1 files changed, 76 insertions, 0 deletions
diff --git a/R/mkinmod.R b/R/mkinmod.R
new file mode 100644
index 0000000..7e64f87
--- /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)
+}