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
|
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>mkinmod. mkin 0.9.42</title>
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="author" content="
Johannes Ranke
">
<link href="css/bootstrap.css" rel="stylesheet">
<link href="css/bootstrap-responsive.css" rel="stylesheet">
<link href="css/highlight.css" rel="stylesheet">
<link href="css/staticdocs.css" rel="stylesheet">
<!--[if lt IE 9]>
<script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
<![endif]-->
<script type="text/x-mathjax-config">
MathJax.Hub.Config({
tex2jax: {
inlineMath: [ ['$','$'], ["\\(","\\)"] ],
processEscapes: true
}
});
</script>
<script type="text/javascript"
src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
</script>
</head>
<body>
<div class="navbar">
<div class="navbar-inner">
<div class="container">
<a class="brand" href="#">mkin 0.9.42</a>
<div class="nav">
<ul class="nav">
<li><a href="index.html"><i class="icon-home icon-white"></i> Index</a></li>
</ul>
</div>
</div>
</div>
</div>
<div class="container">
<header>
</header>
<h1>
Function to set up a kinetic model with one or more state variables
</h1>
<div class="row">
<div class="span8">
<h2>Usage</h2>
<pre><div>mkinmod(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verbose = FALSE)</div></pre>
<h2>Arguments</h2>
<dl>
<dt>...</dt>
<dd>
For each observed variable, a list has to be specified as an argument, containing
at least a component <code>type</code>, specifying the type of kinetics to use
for the variable. Currently, single first order kinetics "SFO",
indeterminate order rate equation kinetics "IORE", or
single first order with reversible binding "SFORB" are implemented for all
variables, while
"FOMC", "DFOP" and "HS" can additionally be chosen for the first
variable which is assumed to be the source compartment.
Additionally, each component of the list can include a character vector <code>to</code>,
specifying names of variables to which a transfer is to be assumed in the
model.
If the argument <code>use_of_ff</code> is set to "min" (default) and the model for
the compartment is "SFO" or "SFORB", an additional component of the list
can be "sink=FALSE" effectively fixing the flux to sink to zero.
</dd>
<dt>use_of_ff</dt>
<dd>
Specification of the use of formation fractions in the model equations and, if
applicable, the coefficient matrix. If "min", a minimum use of formation
fractions is made in order to avoid fitting the product of formation fractions
and rate constants. If "max", formation fractions are always used.
</dd>
<dt>speclist</dt>
<dd>
The specification of the observed variables and their submodel types and
pathways can be given as a single list using this argument. Default is NULL.
</dd>
<dt>quiet</dt>
<dd>
Should messages be suppressed?
</dd>
<dt>verbose</dt>
<dd>
If <code>TRUE</code>, passed to <code><a href='http://www.inside-r.org/packages/cran/inline/docs/cfunction'>cfunction</a></code> if applicable to give
detailed information about the C function being built.
</dd>
</dl>
<div class="Description">
<h2>Description</h2>
<p>The function usually takes several expressions, each assigning a compound name to
a list, specifying the kinetic model type and reaction or transfer to other
observed compartments. Instead of specifying several expressions, a list
of lists can be given in the speclist argument.</p>
<p>For the definition of model types and their parameters, the equations given
in the FOCUS and NAFTA guidance documents are used.</p>
</div>
<div class="Value">
<h2>Value</h2>
<p><dl>
A list of class <code>mkinmod</code> for use with <code><a href='mkinfit.html'>mkinfit</a></code>, containing
<dt>diffs</dt><dd> A vector of string representations of differential equations,
one for each modelling variable. </dd></p>
<p><dt>parms</dt><dd> A vector of parameter names occurring in the differential equations. </dd></p>
<p><dt>map</dt><dd> A list containing named character vectors for each observed variable, specifying
the modelling variables by which it is represented. </dd></p>
<p><dt>use_of_ff</dt><dd> The content of <code>use_of_ff</code> is passed on in this list component. </dd></p>
<p><dt>coefmat</dt><dd> The coefficient matrix, if the system of differential equations can be
represented by one. </dd></p>
<p></dl></p>
</div>
<div class="Note">
<h2>Note</h2>
<p>The IORE submodel is not well tested (yet). When using this model for metabolites,
you may want to read the second note in the help page to
<code><a href='mkinfit.html'>mkinfit</a></code>.</p>
</div>
<div class="References">
<h2>References</h2>
<p>FOCUS (2006) “Guidance Document on Estimating Persistence and
Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
Registration” Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
<a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p>
<p>NAFTA Technical Working Group on Pesticides (not dated) Guidance for
Evaluating and Calculating Degradation Kinetics in Environmental
Media</p>
</div>
<h2 id="examples">Examples</h2>
<pre class="examples"><div class='input'># Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)
SFO <- mkinmod(parent = list(type = "SFO"))
# One parent compound, one metabolite, both single first order
SFO_SFO <- mkinmod(
parent = mkinsub("SFO", "m1"),
m1 = mkinsub("SFO"))
</div>
<strong class='message'>Successfully compiled differential equation model from auto-generated C code.</strong>
<div class='input'>
## Not run:
# # The above model used to be specified like this, before the advent of mkinsub()
# SFO_SFO <- mkinmod(
# parent = list(type = "SFO", to = "m1"),
# m1 = list(type = "SFO"))
#
# # Show details of creating the C function
# SFO_SFO <- mkinmod(
# parent = mkinsub("SFO", "m1"),
# m1 = mkinsub("SFO"), verbose = TRUE)
#
# # If we have several parallel metabolites
# # (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)
# m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
# M1 = mkinsub("SFO"),
# M2 = mkinsub("SFO"),
# use_of_ff = "max", quiet = TRUE)
#
# fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par,
# synthetic_data_for_UBA_2014[[12]]$data,
# quiet = TRUE)
# ## End(Not run)
</div></pre>
</div>
<div class="span4">
<!-- <ul>
<li>mkinmod</li>
</ul>
<ul>
<li> models </li>
</ul> -->
<h2>Author</h2>
Johannes Ranke
</div>
</div>
<footer>
<p class="pull-right"><a href="#">Back to top</a></p>
<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="http://twitter.github.com/bootstrap">bootstrap</a>.</p>
</footer>
</div>
</body>
</html>
|
