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
|
\name{synthetic_data_for_UBA_2014}
\alias{synthetic_data_for_UBA_2014}
\docType{data}
\title{
Synthetic datasets for one parent compound with two metabolites
}
\description{
The 12 datasets were generated using four different models and three different
variance components. The four models are either the SFO or the DFOP model with either
two sequential or two parallel metabolites.
Variance component 'a' is based on a normal distribution with standard deviation of 3,
Variance component 'b' is also based on a normal distribution, but with a standard deviation of 7.
Variance component 'c' is based on the error model from Rocke and Lorenzato (1995), with the
minimum standard deviation (for small y values) of 0.5, and a proportionality constant of 0.07
for the increase of the standard deviation with y.
Initial concentrations for metabolites and all values where adding the variance component resulted
in a value below the assumed limit of detection of 0.1 were set to \code{NA}.
As an example, the first dataset has the title \code{SFO_lin_a} and is based on the SFO model
with two sequential metabolites (linear pathway), with added variance component 'a'.
Compare also the code in the example section to see the degradation models.
}
\usage{synthetic_data_for_UBA_2014}
\format{
A list containing datasets in the form internally used by the 'gmkin' package.
The list has twelfe components. Each of the components is one dataset that has,
among others, the following components
\describe{
\item{\code{title}}{The name of the dataset, e.g. \code{SFO_lin_a}}
\item{\code{data}}{A data frame with the data in the form expected by \code{\link{mkinfit}}}
}
}
\source{
Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative
zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452
Rocke, David M. und Lorenzato, Stefan (1995) A two-component model for
measurement error in analytical chemistry. Technometrics 37(2), 176-184.
}
\examples{
\dontrun{
# The data have been generated using the following kinetic models
m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"),
M1 = list(type = "SFO", to = "M2"),
M2 = list(type = "SFO"), use_of_ff = "max")
m_synth_SFO_par <- mkinmod(parent = list(type = "SFO", to = c("M1", "M2"),
sink = FALSE),
M1 = list(type = "SFO"),
M2 = list(type = "SFO"), use_of_ff = "max")
m_synth_DFOP_lin <- mkinmod(parent = list(type = "DFOP", to = "M1"),
M1 = list(type = "SFO", to = "M2"),
M2 = list(type = "SFO"), use_of_ff = "max")
m_synth_DFOP_par <- mkinmod(parent = list(type = "DFOP", to = c("M1", "M2"),
sink = FALSE),
M1 = list(type = "SFO"),
M2 = list(type = "SFO"), use_of_ff = "max")
# The model predictions without intentional error were generated as follows
sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
d_synth_SFO_lin <- mkinpredict(m_synth_SFO_lin,
c(k_parent = 0.7, f_parent_to_M1 = 0.8,
k_M1 = 0.3, f_M1_to_M2 = 0.7,
k_M2 = 0.02),
c(parent = 100, M1 = 0, M2 = 0),
sampling_times)
d_synth_DFOP_lin <- mkinpredict(m_synth_DFOP_lin,
c(k1 = 0.2, k2 = 0.02, g = 0.5,
f_parent_to_M1 = 0.5, k_M1 = 0.3,
f_M1_to_M2 = 0.7, k_M2 = 0.02),
c(parent = 100, M1 = 0, M2 = 0),
sampling_times)
d_synth_SFO_par <- mkinpredict(m_synth_SFO_par,
c(k_parent = 0.2,
f_parent_to_M1 = 0.8, k_M1 = 0.01,
f_parent_to_M2 = 0.2, k_M2 = 0.02),
c(parent = 100, M1 = 0, M2 = 0),
sampling_times)
d_synth_DFOP_par <- mkinpredict(m_synth_DFOP_par,
c(k1 = 0.3, k2 = 0.02, g = 0.7,
f_parent_to_M1 = 0.6, k_M1 = 0.04,
f_parent_to_M2 = 0.4, k_M2 = 0.01),
c(parent = 100, M1 = 0, M2 = 0),
sampling_times)
# Construct names for datasets with errors
d_synth_names = paste0("d_synth_", c("SFO_lin", "SFO_par",
"DFOP_lin", "DFOP_par"))
# Function for adding errors. The add_err function now published with this
# package is a slightly generalised version where the names of secondary
# compartments that should have an initial value of zero (M1 and M2 in this
# case) are not hardcoded any more.
add_err = function(d, sdfunc, LOD = 0.1, reps = 2, seed = 123456789)
{
set.seed(seed)
d_long = mkin_wide_to_long(d, time = "time")
d_rep = data.frame(lapply(d_long, rep, each = 2))
d_rep$value = rnorm(length(d_rep$value), d_rep$value, sdfunc(d_rep$value))
d_rep[d_rep$time == 0 & d_rep$name %in% c("M1", "M2"), "value"] <- 0
d_NA <- transform(d_rep, value = ifelse(value < LOD, NA, value))
d_NA$value <- round(d_NA$value, 1)
return(d_NA)
}
# The following is the two-component model of Rocke and Lorenzato (1995)
sdfunc_twocomp = function(value, sd_low, rsd_high) {
sqrt(sd_low^2 + value^2 * rsd_high^2)
}
# Add the errors.
for (d_synth_name in d_synth_names)
{
d_synth = get(d_synth_name)
assign(paste0(d_synth_name, "_a"), add_err(d_synth, function(value) 3))
assign(paste0(d_synth_name, "_b"), add_err(d_synth, function(value) 7))
assign(paste0(d_synth_name, "_c"), add_err(d_synth,
function(value) sdfunc_twocomp(value, 0.5, 0.07)))
}
d_synth_err_names = c(
paste(rep(d_synth_names, each = 3), letters[1:3], sep = "_")
)
# This is just one example of an evaluation using the kinetic model used for
# the generation of the data
fit <- mkinfit(m_synth_SFO_lin, synthetic_data_for_UBA_2014[[1]]$data,
quiet = TRUE)
plot_sep(fit)
summary(fit)
}
}
\keyword{datasets}
|
