fix for plotting

R/cor_test.R

@@ -17,7 +17,7 @@ cor_test <- function(data, x, y, ci = "default", method = "pearson", bayesian =
     out <- .cor_test_bayes(data, x, y, ci = ci, iterations = iterations, rope_full = rope_full, rope_bounds = rope_bounds)
   }
 
-  return(out)
+  out
 }
 
 
@@ -49,7 +49,7 @@ cor_test <- function(data, x, y, ci = "default", method = "pearson", bayesian =
     if("S" %in% names(params)) params$S <- Inf
   }
 
-  return(params)
+  params
 }
 
 
@@ -62,9 +62,7 @@ cor_test <- function(data, x, y, ci = "default", method = "pearson", bayesian =
 #' @keywords internal
 .cor_test_bayes <- function(data, x, y, ci = 0.90, iterations = 10^4, rope_full = TRUE, rope_range = c(-0.05, 0.05), prior="medium",  ...) {
   if (!requireNamespace("BayesFactor")) {
-    warning("This function needs `BayesFactor` to be installed... installing now.")
-    install.packages("BayesFactor")
-    requireNamespace("BayesFactor")
+    stop("This function needs `BayesFactor` to be installed. Please install by running `install.packages('BayesFactor')`.")
   }
 
   var_x <- data[[x]]
@@ -112,5 +110,26 @@ cor_test <- function(data, x, y, ci = "default", method = "pearson", bayesian =
   }
 
 
-  return(params)
+  params
 }
+
+
+
+
+#' #' @examples
+#' #' x <- ifelse(iris$Sepal.Width > median(iris$Sepal.Width), 1, 0)
+#' #' y <- ifelse(iris$Petal.Width > median(iris$Petal.Width), 1, 0)
+#' #' @keywords internal
+#' .cor_test_tetrachoric <- function(x, y, ci = 0.95, ...) {
+#'
+#'   if (!requireNamespace("psych", quietly = TRUE)) {
+#'     stop("Package `psych` required for tetrachoric correlations. Please install it.", call. = FALSE)
+#'   }
+#'
+#'   data <- data.frame(x=x, y=y)
+#'   rez <- psych::tetrachoric(data)
+#'
+#'   rez$rho
+#'
+#' }
+

R/correlation.R

@@ -33,11 +33,20 @@
 #' @importFrom dplyr enquos
 #' @export
 correlation <- function(data, data2 = NULL, ci = "default", method = "pearson", p_adjust = "holm", partial = FALSE, bayesian = FALSE, iterations = 10^4, rope_full = TRUE, rope_bounds = c(-0.05, 0.05), prior="medium", ...) {
+
+  # Sanity checks
   if (partial == TRUE & bayesian == TRUE) {
     warning("Bayesian partial correlations are not supported yet. Running frequentist analysis...")
     bayesian <- FALSE
   }
 
+  # CI level
+  if (bayesian == FALSE) {
+    if (ci == "default") ci <- 0.95
+  } else {
+    if (ci == "default") ci <- 0.9
+  }
+
   if (inherits(data, "grouped_df")) {
     groups <- dplyr::group_vars(data)
     ungrouped_x <- dplyr::ungroup(data)

pkgdown/extra.css

@@ -0,0 +1,24 @@
+/* Syntax highlighting ---------------------------------------------------- */ 
+
+/*pre {*/ 
+/*  overflow: auto;*/ 
+/*  word-wrap: normal;*/ 
+/*  word-break: normal;*/ 
+/*  border: 1px solid #eee;*/ 
+/*  background-color: #455A64;*/ 
+/*}*/ 
+
+
+
+/*.fl      {color: #1514b5;}*/ 
+/*.fu      {color: #FF9800;}*/  /* function */
+/*.ch,.st  {color: #CDDC39;}*/  /* string */
+/*.kw      {color: #FFC107;}*/  /* keyword */
+/*.co      {color: #9E9E9E;}*/  /* comment */
+
+/*.message { color: #EEEEEE;   font-weight: bolder;}*/ 
+/*.error   { color: #f44336;  font-weight: bolder;}*/ 
+/*.warning { color: #9C27B0; font-weight: bolder;}*/ 
+
+.ch,.st  {color: orange;} /* string */
+.co      {color: #BDBDBD;}  /* comment */