diff options
Diffstat (limited to 'docs/reference')
157 files changed, 400 insertions, 152 deletions
diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html index 15df31b6..78296f28 100644 --- a/docs/reference/AIC.mmkin.html +++ b/docs/reference/AIC.mmkin.html @@ -18,7 +18,7 @@ same dataset."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/li </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -55,6 +55,9 @@ same dataset."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/CAKE_export.html b/docs/reference/CAKE_export.html index 50f4599f..92cb2755 100644 --- a/docs/reference/CAKE_export.html +++ b/docs/reference/CAKE_export.html @@ -18,7 +18,7 @@ specified as well."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/aj </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -55,6 +55,9 @@ specified as well."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/aj <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/DFOP.solution-1.png b/docs/reference/DFOP.solution-1.png Binary files differindex 6b78836f..5ebba336 100644 --- a/docs/reference/DFOP.solution-1.png +++ b/docs/reference/DFOP.solution-1.png diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index ee7f7888..b526ac9e 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -18,7 +18,7 @@ two exponential decline functions."><!-- mathjax --><script src="https://cdnjs.c </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -55,6 +55,9 @@ two exponential decline functions."><!-- mathjax --><script src="https://cdnjs.c <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 81995a34..76a2cda8 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -17,7 +17,7 @@ </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -54,6 +54,9 @@ <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html index b9d4e4cf..2483a632 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -21,7 +21,7 @@ in this fit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/lib </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -58,6 +58,9 @@ in this fit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/lib <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html index 0f62dc27..d3ee5aba 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -21,7 +21,7 @@ in this fit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/lib </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -58,6 +58,9 @@ in this fit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/lib <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html index 4339fd5d..cb563cdf 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -21,7 +21,7 @@ in this fit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/lib </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -58,6 +58,9 @@ in this fit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/lib <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html index eb7162a1..93fc9030 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -21,7 +21,7 @@ in this fit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/lib </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -58,6 +58,9 @@ in this fit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/lib <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index 51e699a1..f1343c5c 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -17,7 +17,7 @@ </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -54,6 +54,9 @@ <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/FOMC.solution-1.png b/docs/reference/FOMC.solution-1.png Binary files differindex 18a4b586..9d222d42 100644 --- a/docs/reference/FOMC.solution-1.png +++ b/docs/reference/FOMC.solution-1.png diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index 4ae477f8..e5087117 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -18,7 +18,7 @@ a decreasing rate constant."><!-- mathjax --><script src="https://cdnjs.cloudfla </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -55,6 +55,9 @@ a decreasing rate constant."><!-- mathjax --><script src="https://cdnjs.cloudfla <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/HS.solution-1.png b/docs/reference/HS.solution-1.png Binary files differindex 61d89dbc..dd7a76c8 100644 --- a/docs/reference/HS.solution-1.png +++ b/docs/reference/HS.solution-1.png diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 61fbc41c..d24015a0 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -18,7 +18,7 @@ between them."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/li </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -55,6 +55,9 @@ between them."