diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2023-04-20 19:53:28 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2023-04-20 20:03:32 +0200 |
| commit | 9ae42bd20bc2543a94cf1581ba9820c2f9e3afbd (patch) | |
| tree | b3539a9689f5930b8444a5fc459781b825e00fa4 /docs/reference/summary.nlme.mmkin.html | |
| parent | ad0efc2d16a84c674307ad2df9d44153b44a9cf8 (diff) | |
Fix and rebuild documentation, see NEWS
I had to fix the two pathway vignettes, as they did not work with
the released version any more. So they and the multistart vignette
which got some small fixes as well were rebuilt.
Complete rebuild of the online docs with the released version. The
documentation of the 'hierarchial_kinetics' format had to be fixed
as well.
Diffstat (limited to 'docs/reference/summary.nlme.mmkin.html')
| -rw-r--r-- | docs/reference/summary.nlme.mmkin.html | 60 |
1 files changed, 38 insertions, 22 deletions
diff --git a/docs/reference/summary.nlme.mmkin.html b/docs/reference/summary.nlme.mmkin.html index eb01ef7a..64ae46c4 100644 --- a/docs/reference/summary.nlme.mmkin.html +++ b/docs/reference/summary.nlme.mmkin.html @@ -21,13 +21,13 @@ endpoints such as formation fractions and DT50 values. Optionally </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"> @@ -38,6 +38,8 @@ endpoints such as formation fractions and DT50 values. Optionally <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> @@ -45,22 +47,29 @@ endpoints such as formation fractions and DT50 values. Optionally <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> @@ -68,6 +77,14 @@ endpoints such as formation fractions and DT50 values. Optionally <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> @@ -233,13 +250,12 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Optimisation did not converge:</span> <span class="r-wrn co"><span class="r-pr">#></span> iteration limit reached without convergence (10)</span> <span class="r-in"><span><span class="va">f_nlme</span> <span class="op"><-</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_mmkin</span><span class="op">)</span></span></span> -<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Iteration 4, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span> <span class="r-in"><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_nlme</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> nlme version used for fitting: 3.1.160 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.0 </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 17 14:03:27 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Nov 17 14:03:27 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> nlme version used for fitting: 3.1.162 </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: Thu Apr 20 07:36:43 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Apr 20 07:36:43 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_parent/dt = - k_parent * parent</span> @@ -249,7 +265,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</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 analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.538 s using 4 iterations</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.187 s using 4 iterations</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> @@ -278,15 +294,15 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-out co"><span class="r-pr">#></span> Formula: list(parent_0 ~ 1, log_k_parent ~ 1)</span> <span class="r-out co"><span class="r-pr">#></span> Level: ds</span> <span class="r-out co"><span class="r-pr">#></span> Structure: Diagonal</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_parent Residual</span> -<span class="r-out co"><span class="r-pr">#></span> StdDev: 6.924e-05 0.5863 1</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_parent Residual</span> +<span class="r-out co"><span class="r-pr">#></span> StdDev: 6.92e-05 0.5863 1</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance function:</span> <span class="r-out co"><span class="r-pr">#></span> Structure: Constant plus proportion of variance covariate</span> <span class="r-out co"><span class="r-pr">#></span> Formula: ~fitted(.) </span> <span class="r-out co"><span class="r-pr">#></span> Parameter estimates:</span> <span class="r-out co"><span class="r-pr">#></span> const prop </span> -<span class="r-out co"><span class="r-pr">#></span> 0.0001208853 0.0789968036 </span> +<span class="r-out co"><span class="r-pr">#></span> 0.0001208154 0.0789968021 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters with asymmetric confidence intervals:</span> <span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> @@ -365,8 +381,8 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-out co"><span class="r-pr">#></span> ds 4 parent 14 104.8 95.234 9.56590 7.5232 1.271521</span> <span class="r-out co"><span class="r-pr">#></span> ds 4 parent 28 85.0 89.274 -4.27372 7.0523 -0.606001</span> <span class="r-out co"><span class="r-pr">#></span> ds 4 parent 28 77.2 89.274 -12.07372 7.0523 -1.712017</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 82.2 77.013 5.18661 6.0838 0.852526</span> -<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 86.1 77.013 9.08661 6.0838 1.493571</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 82.2 77.013 5.18660 6.0838 0.852526</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 86.1 77.013 9.08660 6.0838 1.493571</span> <span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 70.5 67.053 3.44692 5.2970 0.650733</span> <span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 61.7 67.053 -5.35308 5.2970 -1.010591</span> <span class="r-out co"><span class="r-pr">#></span> ds 4 parent 120 60.0 58.381 1.61905 4.6119 0.351058</span> @@ -376,7 +392,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-out co"><span class="r-pr">#></span> ds 5 parent 1 108.0 99.914 8.08560 7.8929 1.024413</span> <span class="r-out co"><span class="r-pr">#></span> ds 5 parent 1 104.9 99.914 4.98560 7.8929 0.631655</span> <span class="r-out co"><span class="r-pr">#></span> ds 5 parent 3 100.5 96.641 3.85898 7.6343 0.505477</span> -<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 3 89.5 96.641 -7.14102 7.6343 -0.935382</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 3 89.5 96.641 -7.14102 7.6343 -0.935383</span> <span class="r-out co"><span class="r-pr">#></span> ds 5 parent 7 91.7 90.412 1.28752 7.1423 0.180267</span> <span class="r-out co"><span class="r-pr">#></span> ds 5 parent 7 95.1 90.412 4.68752 7.1423 0.656304</span> <span class="r-out co"><span class="r-pr">#></span> ds 5 parent 14 82.2 80.463 1.73715 6.3563 0.273295</span> @@ -405,7 +421,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</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> + <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> |