From 39b6b1395714969f2f9270534799444252a71e82 Mon Sep 17 00:00:00 2001
From: "Mattan S. Ben-Shachar" <mattansb@msbstats.info>
Date: Sun, 23 Jul 2023 23:22:07 +0300
Subject: [PATCH] detrend without qqplotr

---
 R/plot.check_normality.R        | 66 ++++++++++++++++++++-------------
 man/plot.see_check_normality.Rd |  6 +--
 2 files changed, 44 insertions(+), 28 deletions(-)

diff --git a/R/plot.check_normality.R b/R/plot.check_normality.R
index b4ff8750b..d3f6a3ffc 100644
--- a/R/plot.check_normality.R
+++ b/R/plot.check_normality.R
@@ -12,8 +12,8 @@
 #' @param alpha Numeric value specifying alpha level of the confidence bands.
 #' @param colors Character vector of length two, indicating the colors (in
 #'   hex-format) for points and line.
-#' @param detrend Logical that decides if Q-Q and P-P plots should be de-trended.
-#'   Defaults to `TRUE` if the *qqplotr* package is installed and `FALSE` otherwise.
+#' @param detrend Logical that decides if Q-Q and P-P plots should be de-trended
+#'   (also known as _worm plots_).
 #' @param method The method used for estimating the qq/pp bands. Default to
 #'   `"ell"` (equal local levels / simultaneous testing - recommended). Can also
 #'   be one of `"pointwise"` or `"boot"` for pointwise confidence bands, or
@@ -43,7 +43,7 @@ plot.see_check_normality <- function(x,
                                      alpha = 0.2,
                                      dot_alpha = 0.8,
                                      colors = c("#3aaf85", "#1b6ca8"),
-                                     detrend = requireNamespace("qqplotr", quietly = TRUE),
+                                     detrend = TRUE,
                                      method = "ell",
                                      ...) {
   type <- match.arg(type)
@@ -209,24 +209,34 @@ plot.see_check_normality <- function(x,
         detrend = detrend
       )
     )
-    y_lab <- "Sample Quantiles"
+    if (detrend) {
+      y_lab <- "Sample Quantile Deviations"
+    } else {
+      y_lab <- "Sample Quantiles"
+    }
   } else {
-    insight::format_alert(
-      paste0(
-        "For confidence bands",
-        if (isTRUE(detrend)) " and detrending",
-        ", please install `qqplotr`."
-      )
-    )
+    insight::format_alert("For confidence bands, please install `qqplotr`.")
 
     gg_init <- ggplot2::ggplot(x, ggplot2::aes(sample = .data$y))
+
     qq_stuff <- list(
-      ggplot2::geom_qq_line(
-        linewidth = size_line,
-        colour = colors[1],
-        na.rm = TRUE
-      ),
+      if (detrend) {
+        ggplot2::geom_hline(
+          yintercept = 0,
+          linewidth = size_line,
+          colour = colors[1],
+          na.rm = TRUE
+        )
+      } else {
+        ggplot2::geom_qq_line(
+          linewidth = size_line,
+          colour = colors[1],
+          na.rm = TRUE
+        )
+      }
+      ,
       ggplot2::geom_qq(
+        mapping = if (detrend) ggplot2::aes(y = ggplot2::after_stat(sample) - ggplot2::after_stat(theoretical)),
         shape = 16,
         na.rm = TRUE,
         stroke = 0,
@@ -234,7 +244,12 @@ plot.see_check_normality <- function(x,
         colour = colors[2] # "#2c3e50"
       )
     )
-    y_lab <- "Sample Quantiles"
+
+    if (detrend) {
+      y_lab <- "Sample Quantile Deviations"
+    } else {
+      y_lab <- "Sample Quantiles"
+    }
   }
 
   if (!isTRUE(show_dots)) {
@@ -284,11 +299,7 @@ plot.see_check_normality <- function(x,
         detrend = detrend
       )
   } else if (requireNamespace("MASS", quietly = TRUE)) {
-    message(
-      "For confidence bands",
-      if (isTRUE(detrend)) " and detrending",
-      ", please install `qqplotr`."
-    )
+    insight::format_alert("For confidence bands, please install `qqplotr`.")
 
     x$probs <- stats::ppoints(x$res)
     dparms <- MASS::fitdistr(x$res, densfun = "normal")
@@ -296,24 +307,29 @@ plot.see_check_normality <- function(x,
 
     p_plot <- ggplot2::ggplot(x, ggplot2::aes(x = .data$probs, y = .data$y)) +
       ggplot2::geom_abline(
-        slope = 1,
+        slope = if (detrend) 0 else 1,
         linewidth = size_line,
         colour = colors[1]
       ) +
       geom_point2(
+        mapping = if (detrend) ggplot2::aes(y = .data$y - .data$probs),
         colour = colors[2],
         size = size_point,
         alpha = dot_alpha_level
       ) # "#2c3e50"
   } else {
-    stop("Package 'qqplotr' OR 'MASS' required for P-P plots. Please install one of them.", call. = FALSE)
+    insight::format_error("Package 'qqplotr' OR 'MASS' required for P-P plots. Please install one of them.")
   }
 
+
+  y_lab <- "Sample Cummulative Probability"
+  if (detrend) y_lab <- paste0(y_lab, " Deviations")
+
   p_plot +
     ggplot2::labs(
       title = "Normality of Residuals",
       subtitle = "Dots should fall along the line",
-      y = "Sample Cummulative Probability",
+      y = y_lab,
       x = "Standard Normal Cumulative Probability"
     ) +
     theme_style(
diff --git a/man/plot.see_check_normality.Rd b/man/plot.see_check_normality.Rd
index 56c788bef..43ece749d 100644
--- a/man/plot.see_check_normality.Rd
+++ b/man/plot.see_check_normality.Rd
@@ -13,7 +13,7 @@
   alpha = 0.2,
   dot_alpha = 0.8,
   colors = c("#3aaf85", "#1b6ca8"),
-  detrend = requireNamespace("qqplotr", quietly = TRUE),
+  detrend = TRUE,
   method = "ell",
   ...
 )
@@ -40,8 +40,8 @@ statistical model.}
 \item{colors}{Character vector of length two, indicating the colors (in
 hex-format) for points and line.}
 
-\item{detrend}{Logical that decides if Q-Q and P-P plots should be de-trended.
-Defaults to \code{TRUE} if the \emph{qqplotr} package is installed and \code{FALSE} otherwise.}
+\item{detrend}{Logical that decides if Q-Q and P-P plots should be de-trended
+(also known as \emph{worm plots}).}
 
 \item{method}{The method used for estimating the qq/pp bands. Default to
 \code{"ell"} (equal local levels / simultaneous testing - recommended). Can also