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/IORE.solution-1.png b/docs/reference/IORE.solution-1.png Binary files differindex 54c9dcae..9b6ab58f 100644 --- a/docs/reference/IORE.solution-1.png +++ b/docs/reference/IORE.solution-1.png diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index 942c86ca..0ab484cd 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -18,7 +18,7 @@ a concentration dependent rate constant."><!-- mathjax --><script src="https://c </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -55,6 +55,9 @@ a concentration dependent rate constant."><!-- mathjax --><script src="https://c <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/NAFTA_SOP_2015-1.png b/docs/reference/NAFTA_SOP_2015-1.png Binary files differindex 98d4246c..5d2d434b 100644 --- a/docs/reference/NAFTA_SOP_2015-1.png +++ b/docs/reference/NAFTA_SOP_2015-1.png diff --git a/docs/reference/NAFTA_SOP_2015.html b/docs/reference/NAFTA_SOP_2015.html index 86610f6e..9a4f668e 100644 --- a/docs/reference/NAFTA_SOP_2015.html +++ b/docs/reference/NAFTA_SOP_2015.html @@ -17,7 +17,7 @@ </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -54,6 +54,9 @@ <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/NAFTA_SOP_Attachment-1.png b/docs/reference/NAFTA_SOP_Attachment-1.png Binary files differindex a6066441..d8951fc3 100644 --- a/docs/reference/NAFTA_SOP_Attachment-1.png +++ b/docs/reference/NAFTA_SOP_Attachment-1.png diff --git a/docs/reference/NAFTA_SOP_Attachment.html b/docs/reference/NAFTA_SOP_Attachment.html index 7f72e172..02b33e7d 100644 --- a/docs/reference/NAFTA_SOP_Attachment.html +++ b/docs/reference/NAFTA_SOP_Attachment.html @@ -17,7 +17,7 @@ </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -54,6 +54,9 @@ <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png Binary files differindex fa2316b9..ca982688 100644 --- a/docs/reference/Rplot001.png +++ b/docs/reference/Rplot001.png diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png Binary files differindex fa2316b9..de2d61aa 100644 --- a/docs/reference/Rplot002.png +++ b/docs/reference/Rplot002.png diff --git a/docs/reference/Rplot003.png b/docs/reference/Rplot003.png Binary files differindex fa2316b9..8fd02b8e 100644 --- a/docs/reference/Rplot003.png +++ b/docs/reference/Rplot003.png diff --git a/docs/reference/Rplot004.png b/docs/reference/Rplot004.png Binary files differindex d5fef0f0..2c12ceb1 100644 --- a/docs/reference/Rplot004.png +++ b/docs/reference/Rplot004.png diff --git a/docs/reference/Rplot005.png b/docs/reference/Rplot005.png Binary files differindex 7274c79d..1d28b587 100644 --- a/docs/reference/Rplot005.png +++ b/docs/reference/Rplot005.png diff --git a/docs/reference/Rplot006.png b/docs/reference/Rplot006.png Binary files differindex f646fa66..48f5bbd8 100644 --- a/docs/reference/Rplot006.png +++ b/docs/reference/Rplot006.png diff --git a/docs/reference/Rplot007.png b/docs/reference/Rplot007.png Binary files differindex d3b6ddd4..21a6ea76 100644 --- a/docs/reference/Rplot007.png +++ b/docs/reference/Rplot007.png diff --git a/docs/reference/SFO.solution-1.png b/docs/reference/SFO.solution-1.png Binary files differindex 34fdd460..a00499cb 100644 --- a/docs/reference/SFO.solution-1.png +++ b/docs/reference/SFO.solution-1.png diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index b5aff531..67c7abc7 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -17,7 +17,7 @@ </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -54,6 +54,9 @@ <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/SFORB.solution-1.png b/docs/reference/SFORB.solution-1.png Binary files differindex 08d25616..7bea3b78 100644 --- a/docs/reference/SFORB.solution-1.png +++ b/docs/reference/SFORB.solution-1.png diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 490fbbb5..a99deac7 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -21,7 +21,7 @@ and no substance in the bound fraction."><!-- mathjax --><script src="https://cd </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -58,6 +58,9 @@ and no substance in the bound fraction."><!-- mathjax --><script src="https://cd <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/add_err-1.png b/docs/reference/add_err-1.png Binary files differindex 68cfb344..4a3b4062 100644 --- a/docs/reference/add_err-1.png +++ b/docs/reference/add_err-1.png diff --git a/docs/reference/add_err-2.png b/docs/reference/add_err-2.png Binary files differindex d2f0cf08..5aec1744 100644 --- a/docs/reference/add_err-2.png +++ b/docs/reference/add_err-2.png diff --git a/docs/reference/add_err-3.png b/docs/reference/add_err-3.png Binary files differindex 17b5416a..2e71f02f 100644 --- a/docs/reference/add_err-3.png +++ b/docs/reference/add_err-3.png diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 09a92fba..4db51d10 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -19,7 +19,7 @@ may depend on the predicted value and is specified as a standard deviation."