From c04d0bb0e795b67b6958150e8524c5265587f618 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Wed, 12 Nov 2014 16:59:48 +0100
Subject: IORE working for parent and metabolites, introduce mkinsub

---
 R/mkinfit.R            |  9 +++++++--
 R/mkinsub.R            | 23 +++++++++++++++++++++++
 R/transform_odeparms.R |  5 +++--
 3 files changed, 33 insertions(+), 4 deletions(-)
 create mode 100644 R/mkinsub.R

(limited to 'R')

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
-- 
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