From 30cbb4092f6d2d3beff5800603374a0d009ad770 Mon Sep 17 00:00:00 2001
From: jranke <jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb>
Date: Tue, 11 May 2010 23:03:37 +0000
Subject: Initial upload of the upcoming multicompartment version of kinfit.
 Some functionality is still missing (chi2), some may never be implemented
 (FOMC model), but in general it is much more powerful than kinfit, owing to
 the powerful FME package.

git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@8 edb9625f-4e0d-4859-8d74-9fd3b1da38cb
---
 R/mkinmod.R | 76 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 76 insertions(+)
 create mode 100644 R/mkinmod.R

(limited to 'R/mkinmod.R')

diff --git a/R/mkinmod.R b/R/mkinmod.R
new file mode 100644
index 00000000..7e64f879
--- /dev/null
+++ b/R/mkinmod.R
@@ -0,0 +1,76 @@
+mkinmod <- function(spec = list(parent = list(type = "SFO", to = NA, sink = TRUE)))
+{
+  if(!is.list(spec)) stop("spec must be a list of model specifications for each observed variable")
+
+  # The returned model will be a list of two character vectors, containing
+  # differential equations and parameter names
+  parms <- vector()
+  diffs <- vector()
+  map <- list()
+
+  # Establish list of differential equations
+  for (varname in names(spec))
+  {
+    if(!spec[[varname]]$type %in% c("SFO", "SFORB")) stop("Available types are SFO and SFORB only")
+    new_parms <- vector()
+
+    # New (sub)compartments (boxes) needed for the model type
+    new_boxes <- switch(spec[[varname]]$type,
+      SFO = varname,
+      SFORB = paste(varname, c("free", "bound"), sep="_")
+    )
+    map[[varname]] <- new_boxes
+
+    # Start a new differential equation for each new box
+    new_diffs <- paste("d_", new_boxes, " =", sep="")
+
+    # Construct terms for transfer to sink and add if appropriate
+    if(spec[[varname]]$sink) {
+      k_compound_sink <- paste("k", new_boxes[[1]], "sink", sep="_")
+      sink_term <- paste("-", k_compound_sink, "*", new_boxes[[1]])
+      # Only add sink term to first (or only) box for SFO and SFORB models
+      if(spec[[varname]]$type %in% c("SFO", "SFORB")) {
+        new_diffs[[1]] <- paste(new_diffs[[1]], sink_term)
+      }
+      new_parms <- k_compound_sink
+    }
+   
+    # Add reversible binding if appropriate
+    if(spec[[varname]]$type == "SFORB") {
+      k_free_bound <- paste("k", varname, "free", "bound", sep="_")      
+      k_bound_free <- paste("k", varname, "bound", "free", sep="_")      
+      reversible_binding_terms <- c(
+        paste("-", k_free_bound, "*", new_boxes[[1]], "+", k_bound_free, "*", new_boxes[[2]]),
+        paste("+", k_free_bound, "*", new_boxes[[1]], "-", k_bound_free, "*", new_boxes[[2]]))
+      new_diffs <- paste(new_diffs, reversible_binding_terms)
+      new_parms <- c(new_parms, k_free_bound, k_bound_free)
+    } 
+
+    # Add observed variable to model
+    parms <- c(parms, new_parms)
+    names(new_diffs) <- new_boxes
+    diffs <- c(diffs, new_diffs)
+  }
+
+  # Transfer between compartments
+  for (varname in names(spec)) {
+    to <- spec[[varname]]$to
+    if(!is.na(to)) {
+      origin_box <- switch(spec[[varname]]$type,
+        SFO = varname,
+        SFORB = paste(varname, "free", sep="_"))
+      for (target in to) {
+        target_box <- switch(spec[[target]]$type,
+          SFO = target,
+          SFORB = paste(target, "free", sep="_"))
+      }
+      k_from_to <- paste("k", origin_box, target_box, sep="_")
+      diffs[[origin_box]] <- paste(diffs[[origin_box]], "-", k_from_to, "*", origin_box)
+      diffs[[target_box]] <- paste(diffs[[target_box]], "+", k_from_to, "*", origin_box)
+      parms <- c(parms, k_from_to)
+    }
+  }
+  model <- list(diffs = diffs, parms = parms, map = map)
+  class(model) <- "mkinmod"
+  return(model)
+}
-- 
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