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# $Id$
# Copyright (C) 2010-2012 Johannes Ranke
# 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/>
mkinmod <- function(...)
{
spec <- list(...)
obs_vars <- names(spec)
# The returned model will be a list of character vectors, containing
# differential equations, parameter names and a mapping from model variables
# to observed variables. If possible, a matrix representation of the
# differential equations is included
parms <- vector()
diffs <- vector()
map <- list()
if(spec[[1]]$type %in% c("FOMC", "DFOP", "HS")) {
mat = FALSE
if(!is.null(spec[[1]]$to)) {
message <- paste(
"Only constant formation fractions over time are implemented.",
"Depending on the reason for the time dependence of degradation",
"this may be unrealistic",
sep="\n")
warning(message)
} else message <- "ok"
} else mat = TRUE
# Establish list of differential equations
# as well as map from observed compartments to differential equations
for (varname in obs_vars)
{
if(is.null(spec[[varname]]$type)) stop(
"Every argument to mkinmod must be a list containing a type component")
if(!spec[[varname]]$type %in% c("SFO", "FOMC", "DFOP", "HS", "SFORB")) stop(
"Available types are SFO, FOMC, DFOP, HS and SFORB only")
if(spec[[varname]]$type %in% c("FOMC", "DFOP", "HS") & match(varname, obs_vars) != 1) {
stop(paste("Types FOMC, DFOP and HS are only implemented for the first compartment,",
"which is assumed to be the source compartment"))
}
# New (sub)compartments (boxes) needed for the model type
new_boxes <- switch(spec[[varname]]$type,
SFO = varname,
FOMC = varname,
DFOP = varname,
HS = varname,
SFORB = paste(varname, c("free", "bound"), sep="_")
)
map[[varname]] <- new_boxes
names(map[[varname]]) <- rep(spec[[varname]]$type, length(new_boxes))
# Start a new differential equation for each new box
new_diffs <- paste("d_", new_boxes, " =", sep="")
names(new_diffs) <- new_boxes
diffs <- c(diffs, new_diffs)
}
# Create content of differential equations and build parameter list
for (varname in obs_vars)
{
# Add first-order term to first (or only) box for SFO and SFORB
box_1 = map[[varname]][[1]] # This is the only box unless type is SFORB
if(spec[[varname]]$type %in% c("SFO", "SFORB")) {
k_compound <- paste("k", box_1, sep="_")
origin_term <- paste(k_compound, "*", box_1)
parms <- c(parms, k_compound)
}
# Construct and add FOMC term and add FOMC parameters if needed
if(spec[[varname]]$type == "FOMC") {
# From p. 53 of the FOCUS kinetics report
origin_term <- paste("(alpha/beta) * ((time/beta) + 1)^-1 *", box_1)
parms <- c(parms, "alpha", "beta")
}
# Construct and add DFOP term and add DFOP parameters if needed
if(spec[[varname]]$type == "DFOP") {
# From p. 57 of the FOCUS kinetics report
origin_term <- paste("((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) *", box_1)
parms <- c(parms, "k1", "k2", "g")
}
# Construct and add HS term and add HS parameters if needed
if(spec[[varname]]$type == "HS") {
# From p. 55 of the FOCUS kinetics report
origin_term <- paste("ifelse(time <= tb, k1, k2)", "*", box_1)
parms <- c(parms, "k1", "k2", "tb")
}
# Add origin decline term to box 1 (usually the only box, unless type is SFORB)
diffs[[box_1]] <- paste(diffs[[box_1]], "-", origin_term)
# Add reversible binding for SFORB models
if(spec[[varname]]$type == "SFORB") {
box_2 = map[[varname]][[2]]
k_free_bound <- paste("k", varname, "free", "bound", sep="_")
k_bound_free <- paste("k", varname, "bound", "free", sep="_")
reversible_binding_term_1 <- paste("-", k_free_bound, "*", box_1, "+",
k_bound_free, "*", box_2)
diffs[[box_1]] <- paste(diffs[[box_1]], reversible_binding_term_1)
reversible_binding_term_2 <- paste("+", k_free_bound, "*", box_1, "-",
k_bound_free, "*", box_2)
diffs[[box_2]] <- paste(diffs[[box_2]], reversible_binding_term_2)
parms <- c(parms, k_free_bound, k_bound_free)
}
# Transfer between compartments
to <- spec[[varname]]$to
if(!is.null(to)) {
# Name of box from which transfer takes place
origin_box <- box_1
# Add transfer terms to listed compartments
for (target in to) {
target_box <- switch(spec[[target]]$type,
SFO = target,
SFORB = paste(target, "free", sep="_"))
fraction_to_target = paste("f", origin_box, "to", target, sep="_")
diffs[[target_box]] <- paste(diffs[[target_box]], "+",
fraction_to_target, "*", origin_term)
parms <- c(parms, fraction_to_target)
}
}
}
model <- list(diffs = diffs, parms = parms, map = map)
# Create coefficient matrix if appropriate
if (mat) {
boxes <- names(diffs)
n <- length(boxes)
m <- matrix(nrow=n, ncol=n, dimnames=list(boxes, boxes))
for (from in boxes) {
for (to in boxes) {
if (from == to) {
k.candidate = paste("k", from, sep="_")
m[from,to] = ifelse(k.candidate %in% model$parms,
paste("-", k.candidate), "0")
} else {
f.candidate = paste("f", from, "to", to, sep="_")
k.candidate = paste("k", from, to, sep="_")
k.candidate = sub("free.*bound", "free_bound", k.candidate)
k.candidate = sub("bound.*free", "bound_free", k.candidate)
m[to, from] = ifelse(f.candidate %in% model$parms,
paste(f.candidate, " * k_", from, sep=""),
ifelse(k.candidate %in% model$parms, k.candidate, "0"))
}
}
}
model$coefmat <- m
}
class(model) <- "mkinmod"
return(model)
}
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