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-rw-r--r--DESCRIPTION4
-rw-r--r--R/mkinfit.R2
-rw-r--r--R/mkinplot.R38
-rw-r--r--R/plot.mkinfit.R45
-rw-r--r--man/mkinplot.Rd34
-rw-r--r--man/plot.mkinfit.Rd70
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 }

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