Automatic Model Generation

[discoleo]

[some initial ideas]

Example:

model = "S ~ Y + O; I ~ .; H ~ .; S %*% I -> I; S %*% H -> I;
   I -> H + R + D; H -> R + D; V ~ .; (time >= t0) & S^0 -> V;"
model = strsplit(model, ";")[[1]];

el = lapply(model, function(e) parse(text = e))
print(el)

# using classic loop:
for(sM in model) {
  eq = parse(text = sM);
}

1.) Stratification:

• stratified compartment: S ~ Y + O;
• stratified compartment inheriting strata from parent compartment: I ~ .;

2.) Evolution

• simple: H -> R + D;
• interaction: S %*% I -> H + R + D;

Note:

• R & D: are unstratified;
• C1 %*% C2: implies C1[compartments] * sum(C2);
• S^0 -> V: implies dS = - const["SV"]; dV = + const["SV"];
• TODO:
  time delay: e.g. (time >t0), how to specify "time" and "t0";
• alternative model specification: package dMod (but it is not practical);
  see https://cran.r-project.org/web/packages/dMod/vignettes/dMod.html

[discoleo]

strata = function(x) {
	len  = length(x);
	vars = list();
	isStratEq = rep(FALSE, len);
	extract.strata = function(e) {
		sStrata = unique(unlist(lapply(e, as.character)));
		sStrata = sStrata[ ! sStrata %in% c("+", "-")];
	}
	
	for(id in seq(len)) {
		e = x[[id]][[1]];
		# Strata:
		if(as.character(e[[1]]) == "~") {
			isStratEq[id] = TRUE;
			sVar = as.character(e[[2]]);
			v = vars[[sVar]];
			if(is.null(v)) {
				if(as.character(e[[3]] == ".")) {
					vars[[sVar]] = list(hasStrata = TRUE, Strata = character(0));
				} else {
					sStrata = extract.strata(e[[3]]);
					vars[[sVar]] = list(hasStrata = TRUE, Strata = sStrata);
				}
			} else if(v$hasStrata == FALSE) {
				stop(paste0("Variable ", sVar, ": inconsistency in strata!"));
			} else if(length(v$Strata) == 0) {
				if(as.character(e[[3]] == ".")) {
					# NOTHING
				} else {
					sStrata = extract.strata(e[[3]]);
					vars[[sVar]]$Strata = sStrata;
				}
			} else {
				# TODO
				warning(paste0("Variable ", sVar, ": strata already defined!"));
			}
		}
	}
	#
	isStratEq = which(isStratEq);
	attr(vars, "expressions") = isStratEq;
	return(vars)
}

TODO:

• extract parents;
• carry forward strata;