- 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

1 files changed, 9 insertions, 6 deletions

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)