aboutsummaryrefslogtreecommitdiff
path: root/docs/dev/articles/prebuilt/2022_dmta_parent.html
diff options
context:
space:
mode:
Diffstat (limited to 'docs/dev/articles/prebuilt/2022_dmta_parent.html')
-rw-r--r--docs/dev/articles/prebuilt/2022_dmta_parent.html579
1 files changed, 259 insertions, 320 deletions
diff --git a/docs/dev/articles/prebuilt/2022_dmta_parent.html b/docs/dev/articles/prebuilt/2022_dmta_parent.html
index 45a925b3..e4943574 100644
--- a/docs/dev/articles/prebuilt/2022_dmta_parent.html
+++ b/docs/dev/articles/prebuilt/2022_dmta_parent.html
@@ -4,143 +4,91 @@
<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">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<title>Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P • 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="Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P">
-<meta property="og:description" content="mkin">
+<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="Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P">
<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-article">
- <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>
-<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>
-<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>
-<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>
-<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>
+<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="nav-item"><a class="nav-link" href="../../reference/index.html">Reference</a></li>
+<li class="active 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>
- <a href="../../news/index.html">News</a>
-</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="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 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>
-<!--/.nav-collapse -->
+
+
</div>
-<!--/.container -->
-</div>
-<!--/.navbar -->
+</nav><div class="container template-article">
+
+
-
- </header><div class="row">
- <div class="col-md-9 contents">
- <div class="page-header toc-ignore">
- <h1 data-toc-skip>Testing hierarchical parent degradation kinetics
-with residue data on dimethenamid and dimethenamid-P</h1>
+<div class="row">
+ <main id="main" class="col-md-9"><div class="page-header">
+
+ <h1>Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</h1>
<h4 data-toc-skip class="author">Johannes
Ranke</h4>
<h4 data-toc-skip class="date">Last change on 5 January
-2023, last compiled on 19 Mai 2023</h4>
+2023, last compiled on 16 Februar 2025</h4>
<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/prebuilt/2022_dmta_parent.rmd" class="external-link"><code>vignettes/prebuilt/2022_dmta_parent.rmd</code></a></small>
- <div class="hidden name"><code>2022_dmta_parent.rmd</code></div>
-
+ <div class="d-none name"><code>2022_dmta_parent.rmd</code></div>
</div>
@@ -155,7 +103,7 @@ FOMC, DFOP and HS can be fitted with the mkin package.</p>
173340 (Application of nonlinear hierarchical models to the kinetic
evaluation of chemical degradation data) of the German Environment
Agency carried out in 2022 and 2023.</p>