><!- </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -56,6 +56,9 @@ may depend on the predicted value and is specified as a standard deviation."><!- <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/anova.saem.mmkin.html b/docs/reference/anova.saem.mmkin.html index df85fc6f..03ca588d 100644 --- a/docs/reference/anova.saem.mmkin.html +++ b/docs/reference/anova.saem.mmkin.html @@ -20,7 +20,7 @@ the model on the previous line."><!-- mathjax --><script src="https://cdnjs.clou </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -57,6 +57,9 @@ the model on the previous line."><!-- mathjax --><script src="https://cdnjs.clou <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/aw.html b/docs/reference/aw.html index ffb9dd82..5740d67d 100644 --- a/docs/reference/aw.html +++ b/docs/reference/aw.html @@ -19,7 +19,7 @@ by Burnham and Anderson (2004)."><!-- mathjax --><script src="https://cdnjs.clou </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -56,6 +56,9 @@ by Burnham and Anderson (2004)."><!-- mathjax --><script src="https://cdnjs.clou <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html index 33c4a939..48240abc 100644 --- a/docs/reference/confint.mkinfit.html +++ b/docs/reference/confint.mkinfit.html @@ -24,7 +24,7 @@ method of Venzon and Moolgavkar (1988)."><!-- mathjax --><script src="https://cd </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -61,6 +61,9 @@ method of Venzon and Moolgavkar (1988)."><!-- mathjax --><script src="https://cd <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> @@ -254,7 +257,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-in"><span><span class="va">f_d_1</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">ci_profile</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_1</span>, method <span class="op">=</span> <span class="st">"profile"</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 1.086 0.000 1.086 </span> +<span class="r-out co"><span class="r-pr">#></span> 2.578 0.005 2.599 </span> <span class="r-in"><span><span class="co"># Using more cores does not save much time here, as parent_0 takes up most of the time</span></span></span> <span class="r-in"><span><span class="co"># If we additionally exclude parent_0 (the confidence of which is often of</span></span></span> <span class="r-in"><span><span class="co"># minor interest), we get a nice performance improvement if we use at least 4 cores</span></span></span> @@ -262,7 +265,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"k_parent_sink"</span>, <span class="st">"k_parent_m1"</span>, <span class="st">"k_m1_sink"</span>, <span class="st">"sigma"</span><span class="op">)</span>, cores <span class="op">=</span> <span class="va">n_cores</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Profiling the likelihood</span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 0.396 0.065 0.263 </span> +<span class="r-out co"><span class="r-pr">#></span> 0.963 0.255 0.636 </span> <span class="r-in"><span><span class="va">ci_profile</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 96.456003640 1.027703e+02</span> diff --git a/docs/reference/create_deg_func.html b/docs/reference/create_deg_func.html index 4735f334..bf02afe3 100644 --- a/docs/reference/create_deg_func.html +++ b/docs/reference/create_deg_func.html @@ -17,7 +17,7 @@ </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -54,6 +54,9 @@ <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> @@ -148,8 +151,8 @@ <span class="r-in"><span> replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Loading required package: rbenchmark</span> <span class="r-out co"><span class="r-pr">#></span> test replications elapsed relative user.self sys.self user.child</span> -<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.218 1.000 0.217 0 0</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 0.273 1.252 0.274 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.421 1.000 0.412 0.000 0</span> +<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 0.601 1.428 0.566 0.024 0</span> <span class="r-out co"><span class="r-pr">#></span> sys.child</span> <span class="r-out co"><span class="r-pr">#></span> 1 0</span> <span class="r-out co"><span class="r-pr">#></span> 2 0</span> @@ -162,8 +165,8 @@ <span class="r-in"><span> deSolve <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">DFOP_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span> <span