From 3410513f55b3f8b5c4331f4fb4487613d3a28208 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Mon, 4 Nov 2019 23:48:20 +0100
Subject: Scaled residual plots

---
 R/mkinresplot.R | 38 ++++++++++++++++++++++++--------------
 1 file changed, 24 insertions(+), 14 deletions(-)

(limited to 'R/mkinresplot.R')

diff --git a/R/mkinresplot.R b/R/mkinresplot.R
index 5377dbf2..0bfdd02f 100644
--- a/R/mkinresplot.R
+++ b/R/mkinresplot.R
@@ -1,23 +1,25 @@
 if(getRversion() >= '2.15.1') utils::globalVariables(c("variable", "residual"))
 
 #' Function to plot residuals stored in an mkin object
-#' 
+#'
 #' This function plots the residuals for the specified subset of the observed
 #' variables from an mkinfit object. A combined plot of the fitted model and
 #' the residuals can be obtained using \code{\link{plot.mkinfit}} using the
 #' argument \code{show_residuals = TRUE}.
-#' 
+#'
+#' @importFrom stats residuals
 #' @param object A fit represented in an \code{\link{mkinfit}} object.
 #' @param obs_vars A character vector of names of the observed variables for
 #'   which residuals should be plotted. Defaults to all observed variables in
 #'   the model
 #' @param xlim plot range in x direction.
-#' @param xlab Label for the x axis. Defaults to "Time [days]".
-#' @param ylab Label for the y axis. Defaults to "Residual [\% of applied
-#'   radioactivity]".
+#' @param xlab Label for the x axis.
+#' @param standardized Should the residuals be standardized by dividing by the
+#'   standard deviation given by the error model of the fit?
+#' @param ylab Label for the y axis.
 #' @param maxabs Maximum absolute value of the residuals. This is used for the
 #'   scaling of the y axis and defaults to "auto".
-#' @param legend Should a legend be plotted? Defaults to "TRUE".
+#' @param legend Should a legend be plotted?
 #' @param lpos Where should the legend be placed? Default is "topright". Will
 #'   be passed on to \code{\link{legend}}.
 #' @param col_obs Colors for the observed variables.
@@ -28,19 +30,21 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("variable", "residual"))
 #'   effect, namely to produce a plot.
 #' @author Johannes Ranke
 #' @seealso \code{\link{mkinplot}}, for a way to plot the data and the fitted
-#'   lines of the mkinfit object.
+#'   lines of the mkinfit object, and \code{\link{plot_res}} for a function
+#'   combining the plot of the fit and the residual plot.
 #' @examples
-#' 
+#'
 #' model <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
 #' fit <- mkinfit(model, FOCUS_2006_D, quiet = TRUE)
 #' mkinresplot(fit, "m1")
-#' 
+#'
 #' @export
 mkinresplot <- function (object,
   obs_vars = names(object$mkinmod$map),
   xlim = c(0, 1.1 * max(object$data$time)),
-  xlab = "Time", ylab = "Residual",
-  maxabs = "auto", legend= TRUE, lpos = "topright", 
+  standardized = FALSE,
+  xlab = "Time", ylab = ifelse(standardized, "Standardized residual", "Residual"),
+  maxabs = "auto", legend = TRUE, lpos = "topright",
   col_obs = "auto", pch_obs = "auto",
   frame = TRUE,
   ...)
@@ -51,9 +55,15 @@ mkinresplot <- function (object,
       obs_vars <- intersect(obs_vars_all, obs_vars)
   } else obs_vars <- obs_vars_all
 
-  residuals <- subset(object$data, variable %in% obs_vars, residual)
+  if (standardized) {
+    res_col <- "standardized"
+    object$data[[res_col]] <- residuals(object, standardized = TRUE)
+  } else {
+    res_col <- "residual"
+  }
+  res <- subset(object$data, variable %in% obs_vars)[res_col]
 
-  if (maxabs == "auto") maxabs = max(abs(residuals), na.rm = TRUE)
+  if (maxabs == "auto") maxabs = max(abs(res), na.rm = TRUE)
 
   # Set colors and symbols
   if (col_obs[1] == "auto") {
@@ -71,7 +81,7 @@ mkinresplot <- function (object,
        ylim = c(-1.2 * maxabs, 1.2 * maxabs), ...)
 
   for(obs_var in obs_vars){
-    residuals_plot <- subset(object$data, variable == obs_var, c("time", "residual"))
+    residuals_plot <- subset(object$data, variable == obs_var, c("time", res_col))
     points(residuals_plot, pch = pch_obs[obs_var], col = col_obs[obs_var])
   }
 
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