From e959fde98f95f3595e01490b67892678bbcd1b27 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Wed, 7 May 2014 14:47:28 +0200
Subject: Fork the gmkin GUI from mkin. See ChangeLog for details

---
 man/mkinmod.Rd | 63 ----------------------------------------------------------
 1 file changed, 63 deletions(-)
 delete mode 100644 man/mkinmod.Rd

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diff --git a/man/mkinmod.Rd b/man/mkinmod.Rd
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-\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(..., use_of_ff = "min", speclist = NULL)
-}
-\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" 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.
-  }
-}
-\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. }
-}
-\author{
-  Johannes Ranke
-}
-\examples{
-# Specify the SFO model
-SFO <- mkinmod(parent = list(type = "SFO"))
-
-# One parent compound, one metabolite, both single first order.
-SFO_SFO <- mkinmod(
-  parent = list(type = "SFO", to = "m1"),
-  m1 = list(type = "SFO"))
-}
-\keyword{ models }
-- 
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