class="r-in"><span> replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> test replications elapsed relative user.self sys.self user.child</span> -<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.352 1.000 0.352 0 0</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 0.486 1.381 0.485 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.762 1.000 0.758 0.004 0</span> +<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 1.194 1.567 1.140 0.052 0</span> <span class="r-out co"><span class="r-pr">#></span> sys.child</span> <span class="r-out co"><span class="r-pr">#></span> 1 0</span> <span class="r-out co"><span class="r-pr">#></span> 2 0</span> diff --git a/docs/reference/ds_mixed-1.png b/docs/reference/ds_mixed-1.png Binary files differindex 7b73613a..053a7253 100644 --- a/docs/reference/ds_mixed-1.png +++ b/docs/reference/ds_mixed-1.png diff --git a/docs/reference/ds_mixed.html b/docs/reference/ds_mixed.html index 9618edae..fdf72593 100644 --- a/docs/reference/ds_mixed.html +++ b/docs/reference/ds_mixed.html @@ -18,7 +18,7 @@ the 'dataset_generation' directory."><!-- mathjax --><script src="https://cdnjs. </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -55,6 +55,9 @@ the 'dataset_generation' directory."><!-- mathjax --><script src="https://cdnjs. <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index b8ccdb2e..4ce6a8ca 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -23,7 +23,7 @@ advantage that the SFORB model can also be used for metabolites."><!-- mathjax - </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -60,6 +60,9 @@ advantage that the SFORB model can also be used for metabolites."><!-- mathjax - <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/experimental_data_for_UBA-1.png b/docs/reference/experimental_data_for_UBA-1.png Binary files differindex f0dfab85..4de80e3a 100644 --- a/docs/reference/experimental_data_for_UBA-1.png +++ b/docs/reference/experimental_data_for_UBA-1.png diff --git a/docs/reference/experimental_data_for_UBA.html b/docs/reference/experimental_data_for_UBA.html index bad2ad49..6a02f430 100644 --- a/docs/reference/experimental_data_for_UBA.html +++ b/docs/reference/experimental_data_for_UBA.html @@ -45,7 +45,7 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -82,6 +82,9 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/f_time_norm_focus.html b/docs/reference/f_time_norm_focus.html index 17a63ce2..ace7c028 100644 --- a/docs/reference/f_time_norm_focus.html +++ b/docs/reference/f_time_norm_focus.html @@ -18,7 +18,7 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369)."><!-- mathjax </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -55,6 +55,9 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369)."><!-- mathjax <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/focus_soil_moisture.html b/docs/reference/focus_soil_moisture.html index 0d460160..4cb95b77 100644 --- a/docs/reference/focus_soil_moisture.html +++ b/docs/reference/focus_soil_moisture.html @@ -18,7 +18,7 @@ corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5."><!-- mathjax --><script </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -55,6 +55,9 @@ corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5."><!-- mathjax --><script <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/get_deg_func.html b/docs/reference/get_deg_func.html index 4963ad94..79c88c54 100644 --- a/docs/reference/get_deg_func.html +++ b/docs/reference/get_deg_func.html @@ -17,7 +17,7 @@ </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -54,6 +54,9 @@ <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/hierarchical_kinetics.html b/docs/reference/hierarchical_kinetics.html index 35edf6b3..ab0b3d04 100644 --- a/docs/reference/hierarchical_kinetics.html +++ b/docs/reference/hierarchical_kinetics.html @@ -24,7 +24,7 @@ includes them.'><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/l </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -61,6 +61,9 @@ includes them.'><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/l <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/illparms.html b/docs/reference/illparms.html index 2dc8f503..bd90c0ed 100644 --- a/docs/reference/illparms.html +++ b/docs/reference/illparms.html @@ -21,7 +21,7 @@ without parameter transformations is used."><!-- mathjax --><script src="https:/ </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -58,6 +58,9 @@ without parameter transformations is used."><!-- mathjax --><script src="https:/ <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index 68041671..7937d770 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -18,7 +18,7 @@ transformations."