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-rw-r--r--R/mkinmod.R76
1 files changed, 76 insertions, 0 deletions
diff --git a/R/mkinmod.R b/R/mkinmod.R
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+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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