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authorjranke <jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb>2012-04-10 21:50:22 +0000
committerjranke <jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb>2012-04-10 21:50:22 +0000
commitc1144753adfa0809003085009ebd85f8af9beda8 (patch)
treec07afafb9e6a3ffd1248167f4e40983bb3ef85fc /man/transform_odeparms.Rd
parentd3df16102c5ed4bf9182b4f1893561e99eaed166 (diff)
- 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
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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 }

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