aboutsummaryrefslogtreecommitdiff
path: root/R
diff options
context:
space:
mode:
Diffstat (limited to 'R')
-rw-r--r--R/mkinresplot.R29
-rw-r--r--R/plot.mkinfit.R28
2 files changed, 41 insertions, 16 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)
+ }
}

Contact - Imprint