-<p>The mkin package is used in version 1.2.5. It contains the test data
+<p>The mkin package is used in version 1.2.10. It contains the test data
and the functions used in the evaluations. The <code>saemix</code>
package is used as a backend for fitting the NLHM, but is also loaded to
make the convergence plot function available.</p>
@@ -1006,7 +954,7 @@ updated assuming two-component error.</p>
<td align="left">DFOP</td>
<td align="left">OK</td>
<td align="left">OK</td>
-<td align="left">C</td>
+<td align="left">OK</td>
<td align="left">OK</td>
<td align="left">C</td>
<td align="left">OK</td>
@@ -1014,7 +962,7 @@ updated assuming two-component error.</p>
<tr class="even">
<td align="left">HS</td>
<td align="left">OK</td>
-<td align="left">C</td>
+<td align="left">OK</td>
<td align="left">OK</td>
<td align="left">OK</td>
<td align="left">OK</td>
@@ -1112,9 +1060,9 @@ the best fits.</p>
<tr class="even">
<td align="left">FOMC tc</td>
<td align="right">8</td>
-<td align="right">720.4</td>
-<td align="right">718.8</td>
-<td align="right">-352.2</td>
+<td align="right">720.7</td>
+<td align="right">719.1</td>
+<td align="right">-352.4</td>
</tr>
<tr class="odd">
<td align="left">DFOP const</td>
@@ -1133,9 +1081,9 @@ the best fits.</p>
<tr class="odd">
<td align="left">DFOP tc</td>
<td align="right">10</td>
-<td align="right">665.5</td>
-<td align="right">663.4</td>
-<td align="right">-322.8</td>
+<td align="right">665.7</td>
+<td align="right">663.6</td>
+<td align="right">-322.9</td>
</tr>
<tr class="even">
<td align="left">HS tc</td>
@@ -1216,12 +1164,12 @@ achieved with the argument <code>test = TRUE</code> to the
<span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>format.args <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>digits <span class="op">=</span> <span class="fl">4</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
<table class="table">
<colgroup>
-<col width="37%">
-<col width="6%">
+<col width="38%">
+<col width="7%">
<col width="8%">
<col width="8%">
<col width="9%">
-<col width="9%">
+<col width="8%">
<col width="4%">
<col width="15%">
</colgroup>
@@ -1239,8 +1187,8 @@ achieved with the argument <code>test = TRUE</code> to the
<tr class="odd">
<td align="left">f_saem_dfop_tc_no_ranef_k2</td>
<td align="right">9</td>
-<td align="right">663.8</td>
-<td align="right">661.9</td>
+<td align="right">663.7</td>
+<td align="right">661.8</td>
<td align="right">-322.9</td>
<td align="right">NA</td>
<td align="right">NA</td>
@@ -1249,12 +1197,12 @@ achieved with the argument <code>test = TRUE</code> to the
<tr class="even">
<td align="left">f_saem[[“DFOP”, “tc”]]</td>
<td align="right">10</td>
-<td align="right">665.5</td>
-<td align="right">663.4</td>
-<td align="right">-322.8</td>
-<td align="right">0.2809</td>
+<td align="right">665.7</td>
+<td align="right">663.6</td>
+<td align="right">-322.9</td>
+<td align="right">0</td>
+<td align="right">1</td>
<td align="right">1</td>
-<td align="right">0.5961</td>
</tr>
</tbody>
</table>
@@ -1286,11 +1234,11 @@ Plot of the final NLHM DFOP fit
