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
|
# Copyright (C) 2019 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/>
CAKE_export <- function(ds, map = c(parent = "Parent"),
links = NA,
filename = "CAKE_export.csf", path = ".", overwrite = FALSE,
study = "Codlemone aerobic soil degradation",
description = "",
time_unit = "days",
res_unit = "% AR",
comment = "Created using mkin::CAKE_export",
date = Sys.Date(),
optimiser = "IRLS")
{
file <- file.path(path, filename)
if (file.exists(file) & !overwrite) stop(file, " already exists, stopping")
csf <- file(file, encoding = "latin1", open = "w+")
on.exit(close(csf))
add <- function(x) cat(paste0(x, "\r\n"), file = csf, append = TRUE)
add0 <- function(x) cat(x, file = csf, append = TRUE)
add("[FileInfo]")
add("CAKE-Version: 3.3 (Release)")
add(paste("Name:", study))
add(paste("Description:", description))
add(paste("MeasurementUnits:", res_unit))
add(paste("TimeUnits:", time_unit))
add(paste("Comments:", comment))
add(paste("Date:", date))
add(paste("Optimiser:", optimiser))
add("")
add("[Data]")
for (i in seq_along(ds)) {
add(paste("NewDataSet:", names(ds)[i]))
d <- mkin_long_to_wide(ds[[i]])
names(d) <- c("Time", map[names(d)[-1]])
write.table(d, csf,
sep = "\t", col.names = TRUE,
row.names = FALSE,
quote = FALSE, eol = "\r\n", na = "")
add("")
}
if (!is.na(links)) {
add("")
add("[Model]")
add(paste0("ParentCompartment: Parent\t", names(map)[1], "\t", names(map)[1]))
for (name in names(map)[-1]) {
add(paste0("Compartment: ", map[name], "\t", name, "\t", name))
}
for (li in names(links)) {
add(paste0("Link: ", map[li], "\t", map[links[li]], "\t0.5\t0\t1\tFree\tExplicit"))
}
}
add("")
add("[ComponentNames]")
for (name in names(map)) {
add(paste0(map[name], ":", name))
}
}
|
