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# Copyright (C) 2010-2015 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 = c("deSolve", "analytical", "eigen", "odeintr"),
method.ode = "lsoda", atol.deSolve = 1e-8, rtol.deSolve = 1e-10,
map_output = TRUE, ...) {
solution_type = match.arg(solution_type)
# 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")),
IORE = IORE.solution(outtimes,
evalparse(parent.name),
ifelse(mkinmod$use_of_ff == "min",
evalparse(paste("k__iore", parent.name, "sink", sep="_")),
evalparse(paste("k__iore", parent.name, sep="_"))),
evalparse("N_parent")),
DFOP = DFOP.solution(outtimes,
evalparse(parent.name),
evalparse("k1"), evalparse("k2"),
evalparse("g")),
HS = HS.solution(outtimes,
evalparse(parent.name),
evalparse("k1"), evalparse("k2"),
evalparse("tb")),
SFORB = SFORB.solution(outtimes,
evalparse(parent.name),
evalparse(paste("k", parent.name, "bound", sep="_")),
evalparse(paste("k", sub("free", "bound", parent.name), "free", sep="_")),
evalparse(paste("k", parent.name, "sink", sep="_")))
)
out <- data.frame(outtimes, o)
names(out) <- c("time", sub("_free", "", parent.name))
}
if (solution_type == "eigen") {
coefmat.num <- matrix(sapply(as.vector(mkinmod$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$diffs[[box]])))
}
return(list(c(diffs)))
}
out <- ode(
y = odeini,
times = outtimes,
func = mkindiff,
parms = odeparms[mkinmod$parms], # Order matters when using compiled models
method = method.ode,
atol = atol.deSolve,
rtol = rtol.deSolve,
...
)
if (sum(is.na(out)) > 0) {
stop("Differential equations were not integrated for all output times because\n",
"NaN values occurred in output from ode()")
}
}
if (solution_type == "odeintr") {
if (is.null(mkinmod$e$m)) stop("Method odeintr can not be used as no compiled version of the model is available")
odeparms_argstring = ""
for (parname in names(odeparms)) {
odeparms_argstring = paste0(odeparms_argstring, parname, " = ", odeparms[parname], ", ")
}
odeparms_argstring = gsub(", $", "", odeparms_argstring)
with(as.list(odeparms_argstring), eval(parse(text=paste0("mkinmod$e$m_set_params(", odeparms_argstring, ")"))))
out <- mkinmod$e$m_at(init = odeini, times = outtimes)
names(out) <- c("time", names(mkinmod$diffs))
}
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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