1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
|
# $Id$
# 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 (grepl("_to_", obs_var)) stop("Sorry, names of observed variables can not contain _to_")
}
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:
|
