Merge pull request #243 from easystats/dev

dev
easystats · Oct 18, 2019 · dcb59fa · dcb59fa
2 parents d46fe0c + 0cd8a04
commit dcb59fa
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: bayestestR
 Type: Package
 Title: Understand and Describe Bayesian Models and Posterior Distributions
-Version: 0.3.3
+Version: 0.4.0
 Authors@R: c(
     person("Dominique", 
 		"Makowski", 
@@ -52,7 +52,7 @@ LazyData: true
 Depends:
   R (>= 3.0)
 Imports:
-	insight (>= 0.5.0),
+	insight (>= 0.6.0),
 	methods,
 	stats,
 	utils

diff --git a/NAMESPACE b/NAMESPACE
@@ -200,9 +200,11 @@ export(bayesfactor_models)
 export(bayesfactor_parameters)
 export(bayesfactor_restricted)
 export(bayesfactor_savagedickey)
+export(bayesian_as_frequentist)
 export(check_prior)
 export(ci)
 export(contr.bayes)
+export(convert_bayesian_as_frequentist)
 export(convert_p_to_pd)
 export(convert_pd_to_p)
 export(density_at)
@@ -267,7 +269,9 @@ importFrom(stats,cor)
 importFrom(stats,cor.test)
 importFrom(stats,density)
 importFrom(stats,getCall)
+importFrom(stats,glm)
 importFrom(stats,integrate)
+importFrom(stats,lm)
 importFrom(stats,mad)
 importFrom(stats,median)
 importFrom(stats,na.omit)

diff --git a/NEWS.md b/NEWS.md
@@ -2,6 +2,7 @@
 
 ## New functions / features
 
+- `convert_bayesian_to_frequentist` Convert (refit) Bayesian model as frequentist
 - `distribution_binomial()` for perfect binomial distributions
 - `simulate_ttest()` Simulate data with a mean difference
 - `simulate_correlation()` Simulate correlated datasets

diff --git a/R/convert_bayesian_to_frequentist.R b/R/convert_bayesian_to_frequentist.R
@@ -0,0 +1,71 @@
+#' Convert (refit) a Bayesian model to frequentist
+#'
+#' Refit Bayesian model as frequentist. Can be useful for comparisons.
+#'
+#' @param model A Bayesian model.
+#' @param data Data used by the model. If \code{NULL}, will try to extract it from the model.
+#' @examples
+#' \donttest{
+#' # Rstanarm ----------------------
+#' library(rstanarm)
+#'
+#' # Simple regressions
+#' model <- stan_glm(Sepal.Length ~ Petal.Length * Species,
+#'                   data = iris, chains = 2, refresh = 0)
+#' bayesian_as_frequentist(model)
+#'
+#' model <- stan_glm(vs ~ mpg, family = "binomial",
+#'                   data = mtcars, chains = 2, refresh = 0)
+#' bayesian_as_frequentist(model)
+#'
+#' # Mixed models
+#' model <- stan_glmer(Sepal.Length ~ Petal.Length + (1|Species),
+#'                     data = iris, chains = 2, refresh = 0)
+#' bayesian_as_frequentist(model)
+#'
+#' model <- stan_glmer(vs ~ mpg + (1|cyl), family = "binomial",
+#'                     data = mtcars, chains = 2, refresh = 0)
+#' bayesian_as_frequentist(model)
+#' }
+#'
+#' @importFrom stats lm glm
+#' @export
+convert_bayesian_as_frequentist <- function(model, data = NULL) {
+
+  if (is.null(data)) {
+    data <- insight::get_data(model)
+  }
+
+  # info
+  info <- insight::model_info(model)
+
+  # Call
+  called <- model$call
+  # fun <- as.character(called)[1]
+  formula <- called$formula
+  family <- called$family
+
+  if (info$is_mixed) {
+    if (!requireNamespace("lme4", quietly = TRUE)) {
+      stop("Package 'lme4' required for this function to work. Please install it by running `install.packages('lme4')`.")
+    }
+    if (info$is_linear) {
+      freq <- lme4::lmer(formula, data = data)
+    } else{
+      freq <- lme4::glmer(formula, data = data, family = family)
+    }
+  } else{
+    if (info$is_linear) {
+      freq <- stats::lm(formula, data = data)
+    } else{
+      freq <- stats::glm(formula, data = data, family = family)
+    }
+  }
+
+  freq
+}
+
+
+#' @rdname convert_bayesian_as_frequentist
+#' @export
+bayesian_as_frequentist <- convert_bayesian_as_frequentist
diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -68,6 +68,7 @@ reference:
 - title: "Utilities"
   contents:
   - simulate_correlation
+  - convert_bayesian_as_frequentist
   - contr.bayes
   - as.numeric.p_direction
   - as.data.frame.density

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/CODE_OF_CONDUCT.html b/docs/CODE_OF_CONDUCT.html
diff --git a/docs/CONTRIBUTING.html b/docs/CONTRIBUTING.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/PULL_REQUEST_TEMPLATE.html b/docs/PULL_REQUEST_TEMPLATE.html
diff --git a/docs/articles/bayes_factors.html b/docs/articles/bayes_factors.html
diff --git a/docs/articles/bayestestR.html b/docs/articles/bayestestR.html
diff --git a/docs/articles/credible_interval.html b/docs/articles/credible_interval.html
diff --git a/docs/articles/example1.html b/docs/articles/example1.html
diff --git a/docs/articles/example2.html b/docs/articles/example2.html
diff --git a/docs/articles/example3.html b/docs/articles/example3.html
diff --git a/docs/articles/guidelines.html b/docs/articles/guidelines.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/indicesEstimationComparison.html b/docs/articles/indicesEstimationComparison.html
diff --git a/docs/articles/indicesExistenceComparison.html b/docs/articles/indicesExistenceComparison.html
diff --git a/docs/articles/probability_of_direction.html b/docs/articles/probability_of_direction.html
diff --git a/docs/articles/region_of_practical_equivalence.html b/docs/articles/region_of_practical_equivalence.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/reference/area_under_curve.html b/docs/reference/area_under_curve.html
diff --git a/docs/reference/as.data.frame.density.html b/docs/reference/as.data.frame.density.html
diff --git a/docs/reference/as.numeric.p_direction.html b/docs/reference/as.numeric.p_direction.html
diff --git a/docs/reference/bayesfactor.html b/docs/reference/bayesfactor.html
diff --git a/docs/reference/bayesfactor_inclusion.html b/docs/reference/bayesfactor_inclusion.html
diff --git a/docs/reference/bayesfactor_models.html b/docs/reference/bayesfactor_models.html
diff --git a/docs/reference/bayesfactor_parameters.html b/docs/reference/bayesfactor_parameters.html
diff --git a/docs/reference/bayesfactor_restricted.html b/docs/reference/bayesfactor_restricted.html
diff --git a/docs/reference/check_prior.html b/docs/reference/check_prior.html