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Diffstat (limited to 'docs/dev/reference/dimethenamid_2018.html')
| -rw-r--r-- | docs/dev/reference/dimethenamid_2018.html | 85 |
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">#></span> saemix version used for fitting: 3.2 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.2 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Nov 24 08:05:16 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Nov 24 08:05:16 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.3 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.3 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Sun Apr 16 08:30:03 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Sun Apr 16 08:30:03 2023 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></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">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type deSolve </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 819.725 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 304.528 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 9 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Two-component variance function </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Mean of starting values for individual parameters:</span> +<span class="r-out co"><span class="r-pr">#></span> Starting values for degradation parameters:</span> <span class="r-out co"><span class="r-pr">#></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">#></span> 95.5662 -2.9048 -3.8130 -4.1600 -4.1486 0.1341 </span> <span class="r-out co"><span class="r-pr">#></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">#></span> Fixed degradation parameter values:</span> <span class="r-out co"><span class="r-pr">#></span> None</span> <span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Starting values for random effects (square root of initial entries in omega):</span> +<span class="r-out co"><span class="r-pr">#></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">#></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">#></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">#></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">#></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">#></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">#></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">#></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">#></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">#></span> f_DMTA_ilr_2 f_DMTA_ilr_3</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_0 0.0000 0.0000</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_DMTA 0.0000 0.0000</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M23 0.0000 0.0000</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M27 0.0000 0.0000</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M31 0.0000 0.0000</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 0.0000 0.0000</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 0.7378 0.0000</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 0.0000 0.4451</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Starting values for error model parameters:</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 b.1 </span> +<span class="r-out co"><span class="r-pr">#></span> 1 1 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Results:</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></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">#></span> f_DMTA_ilr_1 0.1346 -0.2150 0.4841</span> <span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 0.1449 -0.2593 0.5491</span> <span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -1.3882 -1.7011 -1.0753</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 0.9156 0.8229 1.0084</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.1383 0.1215 0.1551</span> -<span class="r-out co"><span class="r-pr">#></span> SD.DMTA_0 3.7280 -0.6951 8.1511</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.9156 0.8217 1.0095</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.1383 0.1216 0.1550</span> +<span class="r-out co"><span class="r-pr">#></span> SD.DMTA_0 3.7280 -0.6949 8.1508</span> <span class="r-out co"><span class="r-pr">#></span> SD.log_k_DMTA 0.6431 0.2781 1.0080</span> <span class="r-out co"><span class="r-pr">#></span> SD.log_k_M23 1.0096 0.3782 1.6409</span> <span class="r-out co"><span class="r-pr">#></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">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Random effects:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> SD.DMTA_0 3.7280 -0.6951 8.1511</span> +<span class="r-out co"><span class="r-pr">#></span> SD.DMTA_0 3.7280 -0.6949 8.1508</span> <span class="r-out co"><span class="r-pr">#></span> SD.log_k_DMTA 0.6431 0.2781 1.0080</span> <span class="r-out co"><span class="r-pr">#></span> SD.log_k_M23 1.0096 0.3782 1.6409</span> <span class="r-out co"><span class="r-pr">#></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">#></span> SD.f_DMTA_ilr_3 0.3657 0.1383 0.5931</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model:</span> -<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 0.9156 0.8229 1.0084</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.1383 0.1215 0.1551</span> +<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.9156 0.8217 1.009</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.1383 0.1216 0.155</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> @@ -335,7 +376,7 @@ specific pieces of information in the comments.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> 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