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-# Copyright (C) 2010-2014 Johannes Ranke
-# Some lines in this code are copyright (C) 2013 Eurofins Regulatory AG
-# Contact: jranke@uni-bremen.de
-
-# This file is part of the R package mkin
-
-# mkin is free software: you can redistribute it and/or modify it under the
-# terms of the GNU General Public License as published by the Free Software
-# Foundation, either version 3 of the License, or (at your option) any later
-# version.
-
-# This program is distributed in the hope that it will be useful, but WITHOUT
-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
-# details.
-
-# You should have received a copy of the GNU General Public License along with
-# this program. If not, see <http://www.gnu.org/licenses/>
-
-mkinpredict <- function(mkinmod, odeparms, odeini,
- outtimes, solution_type = "deSolve",
- method.ode = "lsoda", atol = 1e-8, rtol = 1e-10,
- map_output = TRUE, ...) {
-
- # Get the names of the state variables in the model
- mod_vars <- names(mkinmod$diffs)
-
- # Order the inital values for state variables if they are named
- if (!is.null(names(odeini))) {
- odeini <- odeini[mod_vars]
- }
-
- # Create function for evaluation of expressions with ode parameters and initial values
- evalparse <- function(string)
- {
- eval(parse(text=string), as.list(c(odeparms, odeini)))
- }
-
- # Create a function calculating the differentials specified by the model
- # if necessary
- if (solution_type == "analytical") {
- parent.type = names(mkinmod$map[[1]])[1]
- parent.name = names(mkinmod$diffs)[[1]]
- o <- switch(parent.type,
- SFO = SFO.solution(outtimes,
- evalparse(parent.name),
- ifelse(mkinmod$use_of_ff == "min",
- evalparse(paste("k", parent.name, "sink", sep="_")),
- evalparse(paste("k", parent.name, sep="_")))),
- FOMC = FOMC.solution(outtimes,
- evalparse(parent.name),
- evalparse("alpha"), evalparse("beta")),
- DFOP = DFOP.solution(outtimes,
- evalparse(parent.name),
- evalparse("k1"), evalparse("k2"),
- evalparse("g")),
- HS = HS.solution(outtimes,
- evalparse(parent.name),
- evalparse("k1"), evalparse("k2"),
- evalparse("tb")),
- SFORB = SFORB.solution(outtimes,
- evalparse(parent.name),
- evalparse(paste("k", parent.name, "bound", sep="_")),
- evalparse(paste("k", sub("free", "bound", parent.name), "free", sep="_")),
- evalparse(paste("k", parent.name, "sink", sep="_")))
- )
- out <- data.frame(outtimes, o)
- names(out) <- c("time", sub("_free", "", parent.name))
- }
- if (solution_type == "eigen") {
- coefmat.num <- matrix(sapply(as.vector(mkinmod$coefmat), evalparse),
- nrow = length(mod_vars))
- e <- eigen(coefmat.num)
- c <- solve(e$vectors, odeini)
- f.out <- function(t) {
- e$vectors %*% diag(exp(e$values * t), nrow=length(mod_vars)) %*% c
- }
- o <- matrix(mapply(f.out, outtimes),
- nrow = length(mod_vars), ncol = length(outtimes))
- out <- data.frame(outtimes, t(o))
- names(out) <- c("time", mod_vars)
- }
- if (solution_type == "deSolve") {
- mkindiff <- function(t, state, parms) {
-
- time <- t
- diffs <- vector()
- for (box in names(mkinmod$diffs))
- {
- diffname <- paste("d", box, sep="_")
- diffs[diffname] <- with(as.list(c(time, state, parms)),
- eval(parse(text=mkinmod$diffs[[box]])))
- }
- return(list(c(diffs)))
- }
- out <- ode(
- y = odeini,
- times = outtimes,
- func = mkindiff,
- parms = odeparms,
- method = method.ode,
- atol = atol,
- rtol = rtol,
- ...
- )
- }
- if (map_output) {
- # Output transformation for models with unobserved compartments like SFORB
- out_mapped <- data.frame(time = out[,"time"])
- for (var in names(mkinmod$map)) {
- if((length(mkinmod$map[[var]]) == 1) || solution_type == "analytical") {
- out_mapped[var] <- out[, var]
- } else {
- out_mapped[var] <- rowSums(out[, mkinmod$map[[var]]])
- }
- }
- return(out_mapped)
- } else {
- return(out)
- }
-}

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