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
|
<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><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>Hierarchical kinetics template — hierarchical_kinetics • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Hierarchical kinetics template — hierarchical_kinetics"><meta property="og:description" content='R markdown format for setting up hierarchical kinetics based on a template
provided with the mkin package. This format is based on rmarkdown::pdf_document.
Chunk options are adapted. Echoing R code from code chunks and caching are
turned on per default. character for prepending output from code chunks is
set to the empty string, code tidying is off, figure alignment defaults to
centering, and positioning of figures is set to "H", which means that
figures will not move around in the document, but stay where the user
includes them.'><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></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 data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<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" aria-expanded="false">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.4</span>
</span>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav"><li>
<a href="../reference/index.html">Reference</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
Articles
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu"><li>
<a href="../articles/mkin.html">Introduction to mkin</a>
</li>
<li class="divider">
<li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</li>
<li>
<a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
</li>
<li>
<a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
</li>
<li>
<a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
</li>
<li class="divider">
<li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li>
<li>
<a href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a>
</li>
<li>
<a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a>
</li>
<li>
<a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a>
</li>
<li>
<a href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a>
</li>
<li>
<a href="../articles/web_only/multistart.html">Short demo of the multistart method</a>
</li>
<li class="divider">
<li class="dropdown-header">Performance</li>
<li>
<a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
</li>
<li>
<a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a>
</li>
<li>
<a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
</li>
<li class="divider">
<li class="dropdown-header">Miscellaneous</li>
<li>
<a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
</li>
<li>
<a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
</li>
</ul></li>
<li>
<a href="../news/index.html">News</a>
</li>
</ul><ul class="nav navbar-nav navbar-right"><li>
<a href="https://github.com/jranke/mkin/" class="external-link">
<span class="fab fa-github fa-lg"></span>
</a>
</li>
</ul></div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
</header><div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Hierarchical kinetics template</h1>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/hierarchical_kinetics.R" class="external-link"><code>R/hierarchical_kinetics.R</code></a></small>
<div class="hidden name"><code>hierarchical_kinetics.Rd</code></div>
</div>
<div class="ref-description">
<p>R markdown format for setting up hierarchical kinetics based on a template
provided with the mkin package. This format is based on <a href="https://pkgs.rstudio.com/rmarkdown/reference/pdf_document.html" class="external-link">rmarkdown::pdf_document</a>.
Chunk options are adapted. Echoing R code from code chunks and caching are
turned on per default. character for prepending output from code chunks is
set to the empty string, code tidying is off, figure alignment defaults to
centering, and positioning of figures is set to "H", which means that
figures will not move around in the document, but stay where the user
includes them.</p>
</div>
<div id="ref-usage">
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">hierarchical_kinetics</span><span class="op">(</span><span class="va">...</span>, keep_tex <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
</div>
<div id="arguments">
<h2>Arguments</h2>
<dl><dt>...</dt>
<dd><p>Arguments to <code><a href="https://pkgs.rstudio.com/rmarkdown/reference/pdf_document.html" class="external-link">rmarkdown::pdf_document</a></code></p></dd>
<dt>keep_tex</dt>
<dd><p>Keep the intermediate tex file used in the conversion to PDF</p></dd>
</dl></div>
<div id="value">
<h2>Value</h2>
<p>R Markdown output format to pass to
<code><a href="https://pkgs.rstudio.com/rmarkdown/reference/render.html" class="external-link">render</a></code></p>
</div>
<div id="details">
<h2>Details</h2>
<p>The latter feature (positioning the figures with "H") depends on the LaTeX
package 'float'. In addition, the LaTeX package 'listing' is used in the
template for showing model fit summaries in the Appendix. This means that
the LaTeX packages 'float' and 'listing' need to be installed in the TeX
distribution used.</p>
<p>On Windows, the easiest way to achieve this (if no TeX distribution
is present before) is to install the 'tinytex' R package, to run
'tinytex::install_tinytex()' to get the basic tiny Tex distribution,
and then to run 'tinytex::tlmgr_install(c("float", "listing"))'.</p>
</div>
<div id="ref-examples">
<h2>Examples</h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># \dontrun{</span></span></span>
<span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/rstudio/rmarkdown" class="external-link">rmarkdown</a></span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="co"># The following is now commented out after the relase of v1.2.3 for the generation</span></span></span>
<span class="r-in"><span><span class="co"># of online docs, as the command creates a directory and opens an editor</span></span></span>
<span class="r-in"><span><span class="co">#draft("example_analysis.rmd", template = "hierarchical_kinetics", package = "mkin")</span></span></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
<span class="r-in"><span></span></span>
</code></pre></div>
</div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
</nav></div>
</div>
<footer><div class="copyright">
<p></p><p>Developed by Johannes Ranke.</p>
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
</div>
</footer></div>
</body></html>
|
