- Fitting and summaries now work with the new parameter transformations.

- The SFORB models with metabolites is broken (see TODO)
- Moved the vignette to the location recommended since R 2.14
- Added the missing documentation
- Commented out the schaefer_complex_case test, as this version of
  mkin is not able to fit a model without sink and therefore 
  mkin estimated parameters are quite different




git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@22 edb9625f-4e0d-4859-8d74-9fd3b1da38cb

1 files changed, 51 insertions, 0 deletions

diff --git a/man/transform_odeparms.Rd b/man/transform_odeparms.Rd
new file mode 100644
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+++ b/man/transform_odeparms.Rd
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+\name{transform_odeparms}
+\alias{transform_odeparms}
+\alias{backtransform_odeparms}
+\title{
+  Functions to transform and backtransform kinetic parameters for fitting
+}
+\description{
+  The transformations are intended to map parameters that should only take 
+  on restricted values to the full scale of real numbers. For kinetic rate
+  constants and other paramters that can only take on positive values, a
+  simple log transformation is used. For compositional parameters, such as
+  the formations fractions that should always sum up to 1 and can not be
+  negative, the \code{\link{ilr}} transformation is used.
+}
+\usage{
+transform_odeparms(parms, mod_vars)
+backtransform_odeparms(transparms, mod_vars)
+}
+\arguments{
+  \item{parms}{
+  Parameters of kinetic models as used in the differential equations.
+}
+  \item{transparms}{
+  Transformed parameters of kinetic models as used in the fitting procedure.
+}
+  \item{mod_vars}{
+  Names of the state variables in the kinetic model. These are used for 
+  grouping the formation fractions before \code{\link{ilr}} transformation.  
+}
+}
+\value{
+  A vector of transformed or backtransformed parameters with the same names
+  as the original parameters.
+}
+\author{
+  Johannes Ranke
+}
+\examples{
+SFO_SFO <- mkinmod(
+  parent = list(type = "SFO", to = "m1", sink = TRUE),
+  m1 = list(type = "SFO"))
+# Fit the model to the FOCUS example dataset D using defaults
+fit <- mkinfit(SFO_SFO, FOCUS_2006_D)
+summary(fit, data=FALSE) # See transformed and backtransformed parameters
+initials <- fit$start$initial
+transformed <- fit$start$transformed
+names(initials) <- names(transformed) <- rownames(fit$start)
+transform_odeparms(initials, c("parent", "m1"))
+backtransform_odeparms(transformed, c("parent", "m1"))
+}
+\keyword{ manip }