blob: e995a75b29d1b551539f7c101cb24a8cdb479fb2 (
plain) (
blame)
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
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
|
<!-- 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>Function reference • 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/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" 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="../jquery.sticky-kit.min.js"></script>
<script src="../pkgdown.js"></script>
<!-- mathjax -->
<script src='https://mathjax.rstudio.com/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 template-reference-index">
<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="../reference/index.html">Functions and data</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" 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>
<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/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
</li>
<li>
<a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
</li>
</ul>
</li>
<li>
<a href="../news/index.html">News</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="http://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="row">
<div class="col-md-9">
<div class="page-header">
<h1>
Reference
<small>version 0.9.45.2</small>
</h1>
</div>
<div class="contents">
<table class="ref-index">
<colgroup>
<col class="alias" />
<col class="title" />
</colgroup>
<tbody>
<tr>
<th colspan="2">
<h2 id="section-main-functions" class="hasAnchor"><a href="#section-main-functions" class="anchor"></a>Main functions</h2>
<p class="section-desc"><p>Essential functionality</p></p>
</th>
</tr>
<tr>
<!-- -->
<td>
<p><code><a href="mkinmod.html">mkinmod</a></code> </p>
</td>
<td><p>Function to set up a kinetic model with one or more state variables</p></td>
</tr><tr>
<!-- -->
<td>
<p><code><a href="mkinfit.html">mkinfit</a></code> </p>
</td>
<td><p>Fit a kinetic model to data with one or more state variables</p></td>
</tr><tr>
<!-- -->
<td>
<p><code><a href="mmkin.html">mmkin</a></code> </p>
</td>
<td><p>Fit one or more kinetic models with one or more state variables to one or more datasets</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-show-results" class="hasAnchor"><a href="#section-show-results" class="anchor"></a>Show results</h2>
<p class="section-desc"><p>Functions working with mkinfit objects</p></p>
</th>
</tr>
<tr>
<!-- -->
<td>
<p><code><a href="plot.mkinfit.html">plot.mkinfit</a></code> </p>
</td>
<td><p>Plot the observed data and the fitted model of an mkinfit object</p></td>
</tr><tr>
<!-- -->
<td>
<p><code><a href="summary.mkinfit.html">summary</a></code> <code><a href="summary.mkinfit.html">print</a></code> </p>
</td>
<td><p>Summary method for class "mkinfit"</p></td>
</tr><tr>
<!-- -->
<td>
<p><code><a href="mkinresplot.html">mkinresplot</a></code> </p>
</td>
<td><p>Function to plot residuals stored in an mkin object</p></td>
</tr><tr>
<!-- -->
<td>
<p><code><a href="mkinparplot.html">mkinparplot</a></code> </p>
</td>
<td><p>Function to plot the confidence intervals obtained using mkinfit</p></td>
</tr><tr>
<!-- -->
<td>
<p><code><a href="endpoints.html">endpoints</a></code> </p>
</td>
<td><p>Function to calculate endpoints for further use from kinetic models fitted with mkinfit</p></td>
</tr><tr>
<!-- -->
<td>
<p><code><a href="mkinerrmin.html">mkinerrmin</a></code> </p>
</td>
<td><p>Calculate the minimum error to assume in order to pass the variance test</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-work-with-mmkin-objects" class="hasAnchor"><a href="#section-work-with-mmkin-objects" class="anchor"></a>Work with mmkin objects</h2>
<p class="section-desc"><p>Functions working with aggregated results</p></p>
</th>
</tr>
<tr>
<!-- -->
<td>
<p><code><a href="Extract.mmkin.html">[.mmkin</a></code> </p>
</td>
<td><p>Subsetting method for mmkin objects</p></td>
</tr><tr>
<!-- -->
<td>
<p><code><a href="plot.mmkin.html">plot</a></code> </p>
</td>
<td><p>Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-datasets-and-known-results" class="hasAnchor"><a href="#section-datasets-and-known-results" class="anchor"></a>Datasets and known results</h2>
<p class="section-desc"></p>
</th>
</tr>
<tr>
<!-- -->
<td>
<p><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_datasets</a></code> </p>
</td>
<td><p>Datasets A to F from the FOCUS Kinetics report from 2006</p></td>
</tr><tr>
<!-- -->
<td>
<p><code><a href="FOCUS_2006_SFO_ref_A_to_F.html">data</a></code> </p>
</td>
<td><p>Results of fitting the SFO model to Datasets A to F of FOCUS (2006)</p></td>
</tr><tr>
<!-- -->
<td>
<p><code><a href="FOCUS_2006_FOMC_ref_A_to_F.html">data</a></code> </p>
</td>
<td><p>Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)</p></td>
</tr><tr>
<!-- -->
<td>
<p><code><a href="FOCUS_2006_HS_ref_A_to_F.html">data</a></code> </p>
</td>
<td><p>Results of fitting the HS model to Datasets A to F of FOCUS (2006)</p></td>
</tr><tr>
<!-- -->
<td>
<p><code><a href="FOCUS_2006_DFOP_ref_A_to_B.html">data</a></code> </p>
</td>
<td><p>Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)</p></td>
</tr><tr>
<!-- -->
<td>
<p><code><a href="mccall81_245T.html">mccall81_245T</a></code> </p>
