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
|
<!-- Generated by pkgdown: do not edit by hand -->
<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>mmkin. mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
<!-- Bootstrap -->
<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
<!-- Font Awesome icons -->
<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
<!-- pkgdown -->
<link href="../pkgdown.css" rel="stylesheet">
<script src="../pkgdown.js"></script>
<!-- mathjax -->
<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
</head>
<body>
<div class="container">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="../index.html">mkin</a>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="../index.html">Home</a>
</li>
<li>
<a href="../reference/index.html">Reference</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin">
<span class="fa fa-github fa-lg"></span>
</a>
</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
</header>
<div class="page-header">
<h1>
</h1>
</div>
<div class="row">
<div class="col-md-9">
<p>This function calls <code>mkinfit</code> on all combinations of models and datasets
specified in its first two arguments.</p>
<pre><span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>,
<span class='kw'>cores</span> <span class='kw'>=</span> <span class='fu'>round</span>(<span class='fu'>detectCores</span>()/<span class='fl'>2</span>), <span class='kw'>cluster</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
<h2>Arguments</h2>
<dl class="dl-horizontal">
<dt>models</dt>
<dd>
Either a character vector of shorthand names ("SFO", "FOMC", "DFOP",
"HS", "SFORB"), or an optionally named list of <code>mkinmod</code>
objects.
</dd>
<dt>datasets</dt>
<dd>
An optionally named list of datasets suitable as observed data for
<code>mkinfit</code>.
</dd>
<dt>cores</dt>
<dd>
The number of cores to be used for multicore processing. This is only
used when the <code>cluster</code> argument is <code>NULL</code>.
</dd>
<dt>cluster</dt>
<dd>
A cluster as returned by <code>makeCluster</code> to be used for parallel
execution.
</dd>
<dt>&#8230;</dt>
<dd>
Further arguments that will be passed to <code>mkinfit</code>.
</dd>
</dl>
<div class="Value">
<h2>Value</h2>
<p>A matrix of <code>mkinfit</code> objects that can be indexed using the model
and dataset names as row and column indices.</p>
</div>
<div class="See also">
<h2>See also</h2>
<p><code>[.mmkin</code> for subsetting, <code>plot.mmkin</code> for plotting.</p>
</div>
<h2 id="examples">Examples</h2>
<pre class="examples"><div class='input'><span class='co'>## Not run: ------------------------------------</span>
<span class='co'># m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),</span>
<span class='co'># M1 = mkinsub("SFO", "M2"),</span>
<span class='co'># M2 = mkinsub("SFO"), use_of_ff = "max")</span>
<span class='co'># </span>
<span class='co'># m_synth_FOMC_lin <- mkinmod(parent = mkinsub("FOMC", "M1"),</span>
<span class='co'># M1 = mkinsub("SFO", "M2"),</span>
<span class='co'># M2 = mkinsub("SFO"), use_of_ff = "max")</span>
<span class='co'># </span>
<span class='co'># models <- list(SFO_lin = m_synth_SFO_lin, FOMC_lin = m_synth_FOMC_lin)</span>
<span class='co'># datasets <- lapply(synthetic_data_for_UBA_2014[1:3], function(x) x$data)</span>
<span class='co'># names(datasets) <- paste("Dataset", 1:3)</span>
<span class='co'># </span>
<span class='co'># time_default <- system.time(fits.0 <- mmkin(models, datasets))</span>
<span class='co'># time_1 <- system.time(fits.1 <- mmkin(models, datasets, cores = 1))</span>
<span class='co'># </span>
<span class='co'># time_default</span>
<span class='co'># time_1</span>
<span class='co'># </span>
<span class='co'># endpoints(fits[["SFO_lin", 2]])</span>
<span class='co'># </span>
<span class='co'># # Plot.mkinfit handles rows or columns of mmkin result objects</span>
<span class='co'># plot(fits.0[1, ])</span>
<span class='co'># plot(fits.0[1, ], obs_var = c("M1", "M2"))</span>
<span class='co'># plot(fits.0[, 1])</span>
<span class='co'># # Use double brackets to extract a single mkinfit object, which will be plotted</span>
<span class='co'># # by plot.mkinfit</span>
<span class='co'># plot(fits.0[[1, 1]], sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE)</span>
<span class='co'># # Plotting with mmkin (single brackets, extracting an mmkin object) does not</span>
<span class='co'># # allow to plot the observed variables separately</span>
<span class='co'># plot(fits.0[1, 1])</span>
<span class='co'>## ---------------------------------------------</span></div></pre>
</div>
<div class="col-md-3">
<h2>Author</h2>
Johannes Ranke
</div>
</div>
<footer>
<p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p>
</footer>
</div>
</body>
</html>
|
