From df916b91c90f80e2c68f3e136a7b6e07b8c6bae1 Mon Sep 17 00:00:00 2001
From: jranke <jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb>
Date: Mon, 26 Nov 2012 23:03:19 +0000
Subject: - 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
---
 man/mkinplot.Rd     | 34 +++-----------------------
 man/plot.mkinfit.Rd | 70 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 73 insertions(+), 31 deletions(-)
 create mode 100644 man/plot.mkinfit.Rd

(limited to 'man')

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 }
-- 
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