Initial upload of the upcoming multicompartment version of kinfit.

Some functionality is still missing (chi2), some may never be implemented
(FOMC model), but in general it is much more powerful than kinfit, owing
to the powerful FME package.



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

3 files changed, 164 insertions, 0 deletions

diff --git a/man/FOCUS_2006_datasets.Rd b/man/FOCUS_2006_datasets.Rd
new file mode 100644
index 0000000..04565f7
--- /dev/null
+++ b/man/FOCUS_2006_datasets.Rd
@@ -0,0 +1,35 @@
+\name{FOCUS_2006_datasets}

+\Rdversion{1.1}

+\alias{FOCUS_2006_A}

+\alias{FOCUS_2006_B}

+\alias{FOCUS_2006_C}

+\alias{FOCUS_2006_D}

+\alias{FOCUS_2006_E}

+\alias{FOCUS_2006_F}

+\docType{data}

+\title{

+Datasets A to F from the FOCUS Kinetics report from 2006

+}

+\description{

+Data taken from an FOCUS (2006), p. 258.

+}

+\usage{FOCUS_2006_datasets}

+\format{

+  6 datasets with observations on the following variables.

+  \describe{

+    \item{\code{name}}{a factor containing the name of the observed variable}

+    \item{\code{time}}{a numeric vector containing time points}

+    \item{\code{value}}{a numeric vector containing concentrations in percent of applied radioactivity}

+  }

+}

+\source{

+  FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence and

+  Degradation Kinetics from Environmental Fate Studies on Pesticides in EU

+  Registration} Report of the FOCUS Work Group on Degradation Kinetics,

+  EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,

+  \url{http://focus.jrc.ec.europa.eu/dk} 

+}

+\examples{

+FOCUS_2006_C

+}

+\keyword{datasets}

diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd
new file mode 100644
index 0000000..7ddc10c
--- /dev/null
+++ b/man/mkinfit.Rd
@@ -0,0 +1,85 @@
+\name{mkinfit}
+\alias{mkinfit}
+\title{
+  Fit a kinetic model to data with one or more state variables.
+}
+\description{
+  This function uses the Flexible Modelling Environment package
+  \code{\link{FME}} to create a function calculating the model cost, which is
+  then minimised, using the specified initial or fixed parameters and starting
+  values.
+}
+\usage{
+mkinfit(mkinmod, observed, parms.ini = rep(0.1, length(mkinmod$parms)), state.ini = c(100, rep(0, length(mkinmod$diffs) - 1)), fixed_parms = rep(FALSE, length(mkinmod$parms)), fixed_initials = c(FALSE, rep(TRUE, length(mkinmod$diffs) - 1)), plot = NULL, err = NULL, weight = "none", scaleVar = FALSE, ...)
+}
+\arguments{
+  \item{mkinmod}{
+    A list of class \code{\link{mkinmod}}, containing the kinetic model to be fitted to the data.
+  }
+  \item{observed}{
+    The observed data. It has to be in the long format as described in
+    \code{\link{modFit}}, i.e. the first column must contain the name of the
+    observed variable for each data point. The second column must contain the
+    times of observation, named "time".  The third column must be named "value"
+    and contain the observed values. Optionally, a further column can contain
+    weights for each data point. If it is not named "err", its name must be
+    passed as a further argument named \code{err} which is then passed on to
+    \code{\link{modFit}}.
+  }
+  \item{parms.ini}{
+    A named vector if initial values for the parameters, including both parameters to
+    be optimised and potentially also fixed parameters as indicated by \code{fixed_parms}.
+}
+  \item{state.ini}{
+    A named vector of initial values for the state variables of the model. In case the 
+    observed variables are represented by more than one model variable, the names will
+    differ from the names of the observed variables (see \code{map} component of 
+    \code{\link{mkinmod}}). The default is to set the initial value of the first model
+    variable to 100 and all others to 0.
+}
+  \item{fixed_parms}{
+    A vector of booleans specifying which parameters are not to be optimised. The default
+    is to include all model parameters in the optimisation.
+}
+  \item{fixed_initials}{
+    A vector of booleans specifying which initial values to include in the optimisation.
+    The default is to optimise the initial value of the first model variable and to
+    keep all other initial values fixed.
+}
+  \item{plot}{
+    Should the observed values and the numerical solutions be plotted at each stage
+    of the optimisation?
+}
+  \item{err }{either \code{NULL}, or the name of the column with the
+    \emph{error} estimates, used to weigh the residuals (see details of
+    \code{\link{modCost}}); if \code{NULL}, then the residuals are not weighed.
+}
+  \item{weight}{only if \code{err}=\code{NULL}: how to weigh the
+    residuals, one of "none", "std", "mean", see details of \code{\link{modCost}}.
+}
+  \item{scaleVar}{
+    Will be passed to \code{\link{modCost}}. Default is not to scale Variables according
+    to the number of observations.
+}
+  \item{\dots}{
+    Further arguments that will be passed to \code{\link{modFit}}. 
+}
+}
+\value{
+    A list of class \code{\link{modFit}}. Thus, at present, a summary can be obtained
+    by \code{\link{summary.modFit}}. 
+}
+\author{
+  Johannes Ranke <jranke@{harlan.com,uni-bremen.de}>
+}
+\examples{
+# One parent compound, one metabolite, both single first order.
+SFO_SFO <- mkinmod(spec = list(
+  parent = list(type = "SFO", to = "m1", sink = TRUE),
+  m1 = list(type = "SFO", to = NA, sink = TRUE)))
+# Fit the model to the FOCUS example dataset D using defaults
+fit <- mkinfit(SFO_SFO, FOCUS_2006_D)
+summary(fit)
+}
+\keyword{ models }
+\keyword{ optimize }
diff --git a/man/mkinmod.Rd b/man/mkinmod.Rd
new file mode 100644
index 0000000..4569b31
--- /dev/null
+++ b/man/mkinmod.Rd
@@ -0,0 +1,44 @@
+\name{mkinmod}

