aboutsummaryrefslogtreecommitdiff
path: root/docs/dev/reference/index.html
blob: d6f859e562be98796d143ee66bc8e9fe78a2068c (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
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
<!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>Function reference • 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="Function reference"><meta name="robots" content="noindex"><!-- 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-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" 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-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.6</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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</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="contents col-md-9">
    <div class="page-header">
      <h1>Reference</h1>
    </div>

    <table class="ref-index"><colgroup><col class="alias"><col class="title"></colgroup><tbody><tr><th colspan="2">
          <h2 id="main-functions">Main functions <a href="#main-functions" class="anchor" aria-hidden="true"></a></h2>
          <p class="section-desc"></p><p>Essential functionality</p>
        </th>
      </tr></tbody><tbody><tr><td>
          <p><code><a href="mkinmod.html">mkinmod()</a></code> <code><a href="mkinmod.html">print(<i>&lt;mkinmod&gt;</i>)</a></code> <code><a href="mkinmod.html">mkinsub()</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> <code><a href="mmkin.html">print(<i>&lt;mmkin&gt;</i>)</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><tr><td>
          <p><code><a href="mhmkin.html">mhmkin()</a></code> <code><a href="mhmkin.html">`[`(<i>&lt;mhmkin&gt;</i>)</a></code> <code><a href="mhmkin.html">print(<i>&lt;mhmkin&gt;</i>)</a></code> </p>
        </td>
        <td><p>Fit nonlinear mixed-effects models built from one or more kinetic
degradation models and one or more error models</p></td>
      </tr></tbody><tbody><tr><th colspan="2">
          <h2 id="generics">Generics <a href="#generics" class="anchor" aria-hidden="true"></a></h2>
          <p class="section-desc"></p><p>Generic functions introduced by the package</p>
        </th>
      </tr></tbody><tbody><tr><td>
          <p><code><a href="parms.html">parms()</a></code> </p>
        </td>
        <td><p>Extract model parameters</p></td>
      </tr><tr><td>
          <p><code><a href="status.html">status()</a></code> <code><a href="status.html">print(<i>&lt;status.mmkin&gt;</i>)</a></code> <code><a href="status.html">print(<i>&lt;status.mhmkin&gt;</i>)</a></code> </p>
        </td>
        <td><p>Method to get status information for fit array objects</p></td>
      </tr><tr><td>
          <p><code><a href="illparms.html">illparms()</a></code> <code><a href="illparms.html">print(<i>&lt;illparms.mkinfit&gt;</i>)</a></code> <code><a href="illparms.html">print(<i>&lt;illparms.mmkin&gt;</i>)</a></code> <code><a href="illparms.html">print(<i>&lt;illparms.saem.mmkin&gt;</i>)</a></code> <code><a href="illparms.html">print(<i>&lt;illparms.mhmkin&gt;</i>)</a></code> </p>
        </td>
        <td><p>Method to get the names of ill-defined parameters</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="aw.html">aw()</a></code> </p>
        </td>
        <td><p>Calculate Akaike weights for model averaging</p></td>
      </tr></tbody><tbody><tr><th colspan="2">
          <h2 id="show-results">Show results <a href="#show-results" class="anchor" aria-hidden="true"></a></h2>
          <p class="section-desc"></p><p>Functions working with mkinfit objects</p>
        </th>
      </tr></tbody><tbody><tr><td>
          <p><code><a href="plot.mkinfit.html">plot(<i>&lt;mkinfit&gt;</i>)</a></code> <code><a href="plot.mkinfit.html">plot_sep()</a></code> <code><a href="plot.mkinfit.html">plot_res()</a></code> <code><a href="plot.mkinfit.html">plot_err()</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(<i>&lt;mkinfit&gt;</i>)</a></code> <code><a href="summary.mkinfit.html">print(<i>&lt;summary.mkinfit&gt;</i>)</a></code> </p>
