diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/mkinresplot.R | 29 | ||||
| -rw-r--r-- | R/plot.mkinfit.R | 28 |
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) + } } |