- 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

1 files changed, 45 insertions, 0 deletions

diff --git a/R/plot.mkinfit.R b/R/plot.mkinfit.R
new file mode 100644
index 00000000..1858aa8a
--- /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)
+  }
+}