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -55,6 +55,9 @@ transformations."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/intervals.saem.mmkin.html b/docs/reference/intervals.saem.mmkin.html index d148140e..d52d8501 100644 --- a/docs/reference/intervals.saem.mmkin.html +++ b/docs/reference/intervals.saem.mmkin.html @@ -17,7 +17,7 @@ </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -54,6 +54,9 @@ <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/llhist.html b/docs/reference/llhist.html index c54796fc..d53d6319 100644 --- a/docs/reference/llhist.html +++ b/docs/reference/llhist.html @@ -18,7 +18,7 @@ original fit is shown as a red vertical line."><!-- mathjax --><script src="http </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -55,6 +55,9 @@ original fit is shown as a red vertical line."><!-- mathjax --><script src="http <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/loftest-1.png b/docs/reference/loftest-1.png Binary files differindex 750a2acf..f1dc5fa7 100644 --- a/docs/reference/loftest-1.png +++ b/docs/reference/loftest-1.png diff --git a/docs/reference/loftest-2.png b/docs/reference/loftest-2.png Binary files differindex d12c26e7..3f1015a9 100644 --- a/docs/reference/loftest-2.png +++ b/docs/reference/loftest-2.png diff --git a/docs/reference/loftest-3.png b/docs/reference/loftest-3.png Binary files differindex 1b2fd838..e876cbab 100644 --- a/docs/reference/loftest-3.png +++ b/docs/reference/loftest-3.png diff --git a/docs/reference/loftest-4.png b/docs/reference/loftest-4.png Binary files differindex 3beb9d1a..ac44c162 100644 --- a/docs/reference/loftest-4.png +++ b/docs/reference/loftest-4.png diff --git a/docs/reference/loftest-5.png b/docs/reference/loftest-5.png Binary files differindex f60f5ff7..14537feb 100644 --- a/docs/reference/loftest-5.png +++ b/docs/reference/loftest-5.png diff --git a/docs/reference/loftest.html b/docs/reference/loftest.html index a5c5e198..b474ad20 100644 --- a/docs/reference/loftest.html +++ b/docs/reference/loftest.html @@ -20,7 +20,7 @@ lrtest.default from the lmtest package."><!-- mathjax --><script src="https://cd </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -57,6 +57,9 @@ lrtest.default from the lmtest package."><!-- mathjax --><script src="https://cd <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index 1dd40d48..07884f26 100644 --- a/docs/reference/logLik.mkinfit.html +++ b/docs/reference/logLik.mkinfit.html @@ -21,7 +21,7 @@ the error model."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -58,6 +58,9 @@ the error model."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/logLik.saem.mmkin.html b/docs/reference/logLik.saem.mmkin.html index 2dd52ebd..92d14aed 100644 --- a/docs/reference/logLik.saem.mmkin.html +++ b/docs/reference/logLik.saem.mmkin.html @@ -17,7 +17,7 @@ </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -54,6 +54,9 @@ <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/logistic.solution-1.png b/docs/reference/logistic.solution-1.png Binary files differindex 23c031de..73dad0a4 100644 --- a/docs/reference/logistic.solution-1.png +++ b/docs/reference/logistic.solution-1.png diff --git a/docs/reference/logistic.solution-2.png b/docs/reference/logistic.solution-2.png Binary files differindex b56db0cb..8d2514a3 100644 --- a/docs/reference/logistic.solution-2.png +++ b/docs/reference/logistic.solution-2.png diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html index c936637b..412a981c 100644 --- a/docs/reference/logistic.solution.html +++ b/docs/reference/logistic.solution.html @@ -18,7 +18,7 @@ an increasing rate constant, supposedly caused by microbial growth"><!-- mathjax </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -55,6 +55,9 @@ an increasing rate constant, supposedly caused by microbial growth"><!-- mathjax <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/lrtest.mkinfit.html b/docs/reference/lrtest.mkinfit.html index aac564fa..45466262 100644 --- a/docs/reference/lrtest.mkinfit.html +++ b/docs/reference/lrtest.mkinfit.html @@ -21,7 +21,7 @@ and can be expressed by fixing the parameters of the other."><!-- mathjax --><sc </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -58,6 +58,9 @@ and can be expressed by fixing the parameters of the other."><!-- mathjax --><sc <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html index 40995e83..892aa4e1 100644 --- a/docs/reference/max_twa_parent.html +++ b/docs/reference/max_twa_parent.html @@ -23,7 +23,7 @@ soil section of the FOCUS guidance."><!-- mathjax --><script src="https://cdnjs. </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -60,6 +60,9 @@ soil section of the FOCUS guidance."