Use roxygen for functions and methods

1 files changed, 69 insertions, 64 deletions

diff --git a/man/mkinpredict.Rd b/man/mkinpredict.Rd
index 24b918dc..53f02dea 100644
--- a/man/mkinpredict.Rd
+++ b/man/mkinpredict.Rd
@@ -1,78 +1,80 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/mkinpredict.R
 \name{mkinpredict}
 \alias{mkinpredict}
 \alias{mkinpredict.mkinmod}
 \alias{mkinpredict.mkinfit}
-\title{
-  Produce predictions from a kinetic model using specific 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.
-}
+\title{Produce predictions from a kinetic model using specific parameters}
 \usage{
-  mkinpredict(x, odeparms, odeini, outtimes = seq(0, 120, by = 0.1),
-    solution_type = "deSolve", use_compiled = "auto", method.ode = "lsoda",
-    atol = 1e-08, rtol = 1e-10, map_output = TRUE, ...)
+mkinpredict(x, odeparms, odeini, outtimes = seq(0, 120, by = 0.1),
+  solution_type = "deSolve", use_compiled = "auto",
+  method.ode = "lsoda", atol = 1e-08, rtol = 1e-10,
+  map_output = TRUE, ...)
+
+\method{mkinpredict}{mkinmod}(x, odeparms = c(k_parent_sink = 0.1),
+  odeini = c(parent = 100), outtimes = seq(0, 120, by = 0.1),
+  solution_type = "deSolve", use_compiled = "auto",
+  method.ode = "lsoda", atol = 1e-08, rtol = 1e-10,
+  map_output = TRUE, ...)
+
+\method{mkinpredict}{mkinfit}(x, odeparms = x$bparms.ode,
+  odeini = x$bparms.state, outtimes = seq(0, 120, by = 0.1),
+  solution_type = "deSolve", use_compiled = "auto",
+  method.ode = "lsoda", atol = 1e-08, rtol = 1e-10,
+  map_output = TRUE, ...)
 }
 \arguments{
-  \item{x}{
-    A kinetic model as produced by \code{\link{mkinmod}}, or a kinetic
-    fit as fitted by \code{\link{mkinfit}}. In the latter case, the fitted
-    parameters are used for the prediction.
-  }
-  \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{use_compiled}{
-    If set to \code{FALSE}, no compiled version of the \code{\link{mkinmod}}
-    model is used, even if is present.
-  }
-  \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.
-  }
+\item{x}{A kinetic model as produced by \code{\link{mkinmod}}, or a kinetic
+fit as fitted by \code{\link{mkinfit}}. In the latter case, the fitted
+parameters are used for the prediction.}
+
+\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{use_compiled}{If set to \code{FALSE}, no compiled version of the
+\code{\link{mkinmod}} model is used, even if is present.}
+
+\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}}.
+A matrix in the same format as the output of \code{\link{ode}}.
 }
-\author{
-  Johannes Ranke
+\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.
 }
 \examples{
+
   SFO <- mkinmod(degradinol = mkinsub("SFO"))
   # Compare solution types
   mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
@@ -124,5 +126,8 @@
     f <- mkinfit(SFO_SFO, FOCUS_2006_C)
     head(mkinpredict(f))
   }
+
+}
+\author{
+Johannes Ranke
 }
-\keyword{ manip }