- Simplified implementation of mkinerrmin (see ChangeLog)

- Improve ChangeLog and add comment to source code
- Simple test of the new mkinerrmin implementation in test.R
- Added some summaries for documenting the changes in mkinerrmin



git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@120 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

3 files changed, 20 insertions, 9 deletions

diff --git a/ChangeLog b/ChangeLog
index a57894d..422deb2 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,9 @@
+2013-10-21  Johannes Ranke <jranke@uni-bremen.de> for mkin (0.9-22)

+

+	* Get rid of the optimisation step in mkinerrmin - this was unnecessary

+	  Thanks to KinGUII for the inspiration - actually this is equation 6-2 

+		in FOCUS kinetics p. 91 that I had overlooked originally

+

 2013-10-17  Johannes Ranke <jranke@uni-bremen.de> for mkin (0.9-22)

 

 	* Fix plot.mkinfit as it passed graphical arguments like main to the solver

@@ -16,11 +22,13 @@
 	* Correct the output of the data in the case of manual weighting

 	* Implement IRLS assuming different variances for observed variables

 

-

 2013-10-09  Johannes Ranke for version (0.9-22)

 

 	* Do not use 0 values at time zero for chi2 error level calculations.

-	  This is the way it is done in KinGUII and it makes sense

+	  This is the way it is done in KinGUII and it makes sense. It does

+		impact the chi2 error levels in the output. Generally they seem to be

+		lower for metabolites now, presumably because the mean of the observed

+		values is higher

 

 Changes performed in earlier versions are documented in the subversion log

 files on R-Forge http://www.r-forge.r-project.org/scm/?group_id=615

diff --git a/DESCRIPTION b/DESCRIPTION
index f7a293d..9e00357 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -3,7 +3,7 @@ Type: Package
 Title: Routines for fitting kinetic models with one or more state
   variables to chemical degradation data
 Version: 0.9-22
-Date: 2013-10-10
+Date: 2013-10-21
 Author: Johannes Ranke, with contributions from Katrin Lindenberger, René Lehmann
 Maintainer: Johannes Ranke <jranke@uni-bremen.de>
 Description: Calculation routines based on the FOCUS Kinetics Report (2006).
diff --git a/R/mkinerrmin.R b/R/mkinerrmin.R
index 7d9d462..074cc56 100644
--- a/R/mkinerrmin.R
+++ b/R/mkinerrmin.R
@@ -22,16 +22,14 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("name", "value_mean"))
 mkinerrmin <- function(fit, alpha = 0.05)

 {

   parms.optim <- fit$par

+

   kinerrmin <- function(errdata, n.parms) {

     means.mean <- mean(errdata$value_mean, na.rm = TRUE)

     df = length(errdata$value_mean) - n.parms

   

-    f <- function(err)

-    {

-      (sum((errdata$value_mean - errdata$value_pred)^2/((err * means.mean)^2)) - 

-       qchisq(1 - alpha,df))^2

-    }

-    err.min <- optimize(f, c(0.01,0.9))$minimum

+    err.min <- sqrt((1 / qchisq(1 - alpha, df)) *

+               sum((errdata$value_mean - errdata$value_pred)^2)/(means.mean^2))

+

     return(list(err.min = err.min, n.optim = n.parms, df = df))

   }

 

@@ -39,7 +37,12 @@ mkinerrmin <- function(fit, alpha = 0.05)
   errdata <- merge(means, fit$predicted, by = c("time", "name"), 

     suffixes = c("_mean", "_pred"))

   errdata <- errdata[order(errdata$time, errdata$name), ]

+

+  # Any value that is set to exactly zero is not really an observed value

+  # Remove those at time 0 - those are caused by the FOCUS recommendation

+  # to set metabolites occurring at time 0 to 0

   errdata <- subset(errdata, !(time == 0 & value_mean == 0))

+

   n.optim.overall <- length(parms.optim)

 

   errmin.overall <- kinerrmin(errdata, n.optim.overall)