1 files changed, 123 insertions, 115 deletions
diff --git a/man/mkinmod.Rd b/man/mkinmod.Rd
index 62b02775..91f285e2 100644
--- a/man/mkinmod.Rd
+++ b/man/mkinmod.Rd
@@ -1,115 +1,123 @@
-\name{mkinmod}
-\alias{mkinmod}
-\title{
-  Function to set up a kinetic model with one or more state variables
-}
-\description{
-  The function usually takes several expressions, each assigning a compound name to 
-  a list, specifying the kinetic model type and reaction or transfer to other
-  observed compartments. Instead of specifying several expressions, a list
-  of lists can be given in the speclist argument.
-
-  For the definition of model types and their parameters, the equations given
-  in the FOCUS and NAFTA guidance documents are used.
-}
-\usage{
-mkinmod(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verbose = FALSE)
-}
-\arguments{
-  \item{...}{
-    For each observed variable, a list has to be specified as an argument, containing
-    at least a component \code{type}, specifying the type of kinetics to use
-    for the variable. Currently, single first order kinetics "SFO", 
-    indeterminate order rate equation kinetics "IORE", or
-    single first order with reversible binding "SFORB" are implemented for all
-    variables, while 
-    "FOMC", "DFOP" and "HS" can additionally be chosen for the first
-    variable which is assumed to be the source compartment.
-    Additionally, each component of the list can include a character vector \code{to},
-    specifying names of variables to which a transfer is to be assumed in the
-    model.
-    If the argument \code{use_of_ff} is set to "min" (default) and the model for 
-    the compartment is "SFO" or "SFORB", an additional component of the list
-    can be "sink=FALSE" effectively fixing the flux to sink to zero.
-  }
-  \item{use_of_ff}{
-    Specification of the use of formation fractions in the model equations and, if 
-    applicable, the coefficient matrix. If "min", a minimum use of formation 
-    fractions is made in order to avoid fitting the product of formation fractions 
-    and rate constants. If "max", formation fractions are always used.
-  }
-  \item{speclist}{
-    The specification of the observed variables and their submodel types and 
-    pathways can be given as a single list using this argument. Default is NULL.
-  }
-  \item{quiet}{
-    Should messages be suppressed?
-  }
-  \item{verbose}{
-    If \code{TRUE}, passed to \code{\link{cfunction}} if applicable to give
-    detailed information about the C function being built.
-  }
-}
-\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. }
-    \item{use_of_ff}{ The content of \code{use_of_ff} is passed on in this list component. }
-    \item{coefmat}{ The coefficient matrix, if the system of differential equations can be
-      represented by one. }
-}
-\note{
-  The IORE submodel is not well tested (yet). When using this model for metabolites, 
-  you may want to read the second note in the help page to 
-  \code{\link{mkinfit}}.
-}
-\references{
-  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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} 
-
-  NAFTA Technical Working Group on Pesticides (not dated) Guidance for
-  Evaluating and Calculating Degradation Kinetics in Environmental 
-  Media
-}
-\author{
-  Johannes Ranke
-}
-\examples{
-# Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)
-SFO <- mkinmod(parent = list(type = "SFO"))
-
-# One parent compound, one metabolite, both single first order
-SFO_SFO <- mkinmod(
-  parent = mkinsub("SFO", "m1"),
-  m1 = mkinsub("SFO"))
-
-\dontrun{
-# The above model used to be specified like this, before the advent of mkinsub()
-SFO_SFO <- mkinmod(
-  parent = list(type = "SFO", to = "m1"),
-  m1 = list(type = "SFO"))
-
-# Show details of creating the C function
-SFO_SFO <- mkinmod(
-  parent = mkinsub("SFO", "m1"),
-  m1 = mkinsub("SFO"), verbose = TRUE)
-
-# If we have several parallel metabolites 
-# (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)
-m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
-                           M1 = mkinsub("SFO"),
-                           M2 = mkinsub("SFO"),
-                           use_of_ff = "max", quiet = TRUE)
-
-fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par, 
-                          synthetic_data_for_UBA_2014[[12]]$data,
-                          quiet = TRUE)
-}
-}
-\keyword{ models }
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mkinmod.R
+\name{mkinmod}
+\alias{mkinmod}
+\title{Function to set up a kinetic model with one or more state variables}
+\usage{
+mkinmod(..., use_of_ff = "min", speclist = NULL, quiet = FALSE,
+  verbose = FALSE)
+}
+\arguments{
+\item{...}{For each observed variable, a list has to be specified as an
+argument, containing at least a component \code{type}, specifying the type
+of kinetics to use for the variable. Currently, single first order
+kinetics "SFO", indeterminate order rate equation kinetics "IORE", or
+single first order with reversible binding "SFORB" are implemented for all
+variables, while "FOMC", "DFOP" and "HS" can additionally be chosen for
+the first variable which is assumed to be the source compartment.
