From 316f1360d1e12eefe491f86b0bbcd6dcf091c736 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Sat, 12 Jul 2014 08:32:08 +0200
Subject: First working fits with IORE model

---
 R/mkinmod.R | 28 ++++++++++++++++++++++------
 1 file changed, 22 insertions(+), 6 deletions(-)

(limited to 'R/mkinmod.R')

diff --git a/R/mkinmod.R b/R/mkinmod.R
index eb290719..321887fc 100644
--- a/R/mkinmod.R
+++ b/R/mkinmod.R
@@ -41,9 +41,8 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL)
   map <- list()
   # }}}
 
-  # Do not return a coefficient matrix mat when FOMC, DFOP or HS are used for
-  # the parent compound {{{
-  if(spec[[1]]$type %in% c("FOMC", "DFOP", "HS")) {
+  # Do not return a coefficient matrix mat when FOMC, IORE, DFOP or HS is used for the parent {{{
+  if(spec[[1]]$type %in% c("FOMC", "IORE", "DFOP", "HS")) {
     mat = FALSE 
   } else mat = TRUE
   #}}}
@@ -55,8 +54,8 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL)
     # Check the type component of the compartment specification {{{
     if(is.null(spec[[varname]]$type)) stop(
       "Every part of the model specification must be a list containing a type component")
-    if(!spec[[varname]]$type %in% c("SFO", "FOMC", "DFOP", "HS", "SFORB")) stop(
-      "Available types are SFO, FOMC, DFOP, HS and SFORB only")
+    if(!spec[[varname]]$type %in% c("SFO", "FOMC", "IORE", "DFOP", "HS", "SFORB")) stop(
+      "Available types are SFO, FOMC, IORE, DFOP, HS and SFORB only")
     if(spec[[varname]]$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"))
@@ -65,6 +64,7 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL)
     new_boxes <- switch(spec[[varname]]$type,
       SFO = varname,
       FOMC = varname,
+      IORE = varname,
       DFOP = varname,
       HS = varname,
       SFORB = paste(varname, c("free", "bound"), sep = "_")
@@ -85,20 +85,36 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL)
     # Turn on sink if this is not explicitly excluded by the user by
     # specifying sink=FALSE
     if(is.null(spec[[varname]]$sink)) spec[[varname]]$sink <- TRUE
-    if(spec[[varname]]$type %in% c("SFO", "SFORB")) { # {{{ Add SFO or SFORB decline term
+    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
           k_compound_sink <- paste("k", box_1, "sink", sep = "_")
+          if(spec[[varname]]$type == "IORE") {
+            k_compound_sink <- paste("k.iore", box_1, "sink", sep = "_")
+          }
           parms <- c(parms, k_compound_sink)
           decline_term <- paste(k_compound_sink, "*", box_1)
+          if(spec[[varname]]$type == "IORE") {
+            N <- paste("N", box_1, sep = "_")
+            parms <- c(parms, N)
+            decline_term <- paste0(decline_term, "^", N)
+          }
         } else { # otherwise no decline term needed here
           decline_term = "0" 
         }
       } else {
         k_compound <- paste("k", box_1, sep = "_")
+        if(spec[[varname]]$type == "IORE") {
+          k_compound <- paste("k.iore", box_1, sep = "_")
+        }
         parms <- c(parms, k_compound)
         decline_term <- paste(k_compound, "*", box_1)
+        if(spec[[varname]]$type == "IORE") {
+          N <- paste("N", box_1, sep = "_")
+          parms <- c(parms, N)
+          decline_term <- paste0(decline_term, "^", N)
+        }
       }
     } #}}}
     if(spec[[varname]]$type == "FOMC") { # {{{ Add FOMC decline term
-- 
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