><!-- mathjax --><script src="https://cdnjs. <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/mccall81_245T-1.png b/docs/reference/mccall81_245T-1.png Binary files differindex 5e4ea6ef..79c45fe6 100644 --- a/docs/reference/mccall81_245T-1.png +++ b/docs/reference/mccall81_245T-1.png diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 0c5cb21a..6b057c9d 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -19,7 +19,7 @@ </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -56,6 +56,9 @@ <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/mean_degparms.html b/docs/reference/mean_degparms.html index 20f539cf..6e17045a 100644 --- a/docs/reference/mean_degparms.html +++ b/docs/reference/mean_degparms.html @@ -17,7 +17,7 @@ </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -54,6 +54,9 @@ <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/mhmkin-1.png b/docs/reference/mhmkin-1.png Binary files differindex 1c99aead..2ecb6759 100644 --- a/docs/reference/mhmkin-1.png +++ b/docs/reference/mhmkin-1.png diff --git a/docs/reference/mhmkin-2.png b/docs/reference/mhmkin-2.png Binary files differindex 3051bddc..70cd7723 100644 --- a/docs/reference/mhmkin-2.png +++ b/docs/reference/mhmkin-2.png diff --git a/docs/reference/mhmkin.html b/docs/reference/mhmkin.html index 08726dfc..7fcb98fb 100644 --- a/docs/reference/mhmkin.html +++ b/docs/reference/mhmkin.html @@ -22,7 +22,7 @@ mixed-effects model fitting functions."><!-- mathjax --><script src="https://cdn </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -59,6 +59,9 @@ mixed-effects model fitting functions."><!-- mathjax --><script src="https://cdn <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/mixed-1.png b/docs/reference/mixed-1.png Binary files differindex 846ca6a1..3992b681 100644 --- a/docs/reference/mixed-1.png +++ b/docs/reference/mixed-1.png diff --git a/docs/reference/mixed.html b/docs/reference/mixed.html index 91bb26ce..b0cce30b 100644 --- a/docs/reference/mixed.html +++ b/docs/reference/mixed.html @@ -17,7 +17,7 @@ </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -54,6 +54,9 @@ <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index ab80a18e..9e1487bd 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -19,7 +19,7 @@ variable and several dependent variables as columns."><!-- mathjax --><script sr </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -56,6 +56,9 @@ variable and several dependent variables as columns."><!-- mathjax --><script sr <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index 0fb06a94..8bf04bdf 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -19,7 +19,7 @@ mkinfit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/ma </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -56,6 +56,9 @@ mkinfit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/ma <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index b3c0e5d5..dda44620 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -20,7 +20,7 @@ provided by this package come as mkinds objects nevertheless."><!-- mathjax -->< </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -57,6 +57,9 @@ provided by this package come as mkinds objects nevertheless."><!-- mathjax -->< <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/mkindsg.html b/docs/reference/mkindsg.html index 118f7650..ac6a2471 100644 --- a/docs/reference/mkindsg.html +++ b/docs/reference/mkindsg.html @@ -20,7 +20,7 @@ dataset if no data are supplied."><!-- mathjax --><script src="https://cdnjs.clo </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -57,6 +57,9 @@ dataset if no data are supplied."><!-- mathjax --><script src="https://cdnjs.clo <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index 517af738..11837e63 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -18,7 +18,7 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006."><!-- ma </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -55,6 +55,9 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006."><!-- ma <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/mkinerrplot-1.png b/docs/reference/mkinerrplot-1.png Binary files differindex 078614fc..49bb1c0e 100644 --- a/docs/reference/mkinerrplot-1.png +++ b/docs/reference/mkinerrplot-1.png diff --git a/docs/reference/mkinerrplot.html b/docs/reference/mkinerrplot.html index 136cddcc..6996eb86 100644 --- a/docs/reference/mkinerrplot.html +++ b/docs/reference/mkinerrplot.html @@ -21,7 +21,7 @@ using the argument show_errplot = TRUE."><!-- mathjax --><script src="https://cd </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -58,6 +58,9 @@ using the argument show_errplot = TRUE."