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authorJohannes Ranke <jranke@uni-bremen.de>2023-04-16 13:42:23 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2023-04-16 13:42:23 +0200
commit34ec60f1b140d788880d84b70cb62b344f7d74b9 (patch)
tree26196c367f037b69f410363a393dad87b5bff233 /docs/dev/reference/dimethenamid_2018.html
parent99b4554a1ce657295b1358509110f3d02155a913 (diff)
Complete rebuild of static docs
Diffstat (limited to 'docs/dev/reference/dimethenamid_2018.html')
-rw-r--r--docs/dev/reference/dimethenamid_2018.html85
1 files changed, 63 insertions, 22 deletions
diff --git a/docs/dev/reference/dimethenamid_2018.html b/docs/dev/reference/dimethenamid_2018.html
index 96ec73c6..0fcd0c61 100644
--- a/docs/dev/reference/dimethenamid_2018.html
+++ b/docs/dev/reference/dimethenamid_2018.html
@@ -22,13 +22,13 @@ constrained by data protection regulations."><meta name="robots" content="noinde
</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">1.2.2</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development 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">
@@ -39,6 +39,8 @@ constrained by data protection regulations."><meta name="robots" content="noinde
<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>
@@ -46,22 +48,29 @@ constrained by data protection regulations."><meta name="robots" content="noinde
<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>
@@ -69,6 +78,14 @@ constrained by data protection regulations."><meta name="robots" content="noinde
<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>
@@ -205,10 +222,10 @@ specific pieces of information in the comments.</p>
<span class="r-in"><span><span class="co">#saemix::plot(f_dmta_saem_tc$so, plot.type = "convergence")</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_dmta_saem_tc</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> saemix version used for fitting: 3.2 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for pre-fitting: 1.2.2 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting: 4.2.2 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit: Thu Nov 24 08:05:16 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Thu Nov 24 08:05:16 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for pre-fitting: 1.2.3 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting: 4.2.3 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit: Sun Apr 16 08:30:03 2023 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Sun Apr 16 08:30:03 2023 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Equations:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> d_DMTA/dt = - k_DMTA * DMTA</span>
@@ -221,12 +238,12 @@ specific pieces of information in the comments.</p>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Model predictions using solution type deSolve </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 819.725 s</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 304.528 s</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Using 300, 100 iterations and 9 chains</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Variance model: Two-component variance function </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Mean of starting values for individual parameters:</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Starting values for degradation parameters:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> DMTA_0 log_k_DMTA log_k_M23 log_k_M27 log_k_M31 f_DMTA_ilr_1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 95.5662 -2.9048 -3.8130 -4.1600 -4.1486 0.1341 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f_DMTA_ilr_2 f_DMTA_ilr_3 </span>
@@ -235,6 +252,30 @@ specific pieces of information in the comments.</p>
<span class="r-out co"><span class="r-pr">#&gt;</span> Fixed degradation parameter values:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> None</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Starting values for random effects (square root of initial entries in omega):</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> DMTA_0 log_k_DMTA log_k_M23 log_k_M27 log_k_M31 f_DMTA_ilr_1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> DMTA_0 4.802 0.0000 0.0000 0.000 0.0000 0.0000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_DMTA 0.000 0.9834 0.0000 0.000 0.0000 0.0000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_M23 0.000 0.0000 0.6983 0.000 0.0000 0.0000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_M27 0.000 0.0000 0.0000 1.028 0.0000 0.0000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_M31 0.000 0.0000 0.0000 0.000 0.9841 0.0000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_DMTA_ilr_1 0.000 0.0000 0.0000 0.000 0.0000 0.7185</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_DMTA_ilr_2 0.000 0.0000 0.0000 0.000 0.0000 0.0000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_DMTA_ilr_3 0.000 0.0000 0.0000 0.000 0.0000 0.0000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_DMTA_ilr_2 f_DMTA_ilr_3</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> DMTA_0 0.0000 0.0000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_DMTA 0.0000 0.0000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_M23 0.0000 0.0000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_M27 0.0000 0.0000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> log_k_M31 0.0000 0.0000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_DMTA_ilr_1 0.0000 0.0000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_DMTA_ilr_2 0.7378 0.0000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> f_DMTA_ilr_3 0.0000 0.4451</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Starting values for error model parameters:</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> a.1 b.1 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Results:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Likelihood computed by importance sampling</span>
@@ -251,9 +292,9 @@ specific pieces of information in the comments.</p>
<span class="r-out co"><span class="r-pr">#&gt;</span> f_DMTA_ilr_1 0.1346 -0.2150 0.4841</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f_DMTA_ilr_2 0.1449 -0.2593 0.5491</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> f_DMTA_ilr_3 -1.3882 -1.7011 -1.0753</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> a.1 0.9156 0.8229 1.0084</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> b.1 0.1383 0.1215 0.1551</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> SD.DMTA_0 3.7280 -0.6951 8.1511</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> a.1 0.9156 0.8217 1.0095</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> b.1 0.1383 0.1216 0.1550</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> SD.DMTA_0 3.7280 -0.6949 8.1508</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> SD.log_k_DMTA 0.6431 0.2781 1.0080</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> SD.log_k_M23 1.0096 0.3782 1.6409</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> SD.log_k_M27 0.4583 0.1541 0.7625</span>
@@ -274,7 +315,7 @@ specific pieces of information in the comments.</p>
<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> est. lower upper</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> SD.DMTA_0 3.7280 -0.6951 8.1511</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> SD.DMTA_0 3.7280 -0.6949 8.1508</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> SD.log_k_DMTA 0.6431 0.2781 1.0080</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> SD.log_k_M23 1.0096 0.3782 1.6409</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> SD.log_k_M27 0.4583 0.1541 0.7625</span>
@@ -284,9 +325,9 @@ specific pieces of information in the comments.</p>
<span class="r-out co"><span class="r-pr">#&gt;</span> SD.f_DMTA_ilr_3 0.3657 0.1383 0.5931</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Variance model:</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> est. lower upper</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> a.1 0.9156 0.8229 1.0084</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> b.1 0.1383 0.1215 0.1551</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> est. lower upper</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> a.1 0.9156 0.8217 1.009</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> b.1 0.1383 0.1216 0.155</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Backtransformed parameters:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> est. lower upper</span>
@@ -335,7 +376,7 @@ specific pieces of information in the comments.</p>
</div>
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- <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>
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