<p>Finally, a summary report of the fit is produced.</p>
<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
<code class="sourceCode R"><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">f_saem_dfop_tc_no_ranef_k2</span><span class="op">)</span></span></code></pre></div>
-<pre><code>saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.5
-R version used for fitting: 4.3.0
-Date of fit: Fri May 19 18:14:27 2023
-Date of summary: Fri May 19 18:14:28 2023
+<pre><code>saemix version used for fitting: 3.3
+mkin version used for pre-fitting: 1.2.10
+R version used for fitting: 4.4.2
+Date of fit: Fri Feb 14 08:13:19 2025
+Date of summary: Fri Feb 14 08:13:19 2025
Equations:
d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -1302,21 +1250,21 @@ Data:
Model predictions using solution type analytical
-Fitted in 4.477 s
+Fitted in 4.154 s
Using 300, 100 iterations and 9 chains
Variance model: Two-component variance function
Starting values for degradation parameters:
- DMTA_0 k1 k2 g
-98.759266 0.087034 0.009933 0.930827
+ DMTA_0 k1 k2 g
+98.71186 0.08675 0.01374 0.93491
Fixed degradation parameter values:
None
Starting values for random effects (square root of initial entries in omega):
DMTA_0 k1 k2 g
-DMTA_0 98.76 0 0 0
+DMTA_0 98.71 0 0 0
k1 0.00 1 0 0
k2 0.00 0 1 0
g 0.00 0 0 1
@@ -1329,40 +1277,40 @@ Results:
Likelihood computed by importance sampling
AIC BIC logLik
- 663.8 661.9 -322.9
+ 663.7 661.8 -322.9
Optimised parameters:
est. lower upper
-DMTA_0 98.228939 96.285869 100.17201
-k1 0.064063 0.033477 0.09465
-k2 0.008297 0.005824 0.01077
-g 0.953821 0.914328 0.99331
-a.1 1.068479 0.869538 1.26742
-b.1 0.029424 0.022406 0.03644
-SD.DMTA_0 2.030437 0.404824 3.65605
-SD.k1 0.594692 0.256660 0.93272
-SD.g 1.006754 0.361327 1.65218
+DMTA_0 98.256267 96.286112 100.22642
+k1 0.064037 0.033281 0.09479
+k2 0.008469 0.006002 0.01094
+g 0.954167 0.914460 0.99387
+a.1 1.061795 0.878608 1.24498
+b.1 0.029550 0.022593 0.03651
+SD.DMTA_0 2.068581 0.427178 3.70998
+SD.k1 0.598285 0.258235 0.93833
+SD.g 1.016689 0.360061 1.67332
Correlation:
DMTA_0 k1 k2
-k1 0.0218
-k2 0.0556 0.0355
-g -0.0516 -0.0284 -0.2800
+k1 0.0213
+k2 0.0541 0.0344
+g -0.0521 -0.0286 -0.2744
Random effects:
est. lower upper
-SD.DMTA_0 2.0304 0.4048 3.6560
-SD.k1 0.5947 0.2567 0.9327
-SD.g 1.0068 0.3613 1.6522
+SD.DMTA_0 2.0686 0.4272 3.7100
+SD.k1 0.5983 0.2582 0.9383
+SD.g 1.0167 0.3601 1.6733
Variance model:
est. lower upper
-a.1 1.06848 0.86954 1.26742
-b.1 0.02942 0.02241 0.03644
+a.1 1.06180 0.87861 1.24498
+b.1 0.02955 0.02259 0.03651
Estimated disappearance times:
- DT50 DT90 DT50back DT50_k1 DT50_k2
-DMTA 11.45 41.4 12.46 10.82 83.54</code></pre>
+ DT50 DT90 DT50back DT50_k1 DT50_k2
+DMTA 11.45 41.32 12.44 10.82 81.85</code></pre>
</div>
<div class="section level3">
<h3 id="alternative-check-of-parameter-identifiability">Alternative check of parameter identifiability<a class="anchor" aria-label="anchor" href="#alternative-check-of-parameter-identifiability"></a>
@@ -1462,11 +1410,11 @@ Erythropoiesis.”</span> <em>BMC Bioinformatics</em> 22 (478). <a href="https:/
