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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(..., use_of_ff = "min")
{
spec <- list(...)
obs_vars <- names(spec)
# Check if any of the names of the observed variables contains any other
for (obs_var in obs_vars) {
if (length(grep(obs_var, obs_vars)) > 1) stop("Sorry, variable names can not contain each other")
}
if (!use_of_ff %in% c("min", "max"))
stop("The use of formation fractions 'use_of_ff' can only be 'min' or 'max'")
# 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()
# }}}
# Give a warning when a model with time dependent degradation uses formation {{{
# fractions
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. You may want to consider using the",
"SFORB model",
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)
{
# Check the type component of the compartment specification {{{
if(is.null(spec[[varname]]$type)) stop(
"Every part of the model specification must be a list containing a type component")
if(!spec[[varname]]$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]]$type, length(new_boxes)) #}}}
# Start a new differential equation for each new box {{{
new_diffs <- paste("d_", new_boxes, " =", sep="")
names(new_diffs) <- new_boxes
diffs <- c(diffs, new_diffs) #}}}
} #}}}
# Create content of differential equations and build parameter list {{{
for (varname in obs_vars)
{
# Get the name of the box(es) we are working on for the decline term(s)
box_1 = map[[varname]][[1]] # This is the only box unless type is SFORB
# Turn on sink if this is not explicitly excluded by the user by
# specifying sink=FALSE
if(is.null(spec[[varname]]$sink)) spec[[varname]]$sink <- TRUE
if(spec[[varname]]$type %in% c("SFO", "SFORB")) { # {{{ Add SFO or SFORB decline term
if (use_of_ff == "min") { # Minimum use of formation fractions
if(spec[[varname]]$sink) {
# If sink is required, add first-order sink term
k_compound_sink <- paste("k", box_1, "sink", sep="_")
parms <- c(parms, k_compound_sink)
decline_term <- paste(k_compound_sink, "*", box_1)
} else { # otherwise no decline term needed here
decline_term = "0"
}
} else {
k_compound <- paste("k", box_1, sep="_")
parms <- c(parms, k_compound)
decline_term <- paste(k_compound, "*", box_1)
}
} #}}}
if(spec[[varname]]$type == "FOMC") { # {{{ Add FOMC decline term
# From p. 53 of the FOCUS kinetics report
decline_term <- paste("(alpha/beta) * ((time/beta) + 1)^-1 *", box_1)
parms <- c(parms, "alpha", "beta")
} #}}}
if(spec[[varname]]$type == "DFOP") { # {{{ Add DFOP decline term
# From p. 57 of the FOCUS kinetics report
decline_term <- paste("((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) *", box_1)
parms <- c(parms, "k1", "k2", "g")
} #}}}
if(spec[[varname]]$type == "HS") { # {{{ Add HS decline term
# From p. 55 of the FOCUS kinetics report
decline_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]], "-", decline_term)#}}}
if(spec[[varname]]$type == "SFORB") { # {{{ Add SFORB reversible binding terms
box_2 = map[[varname]][[2]]
if (use_of_ff == "min") { # Minimum use of formation fractions
k_free_bound <- paste("k", varname, "free", "bound", sep="_")
k_bound_free <- paste("k", varname, "bound", "free", sep="_")
parms <- c(parms, k_free_bound, k_bound_free)
reversible_binding_term_1 <- paste("-", k_free_bound, "*", box_1, "+",
k_bound_free, "*", box_2)
reversible_binding_term_2 <- paste("+", k_free_bound, "*", box_1, "-",
k_bound_free, "*", box_2)
} else { # Use formation fractions also for the free compartment
stop("The maximum use of formation fractions is not supported for SFORB models")
