- 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, 63 insertions, 0 deletions

diff --git a/man/mkinpredict.Rd b/man/mkinpredict.Rd
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+\name{mkinpredict}
+\alias{mkinpredict}
+\title{
+  Produce predictions from a kinetic model using specifc parameters
+}
+\description{
+  This function produces a time series for all the observed variables in a kinetic model
+  as specified by \code{\link{mkinmod}}, using a specific set of kinetic parameters and
+  initial values for the state variables.
+}
+\usage{
+mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = "deSolve", map_output = TRUE, atol = 1e-06, ...)
+}
+\arguments{
+  \item{mkinmod}{
+  A kinetic model as produced by \code{\link{mkinmod}}.
+}
+  \item{odeparms}{
+  A numeric vector specifying the parameters used in the kinetic model, which is generally
+  defined as a set of ordinary differential equations.
+}
+  \item{odeini}{
+  A numeric vectory containing the initial values of the state variables of the model. Note
+  that the state variables can differ from the observed variables, for example in the case
+  of the SFORB model.
+}
+  \item{outtimes}{
+  A numeric vector specifying the time points for which model predictions should be 
+  generated.
+}
+  \item{solution_type}{
+  The method that should be used for producing the predictions. This should
+  generally be "analytical" if there is only one observed variable, and usually
+  "deSolve" in the case of several observed variables. The third possibility "eigen"
+  is faster but produces results that the author believes to be less accurate.
+}
+  \item{map_output}{
+  Boolean to specify if the output should list values for the observed variables (default)
+  or for all state variables (if set to FALSE). 
+}
+  \item{atol}{
+  Absolute error tolerance, passed to \code{\link{ode}}. Default is 1e-6 as in 
+  \code{\link{lsoda}}.
+}
+  \item{\dots}{
+  Further arguments passed to the ode solver in case such a solver is used.
+}
+}
+\value{
+  A matrix in the same format as the output of \code{\link{ode}}.
+}
+\author{
+  Johannes Ranke
+}
+\examples{
+  SFO <- mkinmod(degradinol = list(type = "SFO"))
+  mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 1:20, solution_type = "analytical")
+  mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 1:20, solution_type = "eigen")
+  mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 1:20, atol = 1e-20)
+  mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 1:20, atol = 1e-20, method = "rk4")
+  mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), (1:200)/10)
+}
+\keyword{ manip }