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/mkin@17 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

1 files changed, 20 insertions, 5 deletions

diff --git a/inst/doc/mkin.Rnw b/inst/doc/mkin.Rnw
index 78b59e67..2f71151a 100644
--- a/inst/doc/mkin.Rnw
+++ b/inst/doc/mkin.Rnw
@@ -1,3 +1,4 @@
+% $Id: mkin.Rnw 66 2010-09-03 08:50:26Z jranke $

 %%\VignetteIndexEntry{Routines for fitting kinetic models with one or more state variables to chemical degradation data}

 %%VignetteDepends{FME}

 %%\usepackage{Sweave}

@@ -78,7 +79,7 @@ barrier for \RR{} newcomers.
 \subsection{Data format}

 

 The following listing shows example dataset C from the FOCUS kinetics

-report as distributed with the \Rpackage{kinfit} package

+report as distributed with the \Rpackage{mkin} package

 

 <<FOCUS_2006_C_data, echo=TRUE, eval=TRUE>>=

 library("mkin")

@@ -101,8 +102,9 @@ as shown in the following listing
 

 <<data_format, echo=TRUE>>=

 example_data <- data.frame(

+  name = rep("parent", 9),

   time = c(0, 1, 3, 7, 14, 28, 63, 91, 119),

-  parent = c(85.1, 57.9, 29.9, 14.6, 9.7, 6.6, 4, 3.9, 0.6)

+  value = c(85.1, 57.9, 29.9, 14.6, 9.7, 6.6, 4, 3.9, 0.6)

 )

 @

 

@@ -122,12 +124,23 @@ SFORB_SFO <- mkinmod(
   m1 = list(type = "SFO"))

 @

 

+The model definitions given above define sets of linear first-order ordinary

+differential equations. In these cases, a coefficient matrix is also returned.

+

+Other models that include time on the right-hand side of the differential 

+equation are the first-order multi-compartment (FOMC) model and the

+Hockey-Stick (HS) model. At present, only the FOMC model can only be used, and

+only for the parent compound.

+

 \subsection{Fitting the model}

 

 Then the model parameters should be fitted to the data. The function

 \Robject{mkinfit} internally creates a cost function using \Robject{modCost}

 from the \Rpackage{FME} package and the produces a fit using \Robject{modFit}

-from the same package.

+from the same package. In cases of linear first-order differential 

+equations, the solution used for calculating the cost function is based

+on the fundamental system of the coefficient matrix, as proposed by 

+\citet{bates88}.

 

 <<model_fitting, echo=TRUE>>=

 # Do not show significance stars as they interfere with vignette generation

@@ -136,8 +149,10 @@ SFO.fit <- mkinfit(SFO, FOCUS_2006_C)
 summary(SFO.fit)

 SFORB.fit <- mkinfit(SFORB, FOCUS_2006_C)

 summary(SFORB.fit)

-SFO_SFO.fit <- mkinfit(SFO_SFO, FOCUS_2006_D)

-summary(SFO_SFO.fit)

+SFO_SFO.fit <- mkinfit(SFO_SFO, FOCUS_2006_D, plot=TRUE)

+summary(SFO_SFO.fit, data=FALSE)

+SFORB_SFO.fit <- mkinfit(SFORB_SFO, FOCUS_2006_D, plot=TRUE)

+summary(SFORB_SFO.fit, data=FALSE)

 @

 

 \bibliographystyle{plainnat}