initialize stanreg

DESCRIPTION

@@ -74,6 +74,7 @@ Collate:
     'report.lme4.R'
     'report.numeric.R'
     'report.sessionInfo.R'
+    'report.stanreg.R'
     'report.survreg.R'
     'report.zeroinfl.R'
     'report_effectsize.R'

NAMESPACE

@@ -37,6 +37,7 @@ S3method(report,logical)
 S3method(report,merMod)
 S3method(report,numeric)
 S3method(report,sessionInfo)
+S3method(report,stanreg)
 S3method(report,survreg)
 S3method(report,zeroinfl)
 S3method(report_effectsize,MixMod)
@@ -49,6 +50,7 @@ S3method(report_effectsize,glmmTMB)
 S3method(report_effectsize,htest)
 S3method(report_effectsize,lm)
 S3method(report_effectsize,merMod)
+S3method(report_effectsize,stanreg)
 S3method(report_effectsize,survreg)
 S3method(report_effectsize,zeroinfl)
 S3method(report_info,MixMod)
@@ -61,6 +63,7 @@ S3method(report_info,glmmTMB)
 S3method(report_info,htest)
 S3method(report_info,lm)
 S3method(report_info,merMod)
+S3method(report_info,stanreg)
 S3method(report_info,survreg)
 S3method(report_info,zeroinfl)
 S3method(report_intercept,MixMod)
@@ -69,6 +72,7 @@ S3method(report_intercept,glm)
 S3method(report_intercept,glmmTMB)
 S3method(report_intercept,lm)
 S3method(report_intercept,merMod)
+S3method(report_intercept,stanreg)
 S3method(report_intercept,survreg)
 S3method(report_intercept,zeroinfl)
 S3method(report_model,MixMod)
@@ -81,6 +85,7 @@ S3method(report_model,glmmTMB)
 S3method(report_model,htest)
 S3method(report_model,lm)
 S3method(report_model,merMod)
+S3method(report_model,stanreg)
 S3method(report_model,survreg)
 S3method(report_model,zeroinfl)
 S3method(report_parameters,MixMod)
@@ -100,6 +105,7 @@ S3method(report_parameters,logical)
 S3method(report_parameters,merMod)
 S3method(report_parameters,numeric)
 S3method(report_parameters,sessionInfo)
+S3method(report_parameters,stanreg)
 S3method(report_parameters,survreg)
 S3method(report_parameters,zeroinfl)
 S3method(report_performance,MixMod)
@@ -108,12 +114,14 @@ S3method(report_performance,glm)
 S3method(report_performance,glmmTMB)
 S3method(report_performance,lm)
 S3method(report_performance,merMod)
+S3method(report_performance,stanreg)
 S3method(report_performance,survreg)
 S3method(report_performance,zeroinfl)
 S3method(report_random,MixMod)
 S3method(report_random,default)
 S3method(report_random,glmmTMB)
 S3method(report_random,merMod)
+S3method(report_random,stanreg)
 S3method(report_statistics,MixMod)
 S3method(report_statistics,anova)
 S3method(report_statistics,aov)
@@ -129,6 +137,7 @@ S3method(report_statistics,htest)
 S3method(report_statistics,lm)
 S3method(report_statistics,merMod)
 S3method(report_statistics,numeric)
+S3method(report_statistics,stanreg)
 S3method(report_statistics,survreg)
 S3method(report_statistics,zeroinfl)
 S3method(report_table,MixMod)
@@ -150,6 +159,7 @@ S3method(report_table,logical)
 S3method(report_table,merMod)
 S3method(report_table,numeric)
 S3method(report_table,sessionInfo)
+S3method(report_table,stanreg)
 S3method(report_table,survreg)
 S3method(report_table,zeroinfl)
 S3method(report_text,MixMod)
@@ -171,6 +181,7 @@ S3method(report_text,logical)
 S3method(report_text,merMod)
 S3method(report_text,numeric)
 S3method(report_text,sessionInfo)
+S3method(report_text,stanreg)
 S3method(report_text,survreg)
 S3method(report_text,zeroinfl)
 S3method(summary,report_effectsize)

R/report.R

@@ -44,28 +44,29 @@
 #' with a short and long description of the model summary, as well as a short
 #' and long table of parameters and fit indices.
 #'
-#' @seealso Aspects of reports:
+#' @seealso Aspects of reports (especially for stats models):
 #' \itemize{
 #'   \item \code{\link{report_table}}
 #'   \item \code{\link{report_parameters}}
 #'   \item \code{\link{report_statistics}}
 #'   \item \code{\link{report_effectsize}}
 #'   \item \code{\link{report_model}}
+#'   \item \code{\link{report_random}}
 #'   \item \code{\link{report_performance}}
 #'   \item \code{\link{report_info}}
 #'   \item \code{\link{report_text}}
 #' }
-#' Methods:
-#' \itemize{
-#'   \item \code{\link{as.report}}
-#' }
 #' Specific reports:
 #' \itemize{
 #'   \item \code{\link{report_system}}
 #'   \item \code{\link{report_packages}}
 #'   \item \code{\link{report_participants}}
 #'   \item \code{\link{report_sample}}
 #' }
+#' Methods:
+#' \itemize{
+#'   \item \code{\link{as.report}}
+#' }
 #'
 #' @examples
 #' library(report)

R/report.stanreg.R

@@ -0,0 +1,33 @@
+#' @include report.lm.R
+#' @export
+report.stanreg <- report.lm
+
+#' @export
+report_effectsize.stanreg <- report_effectsize.lm
+
+#' @export
+report_table.stanreg <- report_table.lm
+
+#' @export
+report_performance.stanreg <- report_performance.lm
+
+#' @export
+report_statistics.stanreg <- report_statistics.lm
+
+#' @export
+report_parameters.stanreg <- report_parameters.lm
+
+#' @export
+report_intercept.stanreg <- report_intercept.lm
+
+#' @export
+report_random.stanreg <- report_random.merMod
+
+#' @export
+report_model.stanreg <- report_model.lm
+
+#' @export
+report_info.stanreg <- report_info.lm
+
+#' @export
+report_text.stanreg <- report_text.lm

R/report_effectsize.R

@@ -28,6 +28,12 @@
 #'   model <- lme4::lmer(Sepal.Length ~ Petal.Length + (1 | Species), data = iris)
 #'   report_effectsize(model)
 #' }
+#'
+#' # Bayesian models
+#' if(require("rstanarm")){
+#'   model <- rstanarm::stan_lmer(Sepal.Length ~ Petal.Length + (1 | Species), data = iris, refresh=0, iter=600)
+#'   report_effectsize(model, method="basic")
+#' }
 #' @export
 report_effectsize <- function(x, ...) {
   UseMethod("report_effectsize")
@@ -129,15 +135,15 @@ print.report_effectsize <- function(x, ...) {
       text <- "SD "
     }
     text <- paste0("Standardized parameters were obtained by standardizing the data by 2 times the ", text, " (see Gelman, 2008).")
-  } else if (method == "smart" | method == "classic") {
+  } else if (method == "smart" | method == "basic") {
     if (robust == TRUE) {
       text <- "median and the MAD (a median-based equivalent of the SD) of the response variable."
     } else {
       text <- "mean and the SD of the response variable."
     }
-    text <- paste0(" Parameters were scaled by the ", text)
+    text <- paste0("Parameters were scaled by the ", text)
   } else {
-    text <- paste0(" Parameters were standardized using the ", text, " method.")
+    text <- paste0("Parameters were standardized using the ", text, " method.")
   }
 
   text