        </td>
        <td><p>Summary method for class "mkinfit"</p></td>
      </tr><tr><td>
          <p><code><a href="confint.mkinfit.html">confint(<i>&lt;mkinfit&gt;</i>)</a></code> </p>
        </td>
        <td><p>Confidence intervals for parameters of mkinfit objects</p></td>
      </tr><tr><td>
          <p><code><a href="update.mkinfit.html">update(<i>&lt;mkinfit&gt;</i>)</a></code> </p>
        </td>
        <td><p>Update an mkinfit model with different arguments</p></td>
      </tr><tr><td>
          <p><code><a href="lrtest.mkinfit.html">lrtest(<i>&lt;mkinfit&gt;</i>)</a></code> <code><a href="lrtest.mkinfit.html">lrtest(<i>&lt;mmkin&gt;</i>)</a></code> </p>
        </td>
        <td><p>Likelihood ratio test for mkinfit models</p></td>
      </tr><tr><td>
          <p><code><a href="loftest.html">loftest()</a></code> </p>
        </td>
        <td><p>Lack-of-fit test for models fitted to data with replicates</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><tr><td>
          <p><code><a href="CAKE_export.html">CAKE_export()</a></code> </p>
        </td>
        <td><p>Export a list of datasets format to a CAKE study file</p></td>
      </tr></tbody><tbody><tr><th colspan="2">
          <h2 id="work-with-mmkin-objects">Work with mmkin objects <a href="#work-with-mmkin-objects" class="anchor" aria-hidden="true"></a></h2>
          <p class="section-desc"></p><p>Functions working with aggregated results</p>
        </th>
      </tr></tbody><tbody><tr><td>
          <p><code><a href="Extract.mmkin.html">`[`(<i>&lt;mmkin&gt;</i>)</a></code> </p>
        </td>
        <td><p>Subsetting method for mmkin objects</p></td>
      </tr><tr><td>
          <p><code><a href="plot.mmkin.html">plot(<i>&lt;mmkin&gt;</i>)</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><tr><td>
          <p><code><a href="AIC.mmkin.html">AIC(<i>&lt;mmkin&gt;</i>)</a></code> <code><a href="AIC.mmkin.html">BIC(<i>&lt;mmkin&gt;</i>)</a></code> </p>
        </td>
        <td><p>Calculate the AIC for a column of an mmkin object</p></td>
      </tr><tr><td>
          <p><code><a href="summary.mmkin.html">summary(<i>&lt;mmkin&gt;</i>)</a></code> <code><a href="summary.mmkin.html">print(<i>&lt;summary.mmkin&gt;</i>)</a></code> </p>
        </td>
        <td><p>Summary method for class "mmkin"</p></td>
      </tr></tbody><tbody><tr><th colspan="2">
          <h2 id="mixed-models">Mixed models <a href="#mixed-models" class="anchor" aria-hidden="true"></a></h2>
          <p class="section-desc"></p><p>Create and work with nonlinear hierarchical models</p>
        </th>
      </tr></tbody><tbody><tr><td>
          <p><code><a href="hierarchical_kinetics.html">hierarchical_kinetics()</a></code> </p>
        </td>
        <td><p>Hierarchical kinetics template</p></td>
      </tr><tr><td>
          <p><code><a href="read_spreadsheet.html">read_spreadsheet()</a></code> </p>
        </td>
        <td><p>Read datasets and relevant meta information from a spreadsheet file</p></td>
      </tr><tr><td>
          <p><code><a href="nlme.mmkin.html">nlme(<i>&lt;mmkin&gt;</i>)</a></code> <code><a href="nlme.mmkin.html">print(<i>&lt;nlme.mmkin&gt;</i>)</a></code> <code><a href="nlme.mmkin.html">update(<i>&lt;nlme.mmkin&gt;</i>)</a></code> </p>
        </td>
        <td><p>Create an nlme model for an mmkin row object</p></td>
      </tr><tr><td>
          <p><code><a href="saem.html">saem()</a></code> <code><a href="saem.html">print(<i>&lt;saem.mmkin&gt;</i>)</a></code> <code><a href="saem.html">saemix_model()</a></code> <code><a href="saem.html">saemix_data()</a></code> </p>
        </td>
        <td><p>Fit nonlinear mixed models with SAEM</p></td>
      </tr><tr><td>
          <p><code><a href="mhmkin.html">mhmkin()</a></code> <code><a href="mhmkin.html">`[`(<i>&lt;mhmkin&gt;</i>)</a></code> <code><a href="mhmkin.html">print(<i>&lt;mhmkin&gt;</i>)</a></code> </p>
        </td>
