From 12934520d7ec3218ce1505787b6066334a24a562 Mon Sep 17 00:00:00 2001
From: jranke <jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb>
Date: Tue, 30 Mar 2010 19:49:44 +0000
Subject: Initial import of the kinfit package developed from 2008-07 to
 2010-03 at Harlan Laboratories Ltd (former RCC Ltd).

Supports fitting of parent data with the usual FOCUS kinetic models.



git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/kinfit@2 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
---
 R/kinfit.R | 94 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 94 insertions(+)
 create mode 100644 R/kinfit.R

(limited to 'R/kinfit.R')

diff --git a/R/kinfit.R b/R/kinfit.R
new file mode 100644
index 0000000..42a6520
--- /dev/null
+++ b/R/kinfit.R
@@ -0,0 +1,94 @@
+kinfit <- function(kindata, kinmodels = c("SFO"), 
+	parent.0.user = NA, 
+	start.SFO = list(parent.0 = NA, k = NA), 
+	start.FOMC = list(parent.0 = NA, alpha = NA, beta = NA), 
+	start.DFOP = list(parent.0 = NA, k1 = NA, k2 = NA, g = NA),
+	start.HS = list(parent.0 = NA, k1 = NA, k2 = NA, tb = NA),
+        algorithm = "port")
+{
+	kindata <- subset(kindata, !is.na(kindata$parent))
+	kinfits <- list()
+
+	if (!is.na(parent.0.user)) {
+		start.SFO$parent.0 = parent.0.user
+		start.FOMC$parent.0 = parent.0.user
+	}
+
+	lmlogged = lm(log(parent) ~ t, data = kindata)
+
+	for (kinmodel in kinmodels)
+	{
+
+		if (kinmodel == "SFO") {
+			if (is.na(start.SFO$parent.0)) {
+                                start.SFO$parent.0 = max(kindata$parent)
+			}
+			if (is.na(start.SFO$k)) {
+				start.SFO$k = - coef(lmlogged)[["t"]]
+			}
+			kinfits[[kinmodel]] = try(
+				nls(parent ~ SFO(t, parent.0, k),
+					data = kindata, model = TRUE,
+					start = start.SFO,
+                                        algorithm = algorithm), silent=TRUE)
+		}	
+		k.est = ifelse(is.na(coef(kinfits$SFO)[["k"]]),
+			-coef(lmlogged)[["t"]],
+			coef(kinfits$SFO)[["k"]])
+		if (kinmodel == "FOMC") {
+			if (is.na(start.FOMC$parent.0)) {
+                                start.FOMC$parent.0 = max(kindata$parent)
+			}
+			if (is.na(start.FOMC$alpha)) {
+				start.FOMC$alpha = 1
+			}
+			if (is.na(start.FOMC$beta)) {
+				start.FOMC$beta = start.FOMC$alpha / k.est 
+			}
+			kinfits[[kinmodel]] = try(
+				nls(parent ~ FOMC(t, parent.0, alpha, beta),
+					data = kindata, model = TRUE,
+					start = start.FOMC,
+                                        algorithm = algorithm), silent=TRUE)
+		}	
+		if (kinmodel == "DFOP") {
+			if (is.na(start.DFOP$parent.0)) {
+                                start.DFOP$parent.0 = max(kindata$parent)
+			}
+			if (is.na(start.DFOP$k1)) {
+				start.DFOP$k1 = k.est * 2
+			}
+			if (is.na(start.DFOP$k2)) {
+				start.DFOP$k2 = k.est / 2
+			}
+			if (is.na(start.DFOP$g)) {
+				start.DFOP$g = 0.5
+			}
+			kinfits[[kinmodel]] = try(
+				nls(parent ~ DFOP(t, parent.0, k1, k2, g),
+					data = kindata, model = TRUE,
+					start = start.DFOP,
+                                        algorithm = algorithm), silent=TRUE)
+		}	
+		if (kinmodel == "HS") {
+			if (is.na(start.HS$parent.0)) {
+                                start.HS$parent.0 = max(kindata$parent)
+			}
+			if (is.na(start.HS$k1)) {
+				start.HS$k1 = k.est
+			}
+			if (is.na(start.HS$k2)) {
+				start.HS$k2 = k.est / 10
+			}
+			if (is.na(start.HS$tb)) {
+				start.HS$tb = 0.05 * max(kindata$t)
+			}
+			kinfits[[kinmodel]] = try(
+				nls(parent ~ HS(t, parent.0, k1, k2, tb),
+					data = kindata, model = TRUE,
+					start = start.HS,
+                                        algorithm = algorithm), silent=TRUE)
+		}	
+	}
+	return(kinfits)		
+}
-- 
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