IORE working for parent and metabolites, introduce mkinsub

3 files changed, 33 insertions, 4 deletions

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