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
|
<!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, shrink-to-fit=no"><title>Calculate mean degradation parameters for an mmkin row object — mean_degparms • mkin</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Calculate mean degradation parameters for an mmkin row object — mean_degparms"><meta name="description" content="Calculate mean degradation parameters for an mmkin row object"><meta property="og:description" content="Calculate mean degradation parameters for an mmkin row object"><meta name="robots" content="noindex"></head><body>
<a href="#main" class="visually-hidden-focusable">Skip to contents</a>
<nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="default" aria-label="Site navigation"><div class="container">
<a class="navbar-brand me-2" href="../index.html">mkin</a>
<small class="nav-text text-info me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="In-development version">1.2.10</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
<span class="navbar-toggler-icon"></span>
</button>
<div id="navbar" class="collapse navbar-collapse ms-3">
<ul class="navbar-nav me-auto"><li class="active nav-item"><a class="nav-link" href="../reference/index.html">Reference</a></li>
<li class="nav-item dropdown">
<button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
<ul class="dropdown-menu" aria-labelledby="dropdown-articles"><li><a class="dropdown-item" href="../articles/mkin.html">Introduction to mkin</a></li>
<li><hr class="dropdown-divider"></li>
<li><h6 class="dropdown-header" data-toc-skip>Example evaluations with (generalised) nonlinear least squares</h6></li>
<li><a class="dropdown-item" href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a></li>
<li><a class="dropdown-item" href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a></li>
<li><a class="dropdown-item" href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a></li>
<li><hr class="dropdown-divider"></li>
<li><h6 class="dropdown-header" data-toc-skip>Example evaluations with hierarchical models (nonlinear mixed-effects models)</h6></li>
<li><a class="dropdown-item" href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a></li>
<li><a class="dropdown-item" href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a></li>
<li><a class="dropdown-item" href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a></li>
<li><a class="dropdown-item" href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a></li>
<li><a class="dropdown-item" href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a></li>
<li><a class="dropdown-item" href="../articles/web_only/multistart.html">Short demo of the multistart method</a></li>
<li><hr class="dropdown-divider"></li>
<li><h6 class="dropdown-header" data-toc-skip>Performance</h6></li>
<li><a class="dropdown-item" href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a></li>
<li><a class="dropdown-item" href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a></li>
<li><a class="dropdown-item" href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a></li>
<li><hr class="dropdown-divider"></li>
<li><h6 class="dropdown-header" data-toc-skip>Miscellaneous</h6></li>
<li><a class="dropdown-item" href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a></li>
<li><a class="dropdown-item" href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a></li>
</ul></li>
<li class="nav-item"><a class="nav-link" href="../coverage/coverage.html">Test coverage</a></li>
<li class="nav-item"><a class="nav-link" href="../news/index.html">News</a></li>
</ul><ul class="navbar-nav"><li class="nav-item"><form class="form-inline" role="search">
<input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="../search.json"></form></li>
<li class="nav-item"><a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
</ul></div>
</div>
</nav><div class="container template-reference-topic">
<div class="row">
<main id="main" class="col-md-9"><div class="page-header">
<h1>Calculate mean degradation parameters for an mmkin row object</h1>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mean_degparms.R" class="external-link"><code>R/mean_degparms.R</code></a></small>
<div class="d-none name"><code>mean_degparms.Rd</code></div>
</div>
<div class="ref-description section level2">
<p>Calculate mean degradation parameters for an mmkin row object</p>
</div>
<div class="section level2">
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mean_degparms</span><span class="op">(</span></span>
<span> <span class="va">object</span>,</span>
<span> random <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> test_log_parms <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> conf.level <span class="op">=</span> <span class="fl">0.6</span>,</span>
<span> default_log_parms <span class="op">=</span> <span class="cn">NA</span></span>
<span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt id="arg-object">object<a class="anchor" aria-label="anchor" href="#arg-object"></a></dt>
<dd><p>An mmkin row object containing several fits of the same model to different datasets</p></dd>
<dt id="arg-random">random<a class="anchor" aria-label="anchor" href="#arg-random"></a></dt>
<dd><p>Should a list with fixed and random effects be returned?</p></dd>
<dt id="arg-test-log-parms">test_log_parms<a class="anchor" aria-label="anchor" href="#arg-test-log-parms"></a></dt>
<dd><p>If TRUE, log parameters are only considered in
the mean calculations if their untransformed counterparts (most likely
rate constants) pass the t-test for significant difference from zero.</p></dd>
<dt id="arg-conf-level">conf.level<a class="anchor" aria-label="anchor" href="#arg-conf-level"></a></dt>
<dd><p>Possibility to adjust the required confidence level
for parameter that are tested if requested by 'test_log_parms'.</p></dd>
<dt id="arg-default-log-parms">default_log_parms<a class="anchor" aria-label="anchor" href="#arg-default-log-parms"></a></dt>
<dd><p>If set to a numeric value, this is used
as a default value for the tested log parameters that failed the
t-test.</p></dd>
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<p>If random is FALSE (default), a named vector containing mean values
of the fitted degradation model parameters. If random is TRUE, a list with
fixed and random effects, in the format required by the start argument of
nlme for the case of a single grouping variable ds.</p>
</div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
</nav></aside></div>
<footer><div class="pkgdown-footer-left">
<p>Developed by Johannes Ranke.</p>
</div>
<div class="pkgdown-footer-right">
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
</div>
</footer></div>
</body></html>
|
