From b4739ba14c5472a23cb3e334d55989f7fbb0afe2 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Mon, 28 Apr 2014 17:59:10 +0200
Subject: Option to add residual plot to plot.mkinfit

---
 R/mkinresplot.R  | 29 ++++++++++++++---------------
 R/plot.mkinfit.R | 28 +++++++++++++++++++++++++++-
 2 files changed, 41 insertions(+), 16 deletions(-)

(limited to 'R')

diff --git a/R/mkinresplot.R b/R/mkinresplot.R
index 524ba78..07bd7df 100644
--- a/R/mkinresplot.R
+++ b/R/mkinresplot.R
@@ -1,7 +1,5 @@
-# $Id$
-
-# Copyright (C) 2008-2011 Katrin Lindenberger and Johannes Ranke
-# Contact: mkin-devel@lists.berlios.de
+# Copyright (C) 2008-2014 Johannes Ranke
+# Contact: jranke@uni-bremen.de
 
 # This file is part of the R package mkin
 
@@ -19,36 +17,37 @@
 # this program. If not, see <http://www.gnu.org/licenses/>
 if(getRversion() >= '2.15.1') utils::globalVariables(c("variable", "residual"))
 
-mkinresplot <- function (object, obs_vars = vector(), 
+mkinresplot <- function (object, 
+  obs_vars = names(object$mkinmod$map),
   xlab = "Time", ylab = "Residual",
 	maxabs = "auto", legend= TRUE, lpos = "topright", ...) 
 {
 	obs_vars_all <- as.character(unique(object$data$variable))
 
   if (length(obs_vars) > 0){
-      vars <- intersect(obs_vars_all, obs_vars)	
-  } else vars <- obs_vars_all
+      obs_vars <- intersect(obs_vars_all, obs_vars)	
+  } else obs_vars <- obs_vars_all
 
-  residuals <- subset(object$data, variable %in% vars, residual)
+  residuals <- subset(object$data, variable %in% obs_vars, residual)
 
   if (maxabs == "auto") maxabs = max(abs(residuals), na.rm = TRUE)
 
-	col_obs <- pch_obs <- 1:length(vars)
- 	names(col_obs) <- names(pch_obs) <- vars
+	col_obs <- pch_obs <- 1:length(obs_vars)
+ 	names(col_obs) <- names(pch_obs) <- obs_vars
 
   plot(0,  xlab = xlab, ylab = ylab, 
        xlim = c(0, 1.1 * max(object$data$time)), 
        ylim = c(-1.2 * maxabs, 1.2 * maxabs), ...)
 
-	for(var in vars){
-		residuals_plot <- subset(object$data, variable == var, c("time", "residual"))
-		points(residuals_plot, pch = pch_obs[var], col = col_obs[var])
+	for(obs_var in obs_vars){
+		residuals_plot <- subset(object$data, variable == obs_var, c("time", "residual"))
+		points(residuals_plot, pch = pch_obs[obs_var], col = col_obs[obs_var])
 	}
 
   abline(h = 0, lty = 2)
 
   if (legend == TRUE) {
-    legend(lpos, inset = c(0.05, 0.05), legend = vars, 
-    col = col_obs, pch = pch_obs)
+    legend(lpos, inset = c(0.05, 0.05), legend = obs_vars, 
+      col = col_obs[obs_vars], pch = pch_obs[obs_vars])
   }
 }
diff --git a/R/plot.mkinfit.R b/R/plot.mkinfit.R
index 80cf45f..23eb30f 100644
--- a/R/plot.mkinfit.R
+++ b/R/plot.mkinfit.R
@@ -21,13 +21,20 @@ plot.mkinfit <- function(x, fit = x,
   obs_vars = names(fit$mkinmod$map),
   xlab = "Time", ylab = "Observed",
   xlim = range(fit$data$time), 
-  ylim = c(0, max(subset(fit$data, variable %in% obs_vars)$observed, na.rm = TRUE)),
+  ylim = "default",
   col_obs = 1:length(fit$mkinmod$map),
   pch_obs = col_obs, 
   lty_obs = rep(1, length(fit$mkinmod$map)),
   add = FALSE, legend = !add, 
+  show_residuals = FALSE, maxabs = "auto",
   lpos = "topright", inset = c(0.05, 0.05), ...)
 {
+  if (add && show_residuals) stop("If adding to an existing plot we can not show residuals")
+
+  if (ylim == "default") {
+    ylim = c(0, max(subset(fit$data, variable %in% obs_vars)$observed, na.rm = TRUE))
+  }
+
   solution_type = fit$solution_type
   parms.all <- c(fit$bparms.optim, fit$bparms.fixed)
 
@@ -52,6 +59,10 @@ plot.mkinfit <- function(x, fit = x,
 
   # Set up the plot if not to be added to an existing plot
   if (add == FALSE) {
+    if (show_residuals) {
+      layout(matrix(c(1, 2), 2, 1), heights = c(2, 1.3))
+      par(mar = c(3, 4, 4, 2) + 0.1)
+    }
     plot(0, type="n", 
       xlim = xlim, ylim = ylim,
       xlab = xlab, ylab = ylab, ...)
@@ -67,4 +78,19 @@ plot.mkinfit <- function(x, fit = x,
     legend(lpos, inset= inset, legend = obs_vars,
       col = col_obs[obs_vars], pch = pch_obs[obs_vars], lty = lty_obs[obs_vars])
   }
+  # Show residuals if requested
+  if (show_residuals) {
+    par(mar = c(5, 4, 0, 2) + 0.1)
+    residuals <- subset(fit$data, variable %in% obs_vars, residual)
+    if (maxabs == "auto") maxabs = max(abs(residuals), na.rm = TRUE)
+    plot(0, type="n", 
+      xlim = xlim, 
+      ylim = c(-1.2 * maxabs, 1.2 * maxabs),
+      xlab = xlab, ylab = ylab)
+    for(obs_var in obs_vars){
+      residuals_plot <- subset(fit$data, variable == obs_var, c("time", "residual"))
+      points(residuals_plot, pch = pch_obs[obs_var], col = col_obs[obs_var])
+    }
+    abline(h = 0, lty = 2)
+  }
 }
-- 
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