+\alias{mkinmod}

+\title{

+  Function to set up a kinetic model with one or more state variables.

+}

+\description{

+  The function takes a specification, consisting of a list of the observed variables

+  in the data. Each observed variable is again represented by a list, specifying the 

+  kinetic model type and reaction or transfer to other observed compartments.

+}

+\usage{

+mkinmod(spec = list(parent = list(type = "SFO", to = NA, sink = TRUE)))

+}

+\arguments{

+  \item{spec}{

+    A list of observed variables to be modelled. Each observed variable has to be 

+    represented by a list with the following entries:

+    \code{type}{ The type of kinetics to use for the variable. Currently, only

+      single first order kinetics "SFO" or single first order with reversible binding

+      "SFORB" are implemented. }

+    \code{to}{ A vector of names of variables to which a transfer is to be assumed

+      in the model. }

+    \code{sink}{ Boolean, specifying if transformation to unspecified compounds (sink) 

+      is to be assumed in the model. }

+  }

+}

+\value{

+  A list of class \code{mkinmod} for use with \code{\link{mkinfit}}, containing 

+    \item{diffs}{ A vector of string representations of differential equations,

+      one for each modelling variable. }

+    \item{parms}{ A vector of parameter names occurring in the differential equations. }

+    \item{map}{ A list containing named character vectors for each observed variable, specifying

+      the modelling variables by which it is represented. }

+}

+\author{

+  Johannes Ranke <jranke@{harlan.com,uni-bremen.de}>

+}

+\examples{

+# One parent compound, one metabolite, both single first order.

+SFO_SFO <- mkinmod(spec = list(

+  parent = list(type = "SFO", to = "m1", sink = TRUE),

+  m1 = list(type = "SFO", to = NA, sink = TRUE)))

+}

+\keyword{ models }