Nearly complete support for IORE, pending mkinerrmin

1 files changed, 16 insertions, 10 deletions

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]], "-",