><!-- mathjax --><script src="https://cd <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/mkinfit-1.png b/docs/reference/mkinfit-1.png Binary files differindex 578f64a5..7c51deb6 100644 --- a/docs/reference/mkinfit-1.png +++ b/docs/reference/mkinfit-1.png diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 88848768..865bdc28 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -25,7 +25,7 @@ likelihood function."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -62,6 +62,9 @@ likelihood function."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> @@ -401,17 +404,17 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-in"><span><span class="co"># Use shorthand notation for parent only degradation</span></span></span> <span class="r-in"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</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">fit</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.4 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.0 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri May 19 09:15:57 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri May 19 09:15:57 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.6 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.1 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Oct 30 09:30:09 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Oct 30 09:30:09 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 = - (alpha/beta) * 1/((time/beta) + 1) * parent</span> <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 using 222 model solutions performed in 0.013 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 222 model solutions performed in 0.031 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Error model: Constant variance </span> <span class="r-out co"><span class="r-pr">#></span> </span> @@ -552,9 +555,9 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"analytical"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="op">}</span></span></span> <span class="r-out co"><span class="r-pr">#></span> test relative elapsed</span> -<span class="r-out co"><span class="r-pr">#></span> 3 analytical 1.000 0.226</span> -<span class="r-out co"><span class="r-pr">#></span> 2 eigen 1.845 0.417</span> -<span class="r-out co"><span class="r-pr">#></span> 1 deSolve_compiled 2.354 0.532</span> +<span class="r-out co"><span class="r-pr">#></span> 3 analytical 1.000 0.465</span> +<span class="r-out co"><span class="r-pr">#></span> 2 eigen 2.260 1.051</span> +<span class="r-out co"><span class="r-pr">#></span> 1 deSolve_compiled 2.282 1.061</span> <span class="r-in"><span><span class="co"># }</span></span></span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO</span></span></span> @@ -581,10 +584,10 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NaNs produced</span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NaNs produced</span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>diag(.) had 0 or NA entries; non-finite result is doubtful</span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.4 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.0 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri May 19 09:16:01 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri May 19 09:16:01 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.6 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.1 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Oct 30 09:30:19 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Oct 30 09:30:19 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 = - (alpha/beta) * 1/((time/beta) + 1) * parent</span> @@ -593,7 +596,7 @@ Degradation Data. <em>Environments</em> 6(12) 124 <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 using 4062 model solutions performed in 0.718 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 4062 model solutions performed in 1.981 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Error model: Two-component variance function </span> <span class="r-out co"><span class="r-pr">#></span> </span> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index e4761e73..11a87acc 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -21,7 +21,7 @@ components."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -58,6 +58,9 @@ components."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> @@ -266,7 +269,7 @@ in the FOCUS and NAFTA guidance documents are used.</p> <p>For kinetic models with more than one observed variable, a symbolic solution of the system of differential equations is included in the resulting mkinmod object in some cases, speeding up the solution.