</td>
<td><p>Datasets on aerobic soil metabolism of 2,4,5-T in six soils</p></td>
</tr><tr>
<!-- -->
<td>
<p><code><a href="schaefer07_complex_case.html">data</a></code> </p>
</td>
<td><p>Metabolism data set used for checking the software quality of KinGUI</p></td>
</tr><tr>
<!-- -->
<td>
<p><code><a href="synthetic_data_for_UBA.html">synthetic_data_for_UBA_2014</a></code> </p>
</td>
<td><p>Synthetic datasets for one parent compound with two metabolites</p></td>
</tr><tr>
<!-- -->
<td>
<p><code><a href="mkinds.html">mkinds</a></code> </p>
</td>
<td><p>A dataset class for mkin</p></td>
</tr><tr>
<!-- -->
<td>
<p><code><a href="print.mkinds.html">print</a></code> </p>
</td>
<td><p>Print mkinds objects</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-helper-functions" class="hasAnchor"><a href="#section-helper-functions" class="anchor"></a>Helper functions</h2>
<p class="section-desc"></p>
</th>
</tr>
<tr>
<!-- -->
<td>
<p><code><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></code> </p>
</td>
<td><p>Convert a dataframe with observations over time into long format</p></td>
</tr><tr>
<!-- -->
<td>
<p><code><a href="mkin_long_to_wide.html">mkin_long_to_wide</a></code> </p>
</td>
<td><p>Convert a dataframe from long to wide format</p></td>
</tr><tr>
<!-- -->
<td>
<p><code><a href="mkinsub.html">mkinsub</a></code> </p>
</td>
<td><p>Function to set up a kinetic submodel for one state variable</p></td>
</tr><tr>
<!-- -->
<td>
<p><code><a href="print.mkinmod.html">print</a></code> </p>
</td>
<td><p>Print mkinmod objects</p></td>
</tr><tr>
<!-- -->
<td>
<p><code><a href="mkinpredict.html">mkinpredict</a></code> </p>
</td>
<td><p>Produce predictions from a kinetic model using specific parameters</p></td>
</tr><tr>
<!-- -->
<td>
<p><code><a href="transform_odeparms.html">transform_odeparms</a></code> <code><a href="transform_odeparms.html">backtransform_odeparms</a></code> </p>
</td>
<td><p>Functions to transform and backtransform kinetic parameters for fitting</p></td>
</tr><tr>
<!-- -->
<td>
<p><code><a href="ilr.html">ilr</a></code> <code><a href="ilr.html">invilr</a></code> </p>
</td>
<td><p>Function to perform isometric log-ratio transformation</p></td>
</tr><tr>
<!-- -->
<td>
<p><code><a href="geometric_mean.html">geometric_mean</a></code> </p>
</td>
<td><p>Calculate the geometric mean</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-analytical-solutions" class="hasAnchor"><a href="#section-analytical-solutions" class="anchor"></a>Analytical solutions</h2>
<p class="section-desc"><p>Parent only model solutions</p></p>
</th>
</tr>
<tr>
<!-- -->
<td>
<p><code><a href="SFO.solution.html">SFO.solution</a></code> </p>
</td>
<td><p>Single First-Order kinetics</p></td>
</tr><tr>
<!-- -->
<td>
<p><code><a href="FOMC.solution.html">FOMC.solution</a></code> </p>
</td>
<td><p>First-Order Multi-Compartment kinetics</p></td>
</tr><tr>
<!-- -->
<td>
<p><code><a href="DFOP.solution.html">DFOP.solution</a></code> </p>
</td>
<td><p>Double First-Order in Parallel kinetics</p></td>
</tr><tr>
<!-- -->
<td>
<p><code><a href="SFORB.solution.html">SFORB.solution</a></code> </p>
</td>
<td><p>Single First-Order Reversible Binding kinetics</p></td>
</tr><tr>
<!-- -->
<td>
<p><code><a href="HS.solution.html">HS.solution</a></code> </p>
</td>
<td><p>Hockey-Stick kinetics</p></td>
</tr><tr>
<!-- -->
<td>
<p><code><a href="IORE.solution.html">IORE.solution</a></code> </p>
</td>
<td><p>Indeterminate order rate equation kinetics</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-generate-synthetic-datasets" class="hasAnchor"><a href="#section-generate-synthetic-datasets" class="anchor"></a>Generate synthetic datasets</h2>
<p class="section-desc"></p>
</th>
</tr>
<tr>
<!-- -->
<td>
<p><code><a href="add_err.html">add_err</a></code> </p>
</td>
<td><p>Add normally distributed errors to simulated kinetic degradation data</p></td>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-deprecated-functions" class="hasAnchor"><a href="#section-deprecated-functions" class="anchor"></a>Deprecated functions</h2>
<p class="section-desc"><p>Functions that have been superseeded</p></p>
</th>
</tr>
<tr>
<!-- -->
<td>
<p><code><a href="mkinplot.html">mkinplot</a></code> </p>
</td>
<td><p>Plot the observed data and the fitted model of an mkinfit object</p></td>
</tr>
</tbody>
</table>
</div>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#section-main-functions">Main functions</a></li>
<li><a href="#section-show-results">Show results</a></li>
<li><a href="#section-work-with-mmkin-objects">Work with mmkin objects</a></li>
<li><a href="#section-datasets-and-known-results">Datasets and known results</a></li>
<li><a href="#section-helper-functions">Helper functions</a></li>
<li><a href="#section-analytical-solutions">Analytical solutions</a></li>
<li><a href="#section-generate-synthetic-datasets">Generate synthetic datasets</a></li>
<li><a href="#section-deprecated-functions">Deprecated functions</a></li>
</ul>
</div>
</div>
<footer>
<div class="copyright">
<p>Developed by Johannes Ranke.</p>
</div>
<div class="pkgdown">
<p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
</div>
</footer>
</div>
</body>
</html>
|