Hierarchical mkin fit of the SFO model with error model const
</caption>
<pre><code>
-saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.5
-R version used for fitting: 4.3.0
-Date of fit: Fri May 19 18:14:19 2023
-Date of summary: Fri May 19 18:15:34 2023
+saemix version used for fitting: 3.3
+mkin version used for pre-fitting: 1.2.10
+R version used for fitting: 4.4.2
+Date of fit: Fri Feb 14 08:13:11 2025
+Date of summary: Fri Feb 14 08:14:22 2025
Equations:
d_DMTA/dt = - k_DMTA * DMTA
@@ -1476,7 +1424,7 @@ Data:
Model predictions using solution type analytical
-Fitted in 1.091 s
+Fitted in 0.869 s
Using 300, 100 iterations and 9 chains
Variance model: Constant variance
@@ -1534,11 +1482,11 @@ DMTA 12.24 40.65
Hierarchical mkin fit of the SFO model with error model tc
</caption>
<pre><code>
-saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.5
-R version used for fitting: 4.3.0
-Date of fit: Fri May 19 18:14:21 2023
-Date of summary: Fri May 19 18:15:34 2023
+saemix version used for fitting: 3.3
+mkin version used for pre-fitting: 1.2.10
+R version used for fitting: 4.4.2
+Date of fit: Fri Feb 14 08:13:13 2025
+Date of summary: Fri Feb 14 08:14:22 2025
Equations:
d_DMTA/dt = - k_DMTA * DMTA
@@ -1548,7 +1496,7 @@ Data:
Model predictions using solution type analytical
-Fitted in 2.517 s
+Fitted in 2.423 s
Using 300, 100 iterations and 9 chains
Variance model: Two-component variance function
@@ -1576,13 +1524,13 @@ Likelihood computed by importance sampling
798.3 797.1 -393.2
Optimised parameters:
- est. lower upper
-DMTA_0 97.271822 95.703157 98.84049
-k_DMTA 0.056638 0.029110 0.08417
-a.1 2.660081 2.230398 3.08976
-b.1 0.001665 -0.006911 0.01024
-SD.DMTA_0 1.545520 0.145035 2.94601
-SD.k_DMTA 0.606422 0.262274 0.95057
+ est. lower upper
+DMTA_0 97.271822 95.70316 98.84049
+k_DMTA 0.056638 0.02911 0.08417
+a.1 2.660081 2.27492 3.04525
+b.1 0.001665 -0.14451 0.14784
+SD.DMTA_0 1.545520 0.14301 2.94803
+SD.k_DMTA 0.606422 0.26227 0.95057
Correlation:
DMTA_0
@@ -1590,13 +1538,13 @@ k_DMTA 0.0169
Random effects:
est. lower upper
-SD.DMTA_0 1.5455 0.1450 2.9460
+SD.DMTA_0 1.5455 0.1430 2.9480
SD.k_DMTA 0.6064 0.2623 0.9506
Variance model:
- est. lower upper
-a.1 2.660081 2.230398 3.08976
-b.1 0.001665 -0.006911 0.01024
+ est. lower upper
+a.1 2.660081 2.2749 3.0452
+b.1 0.001665 -0.1445 0.1478
Estimated disappearance times:
DT50 DT90
@@ -1608,11 +1556,11 @@ DMTA 12.24 40.65
Hierarchical mkin fit of the FOMC model with error model const
</caption>
<pre><code>
-saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.5
-R version used for fitting: 4.3.0
-Date of fit: Fri May 19 18:14:20 2023
-Date of summary: Fri May 19 18:15:34 2023
+saemix version used for fitting: 3.3
+mkin version used for pre-fitting: 1.2.10
+R version used for fitting: 4.4.2
+Date of fit: Fri Feb 14 08:13:11 2025
+Date of summary: Fri Feb 14 08:14:22 2025
Equations:
d_DMTA/dt = - (alpha/beta) * 1/((time/beta) + 1) * DMTA
@@ -1622,7 +1570,7 @@ Data:
Model predictions using solution type analytical
-Fitted in 1.25 s
+Fitted in 1.228 s
Using 300, 100 iterations and 9 chains