# The problems were: Calculation of dissipation times did not work in this case
# and the coefficient matrix is not generated correctly by the code present
# in this file in this case
f_free_bound <- paste("f", varname, "free", "bound", sep="_")
k_bound_free <- paste("k", varname, "bound", "free", sep="_")
parms <- c(parms, f_free_bound, k_bound_free)
reversible_binding_term_1 <- paste("+", k_bound_free, "*", box_2)
reversible_binding_term_2 <- paste("+", f_free_bound, "*", k_compound, "*", box_1, "-",
k_bound_free, "*", box_2)
}
diffs[[box_1]] <- paste(diffs[[box_1]], reversible_binding_term_1)
diffs[[box_2]] <- paste(diffs[[box_2]], reversible_binding_term_2)
} #}}}
# Transfer between compartments#{{{
to <- spec[[varname]]$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]]$type,
SFO = target,
SFORB = paste(target, "free", sep="_"))
if (use_of_ff == "min" && spec[[varname]]$type %in% c("SFO",
"SFORB")) {
k_from_to <- paste("k", origin_box, target_box, sep="_")
parms <- c(parms, k_from_to)
diffs[[origin_box]] <- paste(diffs[[origin_box]], "-",
k_from_to, "*", origin_box)
diffs[[target_box]] <- paste(diffs[[target_box]], "+",
k_from_to, "*", origin_box)
} else {
if (!spec[[varname]]$sink) {
stop("Turning off the sink when using formation fractions is not supported")
}
fraction_to_target = paste("f", origin_box, "to", target, sep="_")
parms <- c(parms, fraction_to_target)
diffs[[target_box]] <- paste(diffs[[target_box]], "+",
fraction_to_target, "*", decline_term)
}
}
} #}}}
} #}}}
model <- list(diffs = diffs, parms = parms, map = map, use_of_ff = use_of_ff)
# Create coefficient matrix if appropriate#{{{
if (mat) {
boxes <- names(diffs)
n <- length(boxes)
m <- matrix(nrow=n, ncol=n, dimnames=list(boxes, boxes))
if (use_of_ff == "min") { # {{{ Minimum use of formation fractions
for (from in boxes) {
for (to in boxes) {
if (from == to) { # diagonal elements
k.candidate = paste("k", from, c(boxes, "sink"), sep="_")
k.candidate = sub("free.*bound", "free_bound", k.candidate)
k.candidate = sub("bound.*free", "bound_free", k.candidate)
k.effective = intersect(model$parms, k.candidate)
m[from,to] = ifelse(length(k.effective) > 0,
paste("-", k.effective, collapse = " "), "0")
} else { # off-diagonal elements
k.candidate = paste("k", from, to, sep="_")
if (sub("_free$", "", from) == sub("_bound$", "", to)) {
k.candidate = paste("k", sub("_free$", "_free_bound", from), sep="_")
}
if (sub("_bound$", "", from) == sub("_free$", "", to)) {
k.candidate = paste("k", sub("_bound$", "_bound_free", from), sep="_")
}
k.effective = intersect(model$parms, k.candidate)
m[to, from] = ifelse(length(k.effective) > 0,
k.effective, "0")
}
}
} # }}}
} else { # {{{ Use formation fractions where possible
for (from in boxes) {
for (to in boxes) {
if (from == to) { # diagonal elements
k.candidate = paste("k", from, sep="_")
m[from,to] = ifelse(k.candidate %in% model$parms,
paste("-", k.candidate), "0")
if(grepl("_free", from)) { # add transfer to bound compartment for SFORB
m[from,to] = paste(m[from,to], "-", paste("k", from, "bound", sep="_"))
}
if(grepl("_bound", from)) { # add backtransfer to free compartment for SFORB
m[from,to] = paste("- k", from, "free", sep="_")
}
m[from,to] = m[from,to]
} else { # off-diagonal elements
f.candidate = paste("f", from, "to", to, sep="_")
k.candidate = paste("k", from, to, sep="_")
# SFORB with maximum use of formation fractions not implemented, see above
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)
}
# vim: set foldmethod=marker ts=2 sw=2 expandtab:
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