        <td><p>Fit nonlinear mixed-effects models built from one or more kinetic
degradation models and one or more error models</p></td>
      </tr><tr><td>
          <p><code><a href="plot.mixed.mmkin.html">plot(<i>&lt;mixed.mmkin&gt;</i>)</a></code> </p>
        </td>
        <td><p>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object</p></td>
      </tr><tr><td>
          <p><code><a href="summary.nlme.mmkin.html">summary(<i>&lt;nlme.mmkin&gt;</i>)</a></code> <code><a href="summary.nlme.mmkin.html">print(<i>&lt;summary.nlme.mmkin&gt;</i>)</a></code> </p>
        </td>
        <td><p>Summary method for class "nlme.mmkin"</p></td>
      </tr><tr><td>
          <p><code><a href="summary.saem.mmkin.html">summary(<i>&lt;saem.mmkin&gt;</i>)</a></code> <code><a href="summary.saem.mmkin.html">print(<i>&lt;summary.saem.mmkin&gt;</i>)</a></code> </p>
        </td>
        <td><p>Summary method for class "saem.mmkin"</p></td>
      </tr><tr><td>
          <p><code><a href="anova.saem.mmkin.html">anova(<i>&lt;saem.mmkin&gt;</i>)</a></code> </p>
        </td>
        <td><p>Anova method for saem.mmkin objects</p></td>
      </tr><tr><td>
          <p><code><a href="logLik.saem.mmkin.html">logLik(<i>&lt;saem.mmkin&gt;</i>)</a></code> </p>
        </td>
        <td><p>logLik method for saem.mmkin objects</p></td>
      </tr><tr><td>
          <p><code><a href="nlme.html">nlme_function()</a></code> <code><a href="nlme.html">nlme_data()</a></code> </p>
        </td>
        <td><p>Helper functions to create nlme models from mmkin row objects</p></td>
      </tr><tr><td>
          <p><code><a href="get_deg_func.html">get_deg_func()</a></code> </p>
        </td>
        <td><p>Retrieve a degradation function from the mmkin namespace</p></td>
      </tr><tr><td>
          <p><code><a href="mixed.html">mixed()</a></code> <code><a href="mixed.html">print(<i>&lt;mixed.mmkin&gt;</i>)</a></code> </p>
        </td>
        <td><p>Create a mixed effects model from an mmkin row object</p></td>
      </tr><tr><td>
          <p><code><a href="reexports.html">reexports</a></code> <code><a href="reexports.html">intervals</a></code> <code><a href="reexports.html">lrtest</a></code> <code><a href="reexports.html">nlme</a></code> </p>
        </td>
        <td><p>Objects exported from other packages</p></td>
      </tr><tr><td>
          <p><code><a href="intervals.saem.mmkin.html">intervals(<i>&lt;saem.mmkin&gt;</i>)</a></code> </p>
        </td>
        <td><p>Confidence intervals for parameters in saem.mmkin objects</p></td>
      </tr><tr><td>
          <p><code><a href="multistart.html">multistart()</a></code> <code><a href="multistart.html">print(<i>&lt;multistart&gt;</i>)</a></code> <code><a href="multistart.html">best()</a></code> <code><a href="multistart.html">which.best()</a></code> </p>
        </td>
        <td><p>Perform a hierarchical model fit with multiple starting values</p></td>
      </tr><tr><td>
          <p><code><a href="llhist.html">llhist()</a></code> </p>
        </td>
        <td><p>Plot the distribution of log likelihoods from multistart objects</p></td>
      </tr><tr><td>
          <p><code><a href="parplot.html">parplot()</a></code> </p>
        </td>
        <td><p>Plot parameter variability of multistart objects</p></td>
      </tr></tbody><tbody><tr><th colspan="2">
          <h2 id="datasets-and-known-results">Datasets and known results <a href="#datasets-and-known-results" class="anchor" aria-hidden="true"></a></h2>
          <p class="section-desc"></p>
        </th>
      </tr></tbody><tbody><tr><td>
          <p><code><a href="ds_mixed.html">ds_mixed</a></code> <code><a href="ds_mixed.html">ds_sfo</a></code> <code><a href="ds_mixed.html">ds_fomc</a></code> <code><a href="ds_mixed.html">ds_dfop</a></code> <code><a href="ds_mixed.html">ds_hs</a></code> <code><a href="ds_mixed.html">ds_dfop_sfo</a></code> </p>
        </td>
        <td><p>Synthetic data for hierarchical kinetic degradation models</p></td>
      </tr><tr><td>
