aboutsummaryrefslogtreecommitdiff
path: root/docs/dev/reference/transform_odeparms.html
blob: 9e81258a9b977a3b2747db690cbc9032a6aac7ac (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
<!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>Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms • 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="Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms"><meta property="og:description" content="The transformations are intended to map parameters that should only take on
restricted values to the full scale of real numbers. For kinetic rate
constants and other parameters that can only take on positive values, a
simple log transformation is used. For compositional parameters, such as the
formations fractions that should always sum up to 1 and can not be negative,
the ilr transformation is used."><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-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-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</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>Functions to transform and backtransform kinetic parameters for fitting</h1>
    <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/transform_odeparms.R" class="external-link"><code>R/transform_odeparms.R</code></a></small>
    <div class="hidden name"><code>transform_odeparms.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>The transformations are intended to map parameters that should only take on
restricted values to the full scale of real numbers. For kinetic rate
constants and other parameters that can only take on positive values, a
simple log transformation is used. For compositional parameters, such as the
formations fractions that should always sum up to 1 and can not be negative,
the <a href="ilr.html">ilr</a> transformation is used.</p>
    </div>

    <div id="ref-usage">
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">transform_odeparms</span><span class="op">(</span></span>
<span>  <span class="va">parms</span>,</span>
<span>  <span class="va">mkinmod</span>,</span>
<span>  transform_rates <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span>  transform_fractions <span class="op">=</span> <span class="cn">TRUE</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="fu">backtransform_odeparms</span><span class="op">(</span></span>
<span>  <span class="va">transparms</span>,</span>
<span>  <span class="va">mkinmod</span>,</span>
<span>  transform_rates <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span>  transform_fractions <span class="op">=</span> <span class="cn">TRUE</span></span>
<span><span class="op">)</span></span></code></pre></div>
    </div>

    <div id="arguments">
    <h2>Arguments</h2>
    <dl><dt>parms</dt>
<dd><p>Parameters of kinetic models as used in the differential
equations.</p></dd>


<dt>mkinmod</dt>
<dd><p>The kinetic model of class <a href="mkinmod.html">mkinmod</a>, containing
the names of the model variables that are needed for grouping the
formation fractions before <a href="ilr.html">ilr</a> transformation, the parameter
names and the information if the pathway to sink is included in the model.</p></dd>


<dt>transform_rates</dt>
<dd><p>Boolean specifying if kinetic rate constants should
be transformed in the model specification used in the fitting for better
compliance with the assumption of normal distribution of the estimator. If
TRUE, also alpha and beta parameters of the FOMC model are
log-transformed, as well as k1 and k2 rate constants for the DFOP and HS
models and the break point tb of the HS model.</p></dd>


<dt>transform_fractions</dt>
<dd><p>Boolean specifying if formation fractions
constants should be transformed in the model specification used in the
fitting for better compliance with the assumption of normal distribution
of the estimator. The default (TRUE) is to do transformations.
The g parameter of the DFOP model is also seen as a fraction.
If a single fraction is transformed (g parameter of DFOP or only a single
target variable e.g. a single metabolite plus a pathway to sink), a
logistic transformation is used <code><a href="https://rdrr.io/r/stats/Logistic.html" class="external-link">stats::qlogis()</a></code>. In other cases, i.e. if
two or more formation fractions need to be transformed whose sum cannot
exceed one, the <a href="ilr.html">ilr</a> transformation is used.</p></dd>


<dt>transparms</dt>
<dd><p>Transformed parameters of kinetic models as used in the
fitting procedure.</p></dd>

