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-rw-r--r--R/mkinresplot.R29
-rw-r--r--R/plot.mkinfit.R28
-rw-r--r--inst/GUI/gmkin.R11
-rw-r--r--man/mkinresplot.Rd11
-rw-r--r--man/plot.mkinfit.Rd14
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.
}

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