From a69bf39427ff4f93eebdc8bceacb8174ff13c085 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Mon, 14 Jul 2014 19:07:54 +0200
Subject: Nearly complete support for IORE, pending mkinerrmin

---
 R/mkinmod.R | 26 ++++++++++++++++----------
 1 file changed, 16 insertions(+), 10 deletions(-)

(limited to 'R/mkinmod.R')

diff --git a/R/mkinmod.R b/R/mkinmod.R
index 321887fc..8b86303f 100644
--- a/R/mkinmod.R
+++ b/R/mkinmod.R
@@ -1,4 +1,4 @@
-# Copyright (C) 2010-2013 Johannes Ranke {{{
+# Copyright (C) 2010-2014 Johannes Ranke {{{
 # Contact: jranke@uni-bremen.de
 
 # This file is part of the R package mkin
@@ -33,12 +33,10 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL)
     stop("The use of formation fractions 'use_of_ff' can only be 'min' or 'max'")
 
   # The returned model will be a list of character vectors, containing {{{
-  # differential equations, parameter names and a mapping from model variables
-  # to observed variables. If possible, a matrix representation of the 
-  # differential equations is included
+  # differential equations (if supported), parameter names and a mapping from
+  # model variables to observed variables. If possible, a matrix representation
+  # of the differential equations is included
   parms <- vector()
-  diffs <- vector()
-  map <- list()
   # }}}
 
   # Do not return a coefficient matrix mat when FOMC, IORE, DFOP or HS is used for the parent {{{
@@ -49,6 +47,8 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL)
 
   # Establish a list of differential equations as well as a map from observed {{{
   # compartments to differential equations
+  diffs <- vector()
+  map <- list()
   for (varname in obs_vars)
   {
     # Check the type component of the compartment specification {{{
@@ -59,7 +59,8 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL)
     if(spec[[varname]]$type %in% c("FOMC", "DFOP", "HS") & match(varname, obs_vars) != 1) {
         stop(paste("Types FOMC, DFOP and HS are only implemented for the first compartment,", 
                    "which is assumed to be the source compartment"))
-    } #}}}
+    }
+    #}}}
     # New (sub)compartments (boxes) needed for the model type {{{
     new_boxes <- switch(spec[[varname]]$type,
       SFO = varname,
@@ -88,7 +89,11 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL)
     if(spec[[varname]]$type %in% c("SFO", "IORE", "SFORB")) { # {{{ Add decline term
       if (use_of_ff == "min") { # Minimum use of formation fractions
         if(spec[[varname]]$sink) {
-          # If sink is required, add first-order sink term
+          if(spec[[varname]]$type == "IORE" && length(spec[[varname]]$to) > 0) {
+             stop("Transformation reactions from compounds modelled with IORE\n",
+                  "are only supported with formation fractions (use_of_ff = 'max')")
+          }
+          # If sink is required, add first-order/IORE sink term
           k_compound_sink <- paste("k", box_1, "sink", sep = "_")
           if(spec[[varname]]$type == "IORE") {
             k_compound_sink <- paste("k.iore", box_1, "sink", sep = "_")
@@ -173,9 +178,10 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL)
       for (target in to) {
         target_box <- switch(spec[[target]]$type,
           SFO = target,
+          IORE = target,
           SFORB = paste(target, "free", sep = "_"))
-        if (use_of_ff == "min" && spec[[varname]]$type %in% c("SFO",
-          "SFORB")) {
+        if (use_of_ff == "min" && spec[[varname]]$type %in% c("SFO", "SFORB"))
+        {
           k_from_to <- paste("k", origin_box, target_box, sep = "_")
           parms <- c(parms, k_from_to)
           diffs[[origin_box]] <- paste(diffs[[origin_box]], "-", 
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