if (information$is_logit) {
-        # Logistic Models (any)
-        # Sigma==pi / sqrt(3)
-        0.1 * pi / sqrt(3)
-      } else if (information$is_probit) {
-        # Probit models
-        # Sigma==1
-        0.1 * 1
-      } else if (information$is_correlation) {
-        # Correlations
-        # https://github.com/easystats/bayestestR/issues/121
-        0.05
-      } else if (information$is_count) {
-        # Not sure about this
-        sig <- stats::sigma(x)
-        if (is.null(sig) || length(sig) == 0 || is.na(sig)) stop()
-        0.1 * sig
-      } else {
-        # Default
-        stop()
-      }
+    if (!is.null(response_transform) && grepl("log", response_transform, fixed = TRUE)) {
+      # for log-transform, we assume that a 1% change represents the ROPE adequately
+      # see https://github.com/easystats/bayestestR/issues/487
+      0.01
+    } else if (information$is_linear && information$link_function == "log") {
+      # for log-transform, we assume that a 1% change represents the ROPE adequately
+      # see https://github.com/easystats/bayestestR/issues/487
+      0.01
+    } else if (information$family == "lognormal") {
+      # for log-transform, we assume that a 1% change represents the ROPE adequately
+      # see https://github.com/easystats/bayestestR/issues/487
+      0.01
+    } else if (!is.null(response) && information$link_function == "identity") {
+      # Linear Models
+      0.1 * stats::sd(response, na.rm = TRUE)
+      # 0.1 * stats::sigma(x) # https://github.com/easystats/bayestestR/issues/364
+    } else if (information$is_logit) {
+      # Logistic Models (any)
+      # Sigma==pi / sqrt(3)
+      0.1 * pi / sqrt(3)
+    } else if (information$is_probit) {
+      # Probit models
+      # Sigma==1
+      0.1 * 1
+    } else if (information$is_correlation) {
+      # Correlations
+      # https://github.com/easystats/bayestestR/issues/121
+      0.05
+    } else if (information$is_count) {
+      # Not sure about this
+      sig <- stats::sigma(x)
+      if (is.null(sig) || length(sig) == 0 || is.na(sig)) stop(call. = FALSE)
+      0.1 * sig
+    } else {
+      # Default
+      stop(call. = FALSE)
     },
     error = function(e) {
       if (isTRUE(verbose)) {

diff --git a/R/si.R b/R/si.R
@@ -126,9 +126,8 @@ si.stanreg <- function(posterior, prior = NULL,
   component <- match.arg(component)
 
   samps <- .clean_priors_and_posteriors(posterior, prior,
-    verbose = verbose,
     effects = effects, component = component,
-    parameters = parameters
+    parameters = parameters, verbose = verbose
   )
 
   # Get SIs
@@ -318,7 +317,7 @@ si.rvar <- si.draws
   x_supported <- stats::na.omit(x_axis[crit])
   if (length(x_supported) < 2) {
     return(c(NA, NA))
-  } else {
-    range(x_supported)
   }
+
+  range(x_supported)
 }
diff --git a/R/utils_bayesfactor.R b/R/utils_bayesfactor.R
@@ -1,15 +1,16 @@
 # clean priors and posteriors ---------------------------------------------
 
 #' @keywords internal
-.clean_priors_and_posteriors <- function(posterior, prior,
-                                         verbose = TRUE, ...) {
+.clean_priors_and_posteriors <- function(posterior, prior, ...) {
   UseMethod(".clean_priors_and_posteriors")
 }
 
 #' @keywords internal
 .clean_priors_and_posteriors.stanreg <- function(posterior, prior,
+                                                 effects, component,
+                                                 parameters = NULL,
                                                  verbose = TRUE,
-                                                 effects, component, ...) {
+                                                 ...) {
   # Get Priors
   if (is.null(prior)) {
     prior <- posterior
@@ -65,7 +66,8 @@
 #' @keywords internal
 .clean_priors_and_posteriors.emmGrid <- function(posterior,
                                                  prior,
-                                                 verbose = TRUE) {
+                                                 verbose = TRUE,
+                                                 ...) {
   insight::check_if_installed("emmeans")
 
   if (is.null(prior)) {
@@ -126,7 +128,7 @@
 }
 
 .clean_priors_and_posteriors.emm_list <- function(posterior, prior,
-                                                  verbose = TRUE) {
+                                                  verbose = TRUE, ...) {
   if (is.null(prior)) {
     prior <- posterior
     insight::format_warning("Prior not specified! Please provide the original model to get meaningful results.")

diff --git a/man/bayestestR-package.Rd b/man/bayestestR-package.Rd
diff --git a/tests/testthat/test-rope.R b/tests/testthat/test-rope.R
@@ -81,7 +81,9 @@ test_that("rope (brms)", {
   expect_equal(rope$ROPE_Percentage, c(0.00, 0.00, 0.50), tolerance = 0.1)
 })
 
-model <- brm(bf(mvbind(mpg, disp) ~ wt + gear) + set_rescor(TRUE), data = mtcars, iter = 500, refresh = 0)
+skip_on_os("mac")
+
+model <- suppressWarnings(brm(bf(mvbind(mpg, disp) ~ wt + gear) + set_rescor(TRUE), data = mtcars, iter = 500, refresh = 0))
 rope <- rope(model, verbose = FALSE)
 
 test_that("rope (brms, multivariate)", {