Fork the gmkin GUI from mkin. See ChangeLog for details

1 files changed, 0 insertions, 91 deletions

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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",
-	      method.ode = "lsoda", atol = 1e-08, rtol = 1e-10, map_output = TRUE, ...)
-}
-\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 not applicable to some models e.g.
-    using FOMC for the parent compound.
-  }
-  \item{method.ode}{
-    The solution method passed via \code{\link{mkinpredict}} to
-    \code{\link{ode}} in case the solution type is "deSolve". The default
-    "lsoda" is performant, but sometimes fails to converge.
-  }
-  \item{atol}{
-    Absolute error tolerance, passed to \code{\link{ode}}. Default is 1e-8,
-    lower than in \code{\link{lsoda}}.
-  }
-  \item{rtol}{
-    Absolute error tolerance, passed to \code{\link{ode}}. Default is 1e-10,
-    much lower than in \code{\link{lsoda}}.
-  }
-  \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{\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_sink = 0.3), c(degradinol = 100), 0:20, 
-	      solution_type = "analytical")
-  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, 
-	      solution_type = "eigen")
-
-  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 1:20, 
-	      solution_type = "analytical")[20,]
-  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, 
-	      atol = 1e-20)[20,]
-
-  # The integration method does not make a lot of difference
-  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, 
-	      atol = 1e-20, method = "ode45")[20,]
-  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, 
-	      atol = 1e-20, method = "rk4")[20,]
-
-  # The number of output times used to make a lot of difference until the
-  # default for atol was adjusted
-  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 
-	      seq(0, 20, by = 0.1))[201,]
-  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 
-	      seq(0, 20, by = 0.01))[2001,]
-}
-\keyword{ manip }