aboutsummaryrefslogtreecommitdiff
path: root/docs/reference/nlme.mmkin.html
diff options
context:
space:
mode:
authorJohannes Ranke <jranke@uni-bremen.de>2023-04-20 20:17:12 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2023-04-20 20:17:12 +0200
commit7b7c4bf493ba15824ea43bed764661678b4aca03 (patch)
tree48de1e32327c36ee49fc476dc76ece8397ab55c6 /docs/reference/nlme.mmkin.html
parent842998b688037c007d8876d7e1110c929fe2374c (diff)
parent9ae42bd20bc2543a94cf1581ba9820c2f9e3afbd (diff)
Merge branch 'v1.2.3_pkgdown'
Diffstat (limited to 'docs/reference/nlme.mmkin.html')
-rw-r--r--docs/reference/nlme.mmkin.html53
1 files changed, 35 insertions, 18 deletions
diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html
index 1e294eaf..d446a2a2 100644
--- a/docs/reference/nlme.mmkin.html
+++ b/docs/reference/nlme.mmkin.html
@@ -19,13 +19,13 @@ have been obtained by fitting the same model to a list of datasets."><!-- mathja
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.3</span>
</span>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav"><li>
- <a href="../reference/index.html">Functions and data</a>
+ <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">
@@ -36,6 +36,8 @@ have been obtained by fitting the same model to a list of datasets."><!-- mathja
<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>
@@ -43,22 +45,29 @@ have been obtained by fitting the same model to a list of datasets."><!-- mathja
<a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
</li>
<li>
- <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
+ <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/web_only/multistart.html">Short demo of the multistart method</a>
+ <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/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+ <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/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a>
</li>
<li>
- <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+ <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/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
+ <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>
@@ -66,6 +75,14 @@ have been obtained by fitting the same model to a list of datasets."><!-- mathja
<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>
@@ -239,7 +256,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_nlme_sfo</span>, <span class="va">f_nlme_dfop</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Model df AIC BIC logLik Test L.Ratio p-value</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f_nlme_sfo 1 5 625.0539 637.5529 -307.5269 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> f_nlme_dfop 2 9 495.1270 517.6253 -238.5635 1 vs 2 137.9269 &lt;.0001</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_nlme_dfop 2 9 495.1270 517.6253 -238.5635 1 vs 2 137.9268 &lt;.0001</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">f_nlme_dfop</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Kinetic nonlinear mixed-effects model fit by maximum likelihood</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
@@ -270,7 +287,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
<span class="r-in"><span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">f_nlme_dfop</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $distimes</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> DT50 DT90 DT50back DT50_k1 DT50_k2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> parent 10.79857 100.7937 30.34193 4.193938 43.85443</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent 10.79857 100.7937 30.34192 4.193936 43.85441</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="va">ds_2</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">experimental_data_for_UBA_2019</span><span class="op">[</span><span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
@@ -321,12 +338,12 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
<span class="r-in"><span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">f_nlme_dfop_sfo</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $ff</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_A1 parent_sink </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 0.2768574 0.7231426 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 0.2768575 0.7231425 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $distimes</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> DT50 DT90 DT50back DT50_k1 DT50_k2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> parent 11.07091 104.6320 31.49737 4.462383 46.20825</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> A1 162.30519 539.1662 NA NA NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> parent 11.07091 104.6320 31.49737 4.462384 46.20825</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> A1 162.30507 539.1658 NA NA NA</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="fu">findFunction</span><span class="op">(</span><span class="st">"varConstProp"</span><span class="op">)</span><span class="op">)</span> <span class="op">&gt;</span> <span class="fl">0</span><span class="op">)</span> <span class="op">{</span> <span class="co"># tc error model for nlme available</span></span></span>
@@ -354,7 +371,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
<span class="r-out co"><span class="r-pr">#&gt;</span> Fixed effects:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent_0 log_k1 log_k2 g_qlogis </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 94.04774 -1.82340 -4.16716 0.05686 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 94.04773 -1.82340 -4.16716 0.05686 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Random effects:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1)</span>
@@ -368,7 +385,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
<span class="r-out co"><span class="r-pr">#&gt;</span> Formula: ~fitted(.) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Parameter estimates:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> const prop </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2.23223147 0.01262395 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2.23223593 0.01262367 </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span> <span class="va">f_2_obs</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_2</span>, error_model <span class="op">=</span> <span class="st">"obs"</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="va">f_nlme_sfo_sfo_obs</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_2_obs</span><span class="op">[</span><span class="st">"SFO-SFO"</span>, <span class="op">]</span><span class="op">)</span></span></span>
@@ -401,7 +418,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
<span class="r-out co"><span class="r-pr">#&gt;</span> Formula: ~1 | name </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Parameter estimates:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent A1 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1.0000000 0.2049995 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1.0000000 0.2049994 </span>
<span class="r-in"><span> <span class="va">f_nlme_dfop_sfo_obs</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_2_obs</span><span class="op">[</span><span class="st">"DFOP-SFO"</span>, <span class="op">]</span>,</span></span>
<span class="r-in"><span> control <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>pnlsMaxIter <span class="op">=</span> <span class="fl">120</span>, tolerance <span class="op">=</span> <span class="fl">5e-4</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
@@ -413,7 +430,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_nlme_dfop_sfo</span>, <span class="va">f_nlme_dfop_sfo_obs</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Model df AIC BIC logLik Test L.Ratio</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9274 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> f_nlme_dfop_sfo_obs 2 14 817.5338 861.4350 -394.7669 1 vs 2 28.32091</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_nlme_dfop_sfo_obs 2 14 817.5338 861.4350 -394.7669 1 vs 2 28.32093</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> p-value</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f_nlme_dfop_sfo </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f_nlme_dfop_sfo_obs &lt;.0001</span>
@@ -433,7 +450,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
</div>
<div class="pkgdown">
- <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+ <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>

Contact - Imprint