- Added an S3 plot method for mkinfit models

- Fixed a bug in the mkinfit summary method which crashed on missing covariance matrices



git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@58 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

6 files changed, 123 insertions, 70 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index 8875c6e..494793c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,8 +2,8 @@ Package: mkin
 Type: Package
 Title: Routines for fitting kinetic models with one or more state
   variables to chemical degradation data
-Version: 0.9-07
-Date: 2012-09-20
+Version: 0.9-08
+Date: 2012-11-26
 Author: Johannes Ranke, Katrin Lindenberger, René Lehmann
 Maintainer: Johannes Ranke <jranke@uni-bremen.de>
 Description: Calculation routines based on the FOCUS Kinetics Report (2006).
diff --git a/R/mkinfit.R b/R/mkinfit.R
index 0215596..3649b20 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -317,7 +317,7 @@ print.summary.mkinfit <- function(x, digits = max(3, getOption("digits") - 3), .
     print(x$SFORB, digits=digits,...)

   }    

 

-  printcor <- !is.null(x$cov.unscaled)

+  printcor <- is.numeric(x$cov.unscaled)

   if (printcor){

     Corr <- cov2cor(x$cov.unscaled)

     rownames(Corr) <- colnames(Corr) <- rownames(x$par)

diff --git a/R/mkinplot.R b/R/mkinplot.R
index 546c506..b9becfd 100644
--- a/R/mkinplot.R
+++ b/R/mkinplot.R
@@ -1,38 +1,4 @@
-mkinplot <- function(fit, xlab = "Time", ylab = "Observed", xlim = range(fit$data$time), ylim = range(fit$data$observed, na.rm = TRUE), legend = TRUE, ...)
+mkinplot <- function(fit, ...)
 {
-  solution_type = fit$solution_type
-  fixed <- fit$fixed$value
-  names(fixed) <- rownames(fit$fixed)
-  parms.all <- c(fit$parms.all, fixed)
-  ininames <- c(
-    rownames(subset(fit$start, type == "state")),
-    rownames(subset(fit$fixed, type == "state")))
-  odeini <- parms.all[ininames]
-  names(odeini) <- names(fit$mkinmod$diffs)
-
-  outtimes <- seq(xlim[1], xlim[2], length.out=100)
-
-  odenames <- c(
-    rownames(subset(fit$start, type == "deparm")),
-    rownames(subset(fit$fixed, type == "deparm")))
-  odeparms <- parms.all[odenames]
-
-  out <- mkinpredict(fit$mkinmod, odeparms, odeini, outtimes, 
-          solution_type = solution_type, atol = fit$atol, rtol = fit$rtol, ...)
-
-  # Plot the data and model output
-  plot(0, type="n", 
-    xlim = xlim, ylim = ylim,
-    xlab = xlab, ylab = ylab, ...)
-  col_obs <- pch_obs <- lty_obs <- 1:length(fit$mkinmod$map)
-  names(col_obs) <- names(pch_obs) <- names(lty_obs) <- names(fit$mkinmod$map)
-  for (obs_var in names(fit$mkinmod$map)) {
-    points(subset(fit$data, variable == obs_var, c(time, observed)), 
-      pch = pch_obs[obs_var], col = col_obs[obs_var])
-  }
-  matlines(out$time, out[-1])
-  if (legend == TRUE) {
-    legend("topright", inset=c(0.05, 0.05), legend=names(fit$mkinmod$map),
-      col=col_obs, pch=pch_obs, lty=lty_obs)
-  }
+  plot(fit, ...)
 }
diff --git a/R/plot.mkinfit.R b/R/plot.mkinfit.R
new file mode 100644
index 0000000..1858aa8
--- /dev/null
+++ b/R/plot.mkinfit.R
@@ -0,0 +1,45 @@
+plot.mkinfit <- function(x, fit = x,
+  xlab = "Time", ylab = "Observed",
+  xlim = range(fit$data$time), ylim = range(fit$data$observed, na.rm = TRUE), 
+  col_obs = 1:length(fit$mkinmod$map),
+  pch_obs = col_obs, lty_obs = rep(1, length(fit$mkinmod$map)),
+  add = FALSE, legend = !add, ...)
+{
+  solution_type = fit$solution_type
+  fixed <- fit$fixed$value
+  names(fixed) <- rownames(fit$fixed)
+  parms.all <- c(fit$parms.all, fixed)
+  ininames <- c(
+    rownames(subset(fit$start, type == "state")),
+    rownames(subset(fit$fixed, type == "state")))
+  odeini <- parms.all[ininames]
+  names(odeini) <- names(fit$mkinmod$diffs)
+
+  outtimes <- seq(xlim[1], xlim[2], length.out=100)
+
+  odenames <- c(
+    rownames(subset(fit$start, type == "deparm")),
+    rownames(subset(fit$fixed, type == "deparm")))
+  odeparms <- parms.all[odenames]
+
+  out <- mkinpredict(fit$mkinmod, odeparms, odeini, outtimes, 
+          solution_type = solution_type, atol = fit$atol, rtol = fit$rtol, ...)
+
+  # Set up the plot if not to be added to an existing plot
+  if (add == FALSE) {
+    plot(0, type="n", 
+      xlim = xlim, ylim = ylim,