Variance model: Constant variance
@@ -1654,7 +1602,7 @@ Optimised parameters:
est. lower upper
DMTA_0 98.3435 96.9033 99.784
alpha 7.2007 2.5889 11.812
-beta 112.8746 34.8816 190.868
+beta 112.8745 34.8816 190.867
a.1 2.0459 1.8054 2.286
SD.DMTA_0 1.4795 0.2717 2.687
SD.alpha 0.6396 0.1509 1.128
@@ -1685,11 +1633,11 @@ DMTA 11.41 42.53 12.8
Hierarchical mkin fit of the FOMC model with error model tc
</caption>
<pre><code>
-saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.5
-R version used for fitting: 4.3.0
-Date of fit: Fri May 19 18:14:21 2023
-Date of summary: Fri May 19 18:15:34 2023
+saemix version used for fitting: 3.3
+mkin version used for pre-fitting: 1.2.10
+R version used for fitting: 4.4.2
+Date of fit: Fri Feb 14 08:13:13 2025
+Date of summary: Fri Feb 14 08:14:22 2025
Equations:
d_DMTA/dt = - (alpha/beta) * 1/((time/beta) + 1) * DMTA
@@ -1699,7 +1647,7 @@ Data:
Model predictions using solution type analytical
-Fitted in 2.666 s
+Fitted in 2.87 s
Using 300, 100 iterations and 9 chains
Variance model: Two-component variance function
@@ -1725,38 +1673,38 @@ Results:
Likelihood computed by importance sampling
AIC BIC logLik
- 720.4 718.8 -352.2
+ 720.7 719.1 -352.4
Optimised parameters:
est. lower upper
-DMTA_0 98.99136 97.26011 100.72261
-alpha 5.86312 2.57485 9.15138
-beta 88.55571 29.20889 147.90254
-a.1 1.51063 1.24384 1.77741
-b.1 0.02824 0.02040 0.03609
-SD.DMTA_0 1.57436 -0.04867 3.19739
-SD.alpha 0.59871 0.17132 1.02611
-SD.beta 0.72994 0.22849 1.23139
+DMTA_0 99.10577 97.33296 100.87859
+alpha 5.46260 2.52199 8.40321
+beta 81.66080 30.46664 132.85497
+a.1 1.50219 1.25801 1.74636
+b.1 0.02893 0.02048 0.03739
+SD.DMTA_0 1.61887 -0.03843 3.27618
+SD.alpha 0.58145 0.17364 0.98925
+SD.beta 0.68205 0.21108 1.15302
Correlation:
DMTA_0 alpha
-alpha -0.1363
-beta -0.1414 0.2542
+alpha -0.1321
+beta -0.1430 0.2467
Random effects:
- est. lower upper
-SD.DMTA_0 1.5744 -0.04867 3.197
-SD.alpha 0.5987 0.17132 1.026
-SD.beta 0.7299 0.22849 1.231
+ est. lower upper
+SD.DMTA_0 1.6189 -0.03843 3.2762
+SD.alpha 0.5814 0.17364 0.9892
+SD.beta 0.6821 0.21108 1.1530
Variance model:
- est. lower upper
-a.1 1.51063 1.2438 1.77741
-b.1 0.02824 0.0204 0.03609
+ est. lower upper
+a.1 1.50219 1.25801 1.74636
+b.1 0.02893 0.02048 0.03739
Estimated disappearance times:
- DT50 DT90 DT50back
-DMTA 11.11 42.6 12.82
+ DT50 DT90 DT50back
+DMTA 11.05 42.81 12.89
</code></pre>
<p></p>
@@ -1764,11 +1712,11 @@ DMTA 11.11 42.6 12.82
Hierarchical mkin fit of the DFOP model with error model const
</caption>
<pre><code>
-saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.5
-R version used for fitting: 4.3.0
-Date of fit: Fri May 19 18:14:20 2023
-Date of summary: Fri May 19 18:15:34 2023
+saemix version used for fitting: 3.3
+mkin version used for pre-fitting: 1.2.10
+R version used for fitting: 4.4.2
+Date of fit: Fri Feb 14 08:13:12 2025
+Date of summary: Fri Feb 14 08:14:22 2025
Equations:
d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -1780,7 +1728,7 @@ Data:
Model predictions using solution type analytical
