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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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