IORE working for parent and metabolites, introduce mkinsub

6 files changed, 84 insertions, 4 deletions

diff --git a/NEWS.md b/NEWS.md
index cd082280..8d4a7782 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -2,6 +2,7 @@
 
 ## NEW FEATURES
 
+- Add the convenience function `mkinsub()` for creating the lists used in `mkinmod()`
 
 - Add the possibility to fit indeterminate order rate equation (IORE) models using an analytical solution (parent only) or a numeric solution. Paths from IORE compounds to metabolites are supported when using of formation fractions (use_of_ff = 'max'). Note that the numerical solution (method.ode = 'deSolve') of the IORE differential equations sometimes fails due to numerical problems.
 
diff --git a/R/mkinfit.R b/R/mkinfit.R
index a6889b0b..7a465c2b 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -43,7 +43,7 @@ mkinfit <- function(mkinmod, observed,
 {

   # Check mkinmod and generate a model for the variable whith the highest value

   # if a suitable string is given

-  parent_models_available = c("SFO", "FOMC", "DFOP", "HS", "SFORB") 

+  parent_models_available = c("SFO", "FOMC", "DFOP", "HS", "SFORB", "IORE") 

   if (class(mkinmod) != "mkinmod") {

     presumed_parent_name = observed[which.max(observed$value), "name"]

     if (mkinmod[[1]] %in% parent_models_available) {

@@ -60,7 +60,10 @@ mkinfit <- function(mkinmod, observed,
   method.modFit = match.arg(method.modFit)

   if (maxit.modFit != "auto") {

     if (method.modFit == "Marq") control.modFit$maxiter = maxit.modFit

-    if (method.modFit == "Port") control.modFit$iter.max = maxit.modFit

+    if (method.modFit == "Port") {

+      control.modFit$iter.max = maxit.modFit

+      control.modFit$eval.max = maxit.modFit

+    }

     if (method.modFit %in% c("SANN", "Nelder-Mead", "BFGS", "CG", "L-BFGS-B")) {

         control.modFit$maxit = maxit.modFit

     }

@@ -308,6 +311,8 @@ mkinfit <- function(mkinmod, observed,
   if (!transform_rates) {

     index_k <- grep("^k_", names(lower))

     lower[index_k] <- 0

+    index_k.iore <- grep("^k.iore_", names(lower))

+    lower[index_k.iore] <- 0

     other_rate_parms <- intersect(c("alpha", "beta", "k1", "k2", "tb"), names(lower))

     lower[other_rate_parms] <- 0

   }

diff --git a/R/mkinsub.R b/R/mkinsub.R
new file mode 100644
index 00000000..f92af54b
--- /dev/null
+++ b/R/mkinsub.R
@@ -0,0 +1,23 @@
+# Copyright (C) 2014 Johannes Ranke
+# Portions of this code are copyright (C) 2013 Eurofins Regulatory AG
+# Contact: jranke@uni-bremen.de
+
+# This file is part of the R package mkin
+
+# mkin is free software: you can redistribute it and/or modify it under the
+# terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+# details.
+
+# You should have received a copy of the GNU General Public License along with
+# this program. If not, see <http://www.gnu.org/licenses/>
+mkinsub <- function(submodel, to = NULL, sink = TRUE)
+{
+  return(list(type = submodel, to = to, sink = sink))
+}
+# vim: set ts=2 sw=2 expandtab:
diff --git a/R/transform_odeparms.R b/R/transform_odeparms.R
index 778f56cd..aa70a0b3 100644
--- a/R/transform_odeparms.R
+++ b/R/transform_odeparms.R
@@ -38,8 +38,7 @@ transform_odeparms <- function(parms, mkinmod,
   if (length(k) > 0) {

     if(transform_rates) {

       transparms[paste0("log_", names(k))] <- log(k)

-    }

-    else transparms[names(k)] <- k

+    } else transparms[names(k)] <- k

   }

 

   # Do not transform exponents in IORE models

@@ -123,6 +122,8 @@ backtransform_odeparms <- function(transparms, mkinmod,
   } else {

     trans_k <- transparms[grep("^k_", names(transparms))]

     parms[names(trans_k)] <- trans_k

+    trans_k.iore <- transparms[grep("^k.iore_", names(transparms))]

+    parms[names(trans_k.iore)] <- trans_k.iore

   }

 

   # Do not transform exponents in IORE models

diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd
index c40dff83..a16ed177 100644
--- a/man/mkinfit.Rd
+++ b/man/mkinfit.Rd
@@ -216,6 +216,12 @@ mkinfit(mkinmod, observed,
   Gao). A similar implemention can also be found in CAKE 2.0, which is the
   other GUI derivative of mkin, sponsored by Syngenta.
 }
+\note{
+  When using the "IORE" submodel for metabolites, fitting with 
+  "transform_rates = TRUE" (the default) often leads to failures of the
+  numerical ODE solver. In this situation it may help to switch off the
+  internal rate transformation.
+}
 \author{
   Johannes Ranke
 }
diff --git a/man/mkinsub.Rd b/man/mkinsub.Rd
new file mode 100644
index 00000000..637a671c
--- /dev/null
+++ b/man/mkinsub.Rd
@@ -0,0 +1,44 @@
+\name{mkinsub}
+\alias{mkinsub}
+\title{
+  Function to set up a kinetic submodel for one state variable
+}
+\description{
+  This is a convenience function to set up the lists used as arguments for 
+  \code{\link{mkinmod}}.
+}
+\usage{
+mkinsub(type, to = NULL, sink = TRUE)
+}
+\arguments{
+  \item{type}{
+    Character vector of length one to specify the submodel type. See 
+    \code{\link{mkinmod}} for the list of allowed submodel names.
+  }
+  \item{to}{
+    Vector of the names of the state variable to which a transformation 
+    shall be included in the model.
+  }
+  \item{sink}{
+    Should a pathway to sink be included in the model in addition to the 
+    pathways to other state variables?
+  }
+}
+\value{
+  A list for use with \code{\link{mkinmod}}.
+}
+\author{
+  Johannes Ranke
+}
+\examples{
+# One parent compound, one metabolite, both single first order.
+SFO_SFO <- mkinmod(
+  parent = list(type = "SFO", to = "m1"),
+  m1 = list(type = "SFO"))
+
+# The same model using mkinsub
+SFO_SFO.2 <- mkinmod(
+  parent = mkinsub("SFO", "m1"),
+  m1 = mkinsub("SFO"))
+}
+