          <p><code><a href="D24_2014.html">D24_2014</a></code> </p>
        </td>
        <td><p>Aerobic soil degradation data on 2,4-D from the EU assessment in 2014</p></td>
      </tr><tr><td>
          <p><code><a href="dimethenamid_2018.html">dimethenamid_2018</a></code> </p>
        </td>
        <td><p>Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018</p></td>
      </tr><tr><td>
          <p><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_A</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_B</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_C</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_D</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_E</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_F</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">FOCUS_2006_SFO_ref_A_to_F</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">FOCUS_2006_FOMC_ref_A_to_F</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">FOCUS_2006_HS_ref_A_to_F</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">FOCUS_2006_DFOP_ref_A_to_B</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="NAFTA_SOP_2015.html">NAFTA_SOP_Appendix_B</a></code> <code><a href="NAFTA_SOP_2015.html">NAFTA_SOP_Appendix_D</a></code> </p>
        </td>
        <td><p>Example datasets from the NAFTA SOP published 2015</p></td>
      </tr><tr><td>
          <p><code><a href="NAFTA_SOP_Attachment.html">NAFTA_SOP_Attachment</a></code> </p>
        </td>
        <td><p>Example datasets from Attachment 1 to the NAFTA SOP published 2015</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">schaefer07_complex_case</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_2014.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="experimental_data_for_UBA.html">experimental_data_for_UBA_2019</a></code> </p>
        </td>
        <td><p>Experimental datasets used for development and testing of error models</p></td>
      </tr><tr><td>
          <p><code><a href="test_data_from_UBA_2014.html">test_data_from_UBA_2014</a></code> </p>
        </td>
        <td><p>Three experimental datasets from two water sediment systems and one soil</p></td>
      </tr><tr><td>
          <p><code><a href="focus_soil_moisture.html">focus_soil_moisture</a></code> </p>
        </td>
        <td><p>FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar</p></td>
      </tr><tr><td>
          <p><code><a href="mkinds.html">print(<i>&lt;mkinds&gt;</i>)</a></code> </p>
        </td>
        <td><p>A dataset class for mkin</p></td>
      </tr><tr><td>
          <p><code><a href="mkindsg.html">print(<i>&lt;mkindsg&gt;</i>)</a></code> </p>
        </td>
        <td><p>A class for dataset groups for mkin</p></td>
      </tr></tbody><tbody><tr><th colspan="2">
          <h2 id="nafta-guidance">NAFTA guidance <a href="#nafta-guidance" class="anchor" aria-hidden="true"></a></h2>
          <p class="section-desc"></p>
        </th>
      </tr></tbody><tbody><tr><td>
          <p><code><a href="nafta.html">nafta()</a></code> <code><a href="nafta.html">print(<i>&lt;nafta&gt;</i>)</a></code> </p>
        </td>
        <td><p>Evaluate parent kinetics using the NAFTA guidance</p></td>
      </tr><tr><td>
          <p><code><a href="plot.nafta.html">plot(<i>&lt;nafta&gt;</i>)</a></code> </p>
        </td>
        <td><p>Plot the results of the three models used in the NAFTA scheme.</p></td>
      </tr></tbody><tbody><tr><th colspan="2">
          <h2 id="utility-functions">Utility functions <a href="#utility-functions" class="anchor" aria-hidden="true"></a></h2>
          <p class="section-desc"></p>
        </th>
      </tr></tbody><tbody><tr><td>
          <p><code><a href="summary_listing.html">summary_listing()</a></code> <code><a href="summary_listing.html">tex_listing()</a></code> <code><a href="summary_listing.html">html_listing()</a></code> </p>
        </td>
        <td><p>Display the output of a summary function according to the output format</p></td>
      </tr><tr><td>