+      xlab = xlab, ylab = ylab, ...)
+  }
+  # Plot the data and model output
+  names(col_obs) <- names(pch_obs) <- names(lty_obs) <- names(fit$mkinmod$map)
+  for (obs_var in names(fit$mkinmod$map)) {
+    points(subset(fit$data, variable == obs_var, c(time, observed)), 
+      pch = pch_obs[obs_var], col = col_obs[obs_var])
+  }
+  matlines(out$time, out[-1], col = col_obs, lty = lty_obs)
+  if (legend == TRUE) {
+    legend("topright", inset=c(0.05, 0.05), legend=names(fit$mkinmod$map),
+      col=col_obs, pch=pch_obs, lty=lty_obs)
+  }
+}
diff --git a/man/mkinplot.Rd b/man/mkinplot.Rd
index b72675a..4b0fef4 100644
--- a/man/mkinplot.Rd
+++ b/man/mkinplot.Rd
@@ -4,50 +4,22 @@
   Plot the observed data and the fitted model of an mkinfit.
 }
 \description{
-  Solves the differential equations with the optimised and fixed parameters
-  from a previous successful call to \code{\link{mkinfit}} and plots 
-  the observed data together with the numerical solution of the fitted model.
+  Deprecated function. It now only calls the plot method \code{\link{plot.mkinfit}}.
 }
 \usage{
-  mkinplot(fit, xlab = "Time", ylab = "Observed", 
-    xlim = range(fit$data$time), ylim = range(fit$data$observed, na.rm=TRUE), 
-    legend = TRUE, ...)
+  mkinplot(fit, ...)
 }
 \arguments{
   \item{fit}{
     an object of class \code{\link{mkinfit}}.
   }
-  \item{xlab}{
-    label for the x axis.
-  }
-  \item{ylab}{
-    label for the y axis.
-  }
-  \item{xlim}{
-    plot range in x direction.
-  }
-  \item{ylim}{
-    plot range in y direction.
-  }
-  \item{legend}{
-    legend specifying if a legend should be included in the plot.
-  }
   \item{\dots}{
-   further arguments passed to \code{\link{plot}}.
+   further arguments passed to \code{\link{plot.mkinfit}}.
 }
 }
 \value{
   The function is called for its side effect.
 }
-\examples{
-# One parent compound, one metabolite, both single first order.
-SFO_SFO <- mkinmod(
-  parent = list(type = "SFO", to = "m1", sink = TRUE),
-  m1 = list(type = "SFO"))
-# Fit the model to the FOCUS example dataset D using defaults
-fit <- mkinfit(SFO_SFO, FOCUS_2006_D)
-\dontrun{mkinplot(fit)}
-}
 \author{
   Johannes Ranke
 }
diff --git a/man/plot.mkinfit.Rd b/man/plot.mkinfit.Rd
new file mode 100644
index 0000000..01b8cec
--- /dev/null
+++ b/man/plot.mkinfit.Rd
@@ -0,0 +1,70 @@
+\name{plot.mkinfit}
+\alias{plot.mkinfit}
+\title{
+  Plot the observed data and the fitted model of an mkinfit object.
+}
+\description{
+  Solves the differential equations with the optimised and fixed parameters
+  from a previous successful call to \code{\link{mkinfit}} and plots 
+  the observed data together with the numerical solution of the fitted model.
+}
+\usage{
+\method{plot}{mkinfit}(x, fit = x, xlab = "Time", ylab = "Observed", 
+  xlim = range(fit$data$time), ylim = range(fit$data$observed, na.rm = TRUE),
+  col_obs = 1:length(fit$mkinmod$map), pch_obs = col_obs, lty_obs = 1, 
+  add = FALSE, legend = !add, ...)
+}
+\arguments{
+  \item{x}{
+    Alias for fit introduced for compatibility with the generic S3 method.  
+}
+  \item{fit}{
+    an object of class \code{\link{mkinfit}}.
+}
+  \item{xlab}{
+    label for the x axis.
+  }
+  \item{ylab}{
+    label for the y axis.
+  }
+  \item{xlim}{
+    plot range in x direction.
+  }
+  \item{ylim}{
+    plot range in y direction.
+  }
+  \item{col_obs}{
+    colors used for plotting the observed data and the corresponding model prediction lines.
+}
+  \item{pch_obs}{
+    symbols to be used for plotting the data.
+}
+  \item{lty_obs}{
+    line types to be used for the model predictions.
+}
+  \item{add}{
+    should the plot be added to an existing plot?
+}
+  \item{legend}{
+    should a legend be added to the plot?
+}
+  \item{\dots}{
+   further arguments passed to \code{\link{plot}}.
+}
+}
+\value{
+  The function is called for its side effect.
+}
+\examples{
+# One parent compound, one metabolite, both single first order.
+SFO_SFO <- mkinmod(
+  parent = list(type = "SFO", to = "m1", sink = TRUE),
+  m1 = list(type = "SFO"))
+# Fit the model to the FOCUS example dataset D using defaults
+fit <- mkinfit(SFO_SFO, FOCUS_2006_D)
+\dontrun{plot(fit)}
+}
+\author{
+  Johannes Ranke
+}
+\keyword{ hplot }