-Fitted in 1.639 s
+Fitted in 1.843 s
Using 300, 100 iterations and 9 chains
Variance model: Constant variance
@@ -1811,10 +1759,10 @@ Likelihood computed by importance sampling
Optimised parameters:
est. lower upper
-DMTA_0 98.092481 96.573898 99.61106
+DMTA_0 98.092481 96.573899 99.61106
k1 0.062499 0.030336 0.09466
k2 0.009065 -0.005133 0.02326
-g 0.948967 0.862079 1.03586
+g 0.948967 0.862080 1.03586
a.1 1.821671 1.604774 2.03857
SD.DMTA_0 1.677785 0.472066 2.88350
SD.k1 0.634962 0.270788 0.99914
@@ -1848,11 +1796,11 @@ DMTA 11.79 42.8 12.88 11.09 76.46
Hierarchical mkin fit of the DFOP model with error model tc
</caption>
<pre><code>
-saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.5
-R version used for fitting: 4.3.0
-Date of fit: Fri May 19 18:14:22 2023
-Date of summary: Fri May 19 18:15:34 2023
+saemix version used for fitting: 3.3
+mkin version used for pre-fitting: 1.2.10
+R version used for fitting: 4.4.2
+Date of fit: Fri Feb 14 08:13:14 2025
+Date of summary: Fri Feb 14 08:14:22 2025
Equations:
d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -1864,21 +1812,21 @@ Data:
Model predictions using solution type analytical
-Fitted in 3.435 s
+Fitted in 3.469 s
Using 300, 100 iterations and 9 chains
Variance model: Two-component variance function
Starting values for degradation parameters:
- DMTA_0 k1 k2 g
-98.759266 0.087034 0.009933 0.930827
+ DMTA_0 k1 k2 g
+98.71186 0.08675 0.01374 0.93491
Fixed degradation parameter values:
None
Starting values for random effects (square root of initial entries in omega):
DMTA_0 k1 k2 g
-DMTA_0 98.76 0 0 0
+DMTA_0 98.71 0 0 0
k1 0.00 1 0 0
k2 0.00 0 1 0
g 0.00 0 0 1
@@ -1891,42 +1839,42 @@ Results:
Likelihood computed by importance sampling
AIC BIC logLik
- 665.5 663.4 -322.8
+ 665.7 663.6 -322.9
Optimised parameters:
est. lower upper
-DMTA_0 98.377019 96.447952 100.30609
-k1 0.064843 0.034607 0.09508
-k2 0.008895 0.006368 0.01142
-g 0.949696 0.903815 0.99558
-a.1 1.065241 0.865754 1.26473
-b.1 0.029340 0.022336 0.03634
-SD.DMTA_0 2.007754 0.387982 3.62753
-SD.k1 0.580473 0.250286 0.91066
-SD.k2 0.006105 -4.920337 4.93255
-SD.g 1.097149 0.412779 1.78152
+DMTA_0 98.347470 96.380815 100.31413
+k1 0.064524 0.034279 0.09477
+k2 0.008304 0.005843 0.01076
+g 0.952128 0.909578 0.99468
+a.1 1.068907 0.883665 1.25415
+b.1 0.029265 0.022318 0.03621
+SD.DMTA_0 2.065796 0.427951 3.70364
+SD.k1 0.583703 0.251796 0.91561
+SD.k2 0.004167 -7.831228 7.83956
+SD.g 1.064450 0.397479 1.73142
Correlation:
DMTA_0 k1 k2
-k1 0.0235
-k2 0.0595 0.0424
-g -0.0470 -0.0278 -0.2731
+k1 0.0223
+k2 0.0568 0.0394
+g -0.0464 -0.0269 -0.2713
Random effects:
est. lower upper
-SD.DMTA_0 2.007754 0.3880 3.6275
-SD.k1 0.580473 0.2503 0.9107
-SD.k2 0.006105 -4.9203 4.9325
-SD.g 1.097149 0.4128 1.7815
+SD.DMTA_0 2.065796 0.4280 3.7036
+SD.k1 0.583703 0.2518 0.9156
+SD.k2 0.004167 -7.8312 7.8396
+SD.g 1.064450 0.3975 1.7314
Variance model:
est. lower upper
-a.1 1.06524 0.86575 1.26473
-b.1 0.02934 0.02234 0.03634
+a.1 1.06891 0.88367 1.25415
+b.1 0.02927 0.02232 0.03621
Estimated disappearance times:
