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-rw-r--r--man/FOCUS_2006_datasets.Rd35
-rw-r--r--man/mkinfit.Rd85
-rw-r--r--man/mkinmod.Rd44
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 }

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