+Additionally, each component of the list can include a character vector
+\code{to}, specifying names of variables to which a transfer is to be
+assumed in the model.  If the argument \code{use_of_ff} is set to "min"
+(default) and the model for the compartment is "SFO" or "SFORB", an
+additional component of the list can be "sink=FALSE" effectively fixing
+the flux to sink to zero.}
+
+\item{use_of_ff}{Specification of the use of formation fractions in the
+model equations and, if applicable, the coefficient matrix. If "min", a
+minimum use of formation fractions is made in order to avoid fitting the
+product of formation fractions and rate constants. If "max", formation
+fractions are always used.}
+
+\item{speclist}{The specification of the observed variables and their
+submodel types and pathways can be given as a single list using this
+argument. Default is NULL.}
+
+\item{quiet}{Should messages be suppressed?}
+
+\item{verbose}{If \code{TRUE}, passed to \code{\link{cfunction}} if
+applicable to give detailed information about the C function being built.}
+}
+\value{
+A list of class \code{mkinmod} for use with \code{\link{mkinfit}},
+  containing, among others,
+  \item{diffs}{
+    A vector of string representations of differential equations, one for
+    each modelling variable.
+  }
+  \item{map}{
+    A list containing named character vectors for each observed variable,
+    specifying the modelling variables by which it is represented.
+  }
+  \item{use_of_ff}{
+    The content of \code{use_of_ff} is passed on in this list component.
+  }
+  \item{coefmat}{
+    The coefficient matrix, if the system of differential equations can be
+    represented by one.
+  }
+  \item{ll}{
+    The likelihood function, taking the parameter vector as the first argument.
+  }
+}
+\description{
+The function usually takes several expressions, each assigning a compound
+name to a list, specifying the kinetic model type and reaction or transfer
+to other observed compartments. Instead of specifying several expressions, a
+list of lists can be given in the speclist argument.
+}
+\details{
+For the definition of model types and their parameters, the equations given
+in the FOCUS and NAFTA guidance documents are used.
+}
+\note{
+The IORE submodel is not well tested for metabolites. When using this
+  model for metabolites, you may want to read the second note in the help
+  page to \code{\link{mkinfit}}.
+}
+\examples{
+
+# Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)
+SFO <- mkinmod(parent = list(type = "SFO"))
+
+# One parent compound, one metabolite, both single first order
+SFO_SFO <- mkinmod(
+  parent = mkinsub("SFO", "m1"),
+  m1 = mkinsub("SFO"))
+
+\dontrun{
+# The above model used to be specified like this, before the advent of mkinsub()
+SFO_SFO <- mkinmod(
+  parent = list(type = "SFO", to = "m1"),
+  m1 = list(type = "SFO"))
+
+# Show details of creating the C function
+SFO_SFO <- mkinmod(
+  parent = mkinsub("SFO", "m1"),
+  m1 = mkinsub("SFO"), verbose = TRUE)
+
+# If we have several parallel metabolites
+# (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)
+m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
+                           M1 = mkinsub("SFO"),
+                           M2 = mkinsub("SFO"),
+                           use_of_ff = "max", quiet = TRUE)
+
+fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par,
+                          synthetic_data_for_UBA_2014[[12]]$data,
+                          quiet = TRUE)
+}
+
+}
+\references{
+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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
+
+  NAFTA Technical Working Group on Pesticides (not dated) Guidance for
+  Evaluating and Calculating Degradation Kinetics in Environmental Media
+}
+\author{
+Johannes Ranke
+}