DT50 DT90 DT50back DT50_k1 DT50_k2
-DMTA 11.36 41.32 12.44 10.69 77.92
+DMTA 11.39 41.36 12.45 10.74 83.48
</code></pre>
<p></p>
@@ -1934,11 +1882,11 @@ DMTA 11.36 41.32 12.44 10.69 77.92
Hierarchical mkin fit of the HS model with error model const
</caption>
<pre><code>
-saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.5
-R version used for fitting: 4.3.0
-Date of fit: Fri May 19 18:14:20 2023
-Date of summary: Fri May 19 18:15:34 2023
+saemix version used for fitting: 3.3
+mkin version used for pre-fitting: 1.2.10
+R version used for fitting: 4.4.2
+Date of fit: Fri Feb 14 08:13:12 2025
+Date of summary: Fri Feb 14 08:14:22 2025
Equations:
d_DMTA/dt = - ifelse(time &lt;= tb, k1, k2) * DMTA
@@ -1948,7 +1896,7 @@ Data:
Model predictions using solution type analytical
-Fitted in 1.946 s
+Fitted in 1.698 s
Using 300, 100 iterations and 9 chains
Variance model: Constant variance
@@ -2016,11 +1964,11 @@ DMTA 8.801 67.91 20.44 8.801 31.13
Hierarchical mkin fit of the HS model with error model tc
</caption>
<pre><code>
-saemix version used for fitting: 3.2
-mkin version used for pre-fitting: 1.2.5
-R version used for fitting: 4.3.0
-Date of fit: Fri May 19 18:14:22 2023
-Date of summary: Fri May 19 18:15:34 2023
+saemix version used for fitting: 3.3
+mkin version used for pre-fitting: 1.2.10
+R version used for fitting: 4.4.2
+Date of fit: Fri Feb 14 08:13:13 2025
+Date of summary: Fri Feb 14 08:14:22 2025
Equations:
d_DMTA/dt = - ifelse(time &lt;= tb, k1, k2) * DMTA
@@ -2030,7 +1978,7 @@ Data:
Model predictions using solution type analytical
-Fitted in 3.626 s
+Fitted in 3.307 s
Using 300, 100 iterations and 9 chains
Variance model: Two-component variance function
@@ -2061,16 +2009,16 @@ Likelihood computed by importance sampling
Optimised parameters:
est. lower upper
-DMTA_0 97.76570 95.81350 99.71791
+DMTA_0 97.76571 95.81350 99.71791
k1 0.05855 0.03080 0.08630
k2 0.02337 0.01664 0.03010
tb 31.09638 29.38289 32.80987
-a.1 1.08835 0.88590 1.29080
-b.1 0.02964 0.02257 0.03671
-SD.DMTA_0 2.04877 0.42607 3.67147
+a.1 1.08835 0.90059 1.27611
+b.1 0.02964 0.02261 0.03667
+SD.DMTA_0 2.04877 0.42553 3.67200
SD.k1 0.59166 0.25621 0.92711
SD.k2 0.30698 0.09561 0.51835
-SD.tb 0.01274 -0.10914 0.13462
+SD.tb 0.01274 -0.10915 0.13464
Correlation:
DMTA_0 k1 k2
@@ -2080,15 +2028,15 @@ tb -0.0668 -0.0103 -0.2013
Random effects:
est. lower upper
-SD.DMTA_0 2.04877 0.42607 3.6715
+SD.DMTA_0 2.04877 0.42553 3.6720
SD.k1 0.59166 0.25621 0.9271
SD.k2 0.30698 0.09561 0.5183
-SD.tb 0.01274 -0.10914 0.1346
+SD.tb 0.01274 -0.10915 0.1346
Variance model:
est. lower upper
-a.1 1.08835 0.88590 1.29080
-b.1 0.02964 0.02257 0.03671
+a.1 1.08835 0.90059 1.27611
+b.1 0.02964 0.02261 0.03667
Estimated disappearance times:
DT50 DT90 DT50back DT50_k1 DT50_k2
@@ -2144,13 +2092,13 @@ Convergence plot for the NLHM HS fit with two-component error
<div class="section level3">
<h3 id="session-info">Session info<a class="anchor" aria-label="anchor" href="#session-info"></a>
</h3>
-<pre><code>R version 4.3.0 (2023-04-21)
-Platform: x86_64-pc-linux-gnu (64-bit)
