diff options
| author | jranke <jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb> | 2010-05-11 23:03:37 +0000 |
|---|---|---|
| committer | jranke <jranke@edb9625f-4e0d-4859-8d74-9fd3b1da38cb> | 2010-05-11 23:03:37 +0000 |
| commit | 30cbb4092f6d2d3beff5800603374a0d009ad770 (patch) | |
| tree | ef75421d92823b5b7add1b2d5da9c7499dfd59e5 /R/mkinmod.R | |
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
Diffstat (limited to 'R/mkinmod.R')
| -rw-r--r-- | R/mkinmod.R | 76 |
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)
+}
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