From 3a6b9f52c74d6ef88a8d32c50e42864b3f251719 Mon Sep 17 00:00:00 2001
From: jranke <jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb>
Date: Thu, 15 Mar 2012 15:54:14 +0000
Subject: Update kinfit and mkin to the latest version published on BerliOS.

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/kinfit@17 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
---
 R/kinplot.R | 128 ++++++++++++++++++++++++++++++++++++++++++------------------
 1 file changed, 90 insertions(+), 38 deletions(-)

(limited to 'R/kinplot.R')

diff --git a/R/kinplot.R b/R/kinplot.R
index ace1270..394e271 100644
--- a/R/kinplot.R
+++ b/R/kinplot.R
@@ -1,61 +1,113 @@
+# $Id: kinplot.R 117 2011-06-14 08:52:14Z kati $
+
+# Copyright (C) 2008-2010 Johannes Ranke
+# Contact: mkin-devel@lists.berlios.de
+
+# This file is part of the R package kinfit
+
+# kinfit is free software: you can redistribute it and/or modify it under the
+# terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+# details.
+
+# You should have received a copy of the GNU General Public License along with
+# this program. If not, see <http://www.gnu.org/licenses/>
+
 kinplot <- function(kinobject, 
+	main = "",
 	xlab = "Time [days]", ylab = "Parent [% of applied radioactivity]",
         ylim = c("auto", "auto"),
 	lpos = "topright")
 {
 	kindata <- na.omit(kinobject$data)
 	kinfits <- kinobject$fits
-        if (ylim[1] == "auto") ylim[1] <- 0
-        if (ylim[2] == "auto") ylim[2] <- max(kindata$parent)
-        ylim <- as.numeric(ylim)
+  if (ylim[1] == "auto") ylim[1] <- 0
+  if (ylim[2] == "auto") ylim[2] <- max(kindata$parent)
+  ylim <- as.numeric(ylim)
         
 	plot(kindata$t, kindata$parent,
+	  main = main,
 	  xlab = xlab,
 	  ylab = ylab,
 	  ylim = ylim
-        )
+  )
 	n.m <- length(kinfits)
 	colors <- ltys <- 1:n.m
 	names(colors) <- names(ltys) <- names(kinfits)
-        ltext <- paste(kinobject$parent, "measured")
+  ltext <- paste(kinobject$parent, "measured")
 	for (kinmodel in names(kinfits))
 	{
 		m = kinfits[[kinmodel]]
 		if(class(m) == "nls") {
-			switch(kinmodel,
-				SFO = curve(SFO(x, 
-					coef(m)[["parent.0"]], 
-					coef(m)[["k"]]),
-					from = min(kindata$t), to = max(kindata$t), add=TRUE,
-					col = colors[[kinmodel]],
-					lty = ltys[[kinmodel]]),
-				FOMC = curve(FOMC(x, 
-					coef(m)[["parent.0"]],
-					coef(m)[["alpha"]],
-					coef(m)[["beta"]]),
-					from = min(kindata$t), to = max(kindata$t), add=TRUE,
-					col = colors[[kinmodel]],
-					lty = ltys[[kinmodel]]),
-				HS = curve(HS(x, 
-					coef(m)[["parent.0"]], 
-					coef(m)[["k1"]],
-					coef(m)[["k2"]],
-					coef(m)[["tb"]]),
-					from = min(kindata$t), to = max(kindata$t), add=TRUE,
-					col = colors[[kinmodel]],
-					lty = ltys[[kinmodel]]),
-				DFOP = curve(DFOP(x, 
-					coef(m)[["parent.0"]], 
-					coef(m)[["k1"]],
-					coef(m)[["k2"]],
-					coef(m)[["g"]]),
-					from = min(kindata$t), to = max(kindata$t), add=TRUE,
-					col = colors[[kinmodel]],
-					lty = ltys[[kinmodel]]))
-                        ltext <- c(ltext, paste("Fitted", kinmodel, "model"))
+      if (!"parent.0" %in% names(coef(m))) {
+        switch(kinmodel,
+          SFO = lines(
+              t <- seq(min(kindata$t), max(kindata$t), length.out=500),
+              predict(m, 
+              newdata = data.frame(t)),
+              col = colors[[kinmodel]],
+              lty = ltys[[kinmodel]]),
+          FOMC = lines(
+              t <- seq(min(kindata$t), max(kindata$t), length.out=500),
+              predict(m, 
+              newdata = data.frame(t)),
+              col = colors[[kinmodel]],
+              lty = ltys[[kinmodel]]), 
+ 	    HS = lines(
+              t <- seq(min(kindata$t), max(kindata$t), length.out=500),
+              predict(m, 
+              newdata = data.frame(t)),
+              col = colors[[kinmodel]],
+              lty = ltys[[kinmodel]]), 
+          DFOP = lines(
+              t <- seq(min(kindata$t), max(kindata$t), length.out=500),
+              predict(m, 
+              newdata = data.frame(t)),
+              col = colors[[kinmodel]],
+              lty = ltys[[kinmodel]])
+		)
+        ltext <- c(ltext, paste("Fitted", kinmodel, "model"))
+      } else {
+        switch(kinmodel,
+          SFO = curve(SFO(x, 
+            coef(m)[["parent.0"]], 
+            coef(m)[["k"]]),
+            from = min(kindata$t), to = max(kindata$t), add=TRUE,
+            col = colors[[kinmodel]],
+            lty = ltys[[kinmodel]]),
+          FOMC = curve(FOMC(x, 
+            coef(m)[["parent.0"]],
+            coef(m)[["alpha"]],
+            coef(m)[["beta"]]),
+            from = min(kindata$t), to = max(kindata$t), add=TRUE,
+            col = colors[[kinmodel]],
+            lty = ltys[[kinmodel]]),
+          HS = curve(HS(x, 
+            coef(m)[["parent.0"]], 
+            coef(m)[["k1"]],
+            coef(m)[["k2"]],
+            coef(m)[["tb"]]),
+            from = min(kindata$t), to = max(kindata$t), add=TRUE,
+            col = colors[[kinmodel]],
+            lty = ltys[[kinmodel]]),
+          DFOP = curve(DFOP(x, 
+            coef(m)[["parent.0"]], 
+            coef(m)[["k1"]],
+            coef(m)[["k2"]],
+            coef(m)[["g"]]),
+            from = min(kindata$t), to = max(kindata$t), add=TRUE,
+            col = colors[[kinmodel]],
+            lty = ltys[[kinmodel]]))
+        ltext <- c(ltext, paste("Fitted", kinmodel, "model"))
+      }
 		} else {
-                        ltext <- c(ltext, paste(kinmodel, "model failed"))
-                        ltys[[kinmodel]] <- NA
+        ltext <- c(ltext, paste(kinmodel, "model failed"))
+            ltys[[kinmodel]] <- NA
 		} 
 	}
 	legend(lpos, bty="n", inset = 0.05, 
-- 
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