diff options
| -rw-r--r-- | NEWS.md | 1 | ||||
| -rw-r--r-- | R/mkinfit.R | 9 | ||||
| -rw-r--r-- | R/mkinsub.R | 23 | ||||
| -rw-r--r-- | R/transform_odeparms.R | 5 | ||||
| -rw-r--r-- | man/mkinfit.Rd | 6 | ||||
| -rw-r--r-- | man/mkinsub.Rd | 44 |
6 files changed, 84 insertions, 4 deletions
@@ -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")) +} + |