          <p><code><a href="f_time_norm_focus.html">f_time_norm_focus()</a></code> </p>
        </td>
        <td><p>Normalisation factors for aerobic soil degradation according to FOCUS guidance</p></td>
      </tr><tr><td>
          <p><code><a href="set_nd_nq.html">set_nd_nq()</a></code> <code><a href="set_nd_nq.html">set_nd_nq_focus()</a></code> </p>
        </td>
        <td><p>Set non-detects and unquantified values in residue series without replicates</p></td>
      </tr><tr><td>
          <p><code><a href="max_twa_parent.html">max_twa_parent()</a></code> <code><a href="max_twa_parent.html">max_twa_sfo()</a></code> <code><a href="max_twa_parent.html">max_twa_fomc()</a></code> <code><a href="max_twa_parent.html">max_twa_dfop()</a></code> <code><a href="max_twa_parent.html">max_twa_hs()</a></code> </p>
        </td>
        <td><p>Function to calculate maximum time weighted average concentrations from
kinetic models fitted with mkinfit</p></td>
      </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></tbody><tbody><tr><th colspan="2">
          <h2 id="helper-functions-mainly-used-internally">Helper functions mainly used internally <a href="#helper-functions-mainly-used-internally" class="anchor" aria-hidden="true"></a></h2>
          <p class="section-desc"></p>
        </th>
      </tr></tbody><tbody><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="logLik.mkinfit.html">logLik(<i>&lt;mkinfit&gt;</i>)</a></code> </p>
        </td>
        <td><p>Calculated the log-likelihood of a fitted mkinfit object</p></td>
      </tr><tr><td>
          <p><code><a href="residuals.mkinfit.html">residuals(<i>&lt;mkinfit&gt;</i>)</a></code> </p>
        </td>
        <td><p>Extract residuals from an mkinfit model</p></td>
      </tr><tr><td>
          <p><code><a href="nobs.mkinfit.html">nobs(<i>&lt;mkinfit&gt;</i>)</a></code> </p>
        </td>
        <td><p>Number of observations on which an mkinfit object was fitted</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="mkinerrplot.html">mkinerrplot()</a></code> </p>
        </td>
        <td><p>Function to plot squared residuals and the error model for an mkin object</p></td>
      </tr><tr><td>
          <p><code><a href="mean_degparms.html">mean_degparms()</a></code> </p>
        </td>
        <td><p>Calculate mean degradation parameters for an mmkin row object</p></td>
      </tr><tr><td>
          <p><code><a href="create_deg_func.html">create_deg_func()</a></code> </p>
        </td>
        <td><p>Create degradation functions for known analytical solutions</p></td>
      </tr></tbody><tbody><tr><th colspan="2">
          <h2 id="analytical-solutions">Analytical solutions <a href="#analytical-solutions" class="anchor" aria-hidden="true"></a></h2>
          <p class="section-desc"></p><p>Parent only model solutions</p>
        </th>
      </tr></tbody><tbody><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><tr><td>
          <p><code><a href="logistic.solution.html">logistic.solution()</a></code> </p>
        </td>
        <td><p>Logistic kinetics</p></td>
      </tr></tbody><tbody><tr><th colspan="2">
          <h2 id="generate-synthetic-datasets">Generate synthetic datasets <a href="#generate-synthetic-datasets" class="anchor" aria-hidden="true"></a></h2>
          <p class="section-desc"></p>
        </th>
      </tr></tbody><tbody><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><tr><td>
          <p><code><a href="sigma_twocomp.html">sigma_twocomp()</a></code> </p>
        </td>
        <td><p>Two-component error model</p></td>
      </tr></tbody><tbody><tr><th colspan="2">
          <h2 id="deprecated-functions">Deprecated functions <a href="#deprecated-functions" class="anchor" aria-hidden="true"></a></h2>
          <p class="section-desc"></p><p>Functions that have been superseded</p>
        </th>
      </tr></tbody><tbody><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 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>

Contact - Imprint