+<pre><code>R version 4.4.2 (2024-10-31)
+Platform: x86_64-pc-linux-gnu
Running under: Debian GNU/Linux 12 (bookworm)
Matrix products: default
-BLAS: /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3
-LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so; LAPACK version 3.11.0
+BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0
+LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0
locale:
[1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C
@@ -2168,60 +2116,51 @@ attached base packages:
[8] base
other attached packages:
-[1] saemix_3.2 npde_3.3 knitr_1.42 mkin_1.2.5
+[1] rmarkdown_2.29 nvimcom_0.9-167 saemix_3.3 npde_3.5
+[5] knitr_1.49 mkin_1.2.10
loaded via a namespace (and not attached):
- [1] sass_0.4.6 utf8_1.2.3 generics_0.1.3 stringi_1.7.12
- [5] lattice_0.21-8 digest_0.6.31 magrittr_2.0.3 evaluate_0.21
- [9] grid_4.3.0 fastmap_1.1.1 rprojroot_2.0.3 jsonlite_1.8.4
-[13] DBI_1.1.3 mclust_6.0.0 gridExtra_2.3 purrr_1.0.1
-[17] fansi_1.0.4 scales_1.2.1 codetools_0.2-19 textshaping_0.3.6
-[21] jquerylib_0.1.4 cli_3.6.1 rlang_1.1.1 munsell_0.5.0
-[25] cachem_1.0.8 yaml_2.3.7 tools_4.3.0 memoise_2.0.1
-[29] dplyr_1.1.2 colorspace_2.1-0 ggplot2_3.4.2 vctrs_0.6.2
-[33] R6_2.5.1 zoo_1.8-12 lifecycle_1.0.3 stringr_1.5.0
-[37] fs_1.6.2 ragg_1.2.5 pkgconfig_2.0.3 desc_1.4.2
-[41] pkgdown_2.0.7 bslib_0.4.2 pillar_1.9.0 gtable_0.3.3
-[45] glue_1.6.2 systemfonts_1.0.4 highr_0.10 xfun_0.39
-[49] tibble_3.2.1 lmtest_0.9-40 tidyselect_1.2.0 htmltools_0.5.5
-[53] nlme_3.1-162 rmarkdown_2.21 compiler_4.3.0 </code></pre>
+ [1] gtable_0.3.6 jsonlite_1.8.9 dplyr_1.1.4 compiler_4.4.2
+ [5] tidyselect_1.2.1 gridExtra_2.3 jquerylib_0.1.4 systemfonts_1.1.0
+ [9] scales_1.3.0 textshaping_0.4.1 yaml_2.3.10 fastmap_1.2.0
+[13] lattice_0.22-6 ggplot2_3.5.1 R6_2.5.1 generics_0.1.3
+[17] lmtest_0.9-40 MASS_7.3-61 htmlwidgets_1.6.4 tibble_3.2.1
+[21] desc_1.4.3 munsell_0.5.1 bslib_0.8.0 pillar_1.9.0
+[25] rlang_1.1.4 utf8_1.2.4 cachem_1.1.0 xfun_0.49
+[29] fs_1.6.5 sass_0.4.9 cli_3.6.3 pkgdown_2.1.1
+[33] magrittr_2.0.3 digest_0.6.37 grid_4.4.2 mclust_6.1.1
+[37] lifecycle_1.0.4 nlme_3.1-166 vctrs_0.6.5 evaluate_1.0.1
+[41] glue_1.8.0 codetools_0.2-20 ragg_1.3.3 zoo_1.8-12
+[45] fansi_1.0.6 colorspace_2.1-1 pkgconfig_2.0.3 tools_4.4.2
+[49] htmltools_0.5.8.1</code></pre>
</div>
<div class="section level3">
<h3 id="hardware-info">Hardware info<a class="anchor" aria-label="anchor" href="#hardware-info"></a>
</h3>
<pre><code>CPU model: AMD Ryzen 9 7950X 16-Core Processor</code></pre>
-<pre><code>MemTotal: 64925476 kB</code></pre>
+<pre><code>MemTotal: 64927788 kB</code></pre>
</div>
</div>
- </div>
-
- <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
-
- <nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2>
- </nav>
-</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="copyright">
- <p></p>
-<p>Developed by Johannes Ranke.</p>
+ <footer><div class="pkgdown-footer-left">
+ <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 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>
+ </footer>
</div>
-
-
+
</body>
</html>

Contact - Imprint