Option to add residual plot to plot.mkinfit

5 files changed, 62 insertions, 31 deletions

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)
+  }
 }
diff --git a/inst/GUI/gmkin.R b/inst/GUI/gmkin.R
index 422be57..4d33b35 100644
--- a/inst/GUI/gmkin.R
+++ b/inst/GUI/gmkin.R
@@ -698,19 +698,12 @@ plot_ftmp_png <- function() {
     obs_vars_plot = names(ftmp$mkinmod$spec)

   }

   png(tf, width = 525, height = 600)

-  layout(matrix(c(1, 2), 2, 1), heights = c(2, 1.3))

-  par(mar = c(3, 4, 4, 2) + 0.1)

   plot(ftmp, main = ftmp$ds$title, obs_vars = obs_vars_plot,

        xlab = ifelse(ftmp$ds$time_unit == "", "Time", 

                      paste("Time in", ftmp$ds$time_unit)),

        ylab = ifelse(ds[[ds.i]]$unit == "", "Observed", 

-                     paste("Observed in", ftmp$ds$unit)))

-  par(mar = c(5, 4, 0, 2) + 0.1)

-  mkinresplot(ftmp, legend = FALSE, obs_vars = obs_vars_plot,

-       xlab = ifelse(ftmp$ds$time_unit == "", "Time", 

-                     paste("Time in", ftmp$ds$time_unit)),

-       ylab = ifelse(ds[[ds.i]]$unit == "", "Observed", 

-                     paste("Residuals in", ftmp$ds$unit)))

+                     paste("Observed in", ftmp$ds$unit)),

+       show_residuals = TRUE)

   dev.off()

   return(tf)

 }

diff --git a/man/mkinresplot.Rd b/man/mkinresplot.Rd
index 8e3f18a..3f53dd1 100644
--- a/man/mkinresplot.Rd
+++ b/man/mkinresplot.Rd
@@ -5,10 +5,13 @@
 }

 \description{

   This function plots the residuals for the specified subset of the 

-  observed variables from an mkinfit object.

+  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}.

 }

 \usage{

-  mkinresplot(object, obs_vars = vector(), 

+  mkinresplot(object, 

+    obs_vars = names(object$mkinmod$map),

     xlab = "Time", ylab = "Residual", 

     maxabs = "auto", legend = TRUE, lpos = "topright", ...)

 }

@@ -18,7 +21,7 @@
 }

   \item{obs_vars}{

     A character vector of names of the observed variables for which residuals

-    should be plotted.

+    should be plotted. Defaults to all observed variables in the model

 }

   \item{xlab}{

     Label for the x axis. Defaults to "Time [days]".

@@ -44,7 +47,7 @@
   Nothing is returned by this function, as it is called for its side effect, namely to produce a plot.

 }

 \author{

-  Katrin Lindenberger and Johannes Ranke

+  Johannes Ranke

 }

 

 \seealso{

diff --git a/man/plot.mkinfit.Rd b/man/plot.mkinfit.Rd
index 4ae82a5..7009e7d 100644
--- a/man/plot.mkinfit.Rd
+++ b/man/plot.mkinfit.Rd
@@ -12,10 +12,13 @@
 \method{plot}{mkinfit}(x, fit = x,
   obs_vars = names(fit$mkinmod$map),
   xlab = "Time", ylab = "Observed", 
-  xlim = range(fit$data$time), ylim = c(0, max(fit$data$observed, na.rm = TRUE)),
+  xlim = range(fit$data$time),
+  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, lpos = "topright", inset = c(0.05, 0.05), ...)
+  add = FALSE, legend = !add,
+  show_residuals = FALSE, maxabs = "auto",
+  lpos = "topright", inset = c(0.05, 0.05), \dots)
 }
 \arguments{
   \item{x}{
@@ -56,6 +59,13 @@
   \item{legend}{
     should a legend be added to the plot?
   }
+  \item{show_residuals}{
+    should residuals be shown in the lower third of the plot?
+  }
+  \item{maxabs}{
+    Maximum absolute value of the residuals. This is used for the scaling of
+    the y axis and defaults to "auto".
+  }
   \item{lpos}{
     position of the legend. Passed to \code{\link{legend}} as the first argument.
   }