</dl></div>
    <div id="value">
    <h2>Value</h2>
    

<p>A vector of transformed or backtransformed parameters</p>
    </div>
    <div id="details">
    <h2>Details</h2>
    <p>The transformation of sets of formation fractions is fragile, as it supposes
the same ordering of the components in forward and backward transformation.
This is no problem for the internal use in <a href="mkinfit.html">mkinfit</a>.</p>
    </div>
    <div id="author">
    <h2>Author</h2>
    <p>Johannes Ranke</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="va">SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span>
<span class="r-in"><span>  parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"m1"</span>, sink <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>  m1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"min"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Fit the model to the FOCUS example dataset D using defaults</span></span></span>
<span class="r-in"><span><span class="va">FOCUS_D</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span> <span class="co"># remove zero values to avoid warning</span></span></span>
<span class="r-in"><span><span class="va">fit</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">fit.s</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="co"># Transformed and backtransformed parameters</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.s</span><span class="op">$</span><span class="va">par</span>, <span class="fl">3</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span>                   Estimate Std. Error Lower  Upper</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0             99.60     1.5702 96.40 102.79</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_parent_sink    -3.04     0.0763 -3.19  -2.88</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_parent_m1      -2.98     0.0403 -3.06  -2.90</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_m1_sink        -5.25     0.1332 -5.52  -4.98</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma                 3.13     0.3585  2.40   3.85</span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.s</span><span class="op">$</span><span class="va">bpar</span>, <span class="fl">3</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span>               Estimate se_notrans t value   Pr(&gt;t)    Lower    Upper</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0      99.59848    1.57022   63.43 2.30e-36 96.40384 102.7931</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent_sink  0.04792    0.00365   13.11 6.13e-15  0.04103   0.0560</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent_m1    0.05078    0.00205   24.80 3.27e-23  0.04678   0.0551</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_m1_sink      0.00526    0.00070    7.51 6.16e-09  0.00401   0.0069</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma          3.12550    0.35852    8.72 2.24e-10  2.39609   3.8549</span>
<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="co"># Compare to the version without transforming rate parameters (does not work</span></span></span>
<span class="r-in"><span><span class="co"># with analytical solution, we get NA values for m1 in predictions)</span></span></span>
<span class="r-in"><span><span class="va">fit.2</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, transform_rates <span class="op">=</span> <span class="cn">FALSE</span>,</span></span>
<span class="r-in"><span>  solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">fit.2.s</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.2</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.2.s</span><span class="op">$</span><span class="va">par</span>, <span class="fl">3</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span>               Estimate Std. Error    Lower    Upper</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0      99.59848    1.57022 96.40384 1.03e+02</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent_sink  0.04792    0.00365  0.04049 5.54e-02</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent_m1    0.05078    0.00205  0.04661 5.49e-02</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_m1_sink      0.00526    0.00070  0.00384 6.69e-03</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma          3.12550    0.35852  2.39609 3.85e+00</span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.2.s</span><span class="op">$</span><span class="va">bpar</span>, <span class="fl">3</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span>               Estimate se_notrans t value   Pr(&gt;t)    Lower    Upper</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0      99.59848    1.57022   63.43 2.30e-36 96.40384 1.03e+02</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent_sink  0.04792    0.00365   13.11 6.13e-15  0.04049 5.54e-02</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent_m1    0.05078    0.00205   24.80 3.27e-23  0.04661 5.49e-02</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_m1_sink      0.00526    0.00070    7.51 6.16e-09  0.00384 6.69e-03</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma          3.12550    0.35852    8.72 2.24e-10  2.39609 3.85e+00</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">initials</span> <span class="op">&lt;-</span> <span class="va">fit</span><span class="op">$</span><span class="va">start</span><span class="op">$</span><span class="va">value</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">initials</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">rownames</a></span><span class="op">(</span><span class="va">fit</span><span class="op">$</span><span class="va">start</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">transformed</span> <span class="op">&lt;-</span> <span class="va">fit</span><span class="op">$</span><span class="va">start_transformed</span><span class="op">$</span><span class="va">value</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">transformed</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">rownames</a></span><span class="op">(</span><span class="va">fit</span><span class="op">$</span><span class="va">start_transformed</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu">transform_odeparms</span><span class="op">(</span><span class="va">initials</span>, <span class="va">SFO_SFO</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>        100.750000         -2.302585         -2.301586         -2.300587 </span>
<span class="r-in"><span><span class="fu">backtransform_odeparms</span><span class="op">(</span><span class="va">transformed</span>, <span class="va">SFO_SFO</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span>      parent_0 k_parent_sink   k_parent_m1     k_m1_sink </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>      100.7500        0.1000        0.1001        0.1002 </span>
<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="co"># The case of formation fractions (this is now the default)</span></span></span>
<span class="r-in"><span><span class="va">SFO_SFO.ff</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span>
<span class="r-in"><span>  parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"m1"</span>, sink <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>  m1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>  use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">fit.ff</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO.ff</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">fit.ff.s</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.ff</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.ff.s</span><span class="op">$</span><span class="va">par</span>, <span class="fl">3</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span>                 Estimate Std. Error  Lower  Upper</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0         99.5985     1.5702 96.404 102.79</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_parent     -2.3157     0.0409 -2.399  -2.23</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_m1         -5.2475     0.1332 -5.518  -4.98</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_qlogis   0.0579     0.0893 -0.124   0.24</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma             3.1255     0.3585  2.396   3.85</span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.ff.s</span><span class="op">$</span><span class="va">bpar</span>, <span class="fl">3</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span>                Estimate se_notrans t value   Pr(&gt;t)    Lower    Upper</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0       99.59848    1.57022   63.43 2.30e-36 96.40383 102.7931</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent        0.09870    0.00403   24.47 4.96e-23  0.09082   0.1073</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_m1            0.00526    0.00070    7.51 6.16e-09  0.00401   0.0069</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_to_m1  0.51448    0.02230   23.07 3.10e-22  0.46912   0.5596</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma           3.12550    0.35852    8.72 2.24e-10  2.39609   3.8549</span>
<span class="r-in"><span><span class="va">initials</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"f_parent_to_m1"</span> <span class="op">=</span> <span class="fl">0.5</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">transformed</span> <span class="op">&lt;-</span> <span class="fu">transform_odeparms</span><span class="op">(</span><span class="va">initials</span>, <span class="va">SFO_SFO.ff</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu">backtransform_odeparms</span><span class="op">(</span><span class="va">transformed</span>, <span class="va">SFO_SFO.ff</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f_parent_to_m1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>            0.5 </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># And without sink</span></span></span>
<span class="r-in"><span><span class="va">SFO_SFO.ff.2</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span>
<span class="r-in"><span>  parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"m1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>  m1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>  use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">fit.ff.2</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO.ff.2</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">fit.ff.2.s</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.ff.2</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.ff.2.s</span><span class="op">$</span><span class="va">par</span>, <span class="fl">3</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span>              Estimate Std. Error Lower Upper</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0        84.79      3.012 78.67 90.91</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_parent    -2.76      0.082 -2.92 -2.59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_m1        -4.21      0.123 -4.46 -3.96</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma            8.22      0.943  6.31 10.14</span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.ff.2.s</span><span class="op">$</span><span class="va">bpar</span>, <span class="fl">3</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span>          Estimate se_notrans t value   Pr(&gt;t)   Lower  Upper</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0  84.7916    3.01203   28.15 1.92e-25 78.6704 90.913</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_parent   0.0635    0.00521   12.19 2.91e-14  0.0538  0.075</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> k_m1       0.0148    0.00182    8.13 8.81e-10  0.0115  0.019</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> sigma      8.2229    0.94323    8.72 1.73e-10  6.3060 10.140</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>

Contact - Imprint