</p> -<p>If a C compiler is found by <code><a href="https://r-lib.github.io/pkgbuild/reference/has_compiler.html" class="external-link">pkgbuild::has_compiler()</a></code> and there +<p>If a C compiler is found by <code><a href="https://pkgbuild.r-lib.org/reference/has_compiler.html" class="external-link">pkgbuild::has_compiler()</a></code> and there is more than one observed variable in the specification, C code is generated for evaluating the differential equations, compiled using <code><a href="https://rdrr.io/pkg/inline/man/cfunction.html" class="external-link">inline::cfunction()</a></code> and added to the resulting mkinmod object.</p> @@ -330,7 +333,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-in"><span> m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, full_name <span class="op">=</span> <span class="st">"Metabolite M1"</span><span class="op">)</span>,</span></span> <span class="r-in"><span> name <span class="op">=</span> <span class="st">"SFO_SFO"</span>, dll_dir <span class="op">=</span> <span class="va">DLL_dir</span>, unload <span class="op">=</span> <span class="cn">TRUE</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-msg co"><span class="r-pr">#></span> Copied DLL from /tmp/RtmpUEfrXw/file723a02cdd855b.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span> +<span class="r-msg co"><span class="r-pr">#></span> Copied DLL from /tmp/RtmpkUSV6I/file244bcd2ba24b1a.so to /home/agsad.admin.ch/f80868656/.local/share/mkin/SFO_SFO.so</span> <span class="r-in"><span><span class="co"># Now we can save the model and restore it in a new session</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS</a></span><span class="op">(</span><span class="va">SFO_SFO.2</span>, file <span class="op">=</span> <span class="st">"~/SFO_SFO.rds"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="co"># Terminate the R session here if you would like to check, and then do</span></span></span> @@ -383,7 +386,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-out co"><span class="r-pr">#></span> })</span> <span class="r-out co"><span class="r-pr">#></span> return(predicted)</span> <span class="r-out co"><span class="r-pr">#></span> }</span> -<span class="r-out co"><span class="r-pr">#></span> <environment: 0x55555f4ce060></span> +<span class="r-out co"><span class="r-pr">#></span> <environment: 0x560630960080></span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># If we have several parallel metabolites</span></span></span> <span class="r-in"><span><span class="co"># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span></span></span> diff --git a/docs/reference/mkinparplot-1.png b/docs/reference/mkinparplot-1.png Binary files differindex 8d34b451..5d6fde87 100644 --- a/docs/reference/mkinparplot-1.png +++ b/docs/reference/mkinparplot-1.png diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index 0e7985d8..71957650 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -18,7 +18,7 @@ mkinfit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/ma </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -55,6 +55,9 @@ mkinfit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/ma <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index 8a35bae9..da047bf7 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -18,7 +18,7 @@ plot.mkinfit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/li </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -55,6 +55,9 @@ plot.mkinfit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 5e016527..d52e57cc 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -19,7 +19,7 @@ kinetic parameters and initial values for the state variables."><!-- mathjax --> </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -56,6 +56,9 @@ kinetic parameters and initial values for the state variables."><!-- mathjax --> <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> @@ -395,10 +398,10 @@ as these always return mapped output.</p></dd> <span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"analytical"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">[</span><span class="fl">201</span>,<span class="op">]</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="op">}</span></span></span> <span class="r-out co"><span class="r-pr">#></span> test relative elapsed</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve_compiled 1.0 0.002</span> -<span class="r-out co"><span class="r-pr">#></span> 4 analytical 1.0 0.002</span> -<span class="r-out co"><span class="r-pr">#></span> 1 eigen 3.5 0.007</span> -<span class="r-out co"><span class="r-pr">#></span> 3 deSolve 29.0 0.058</span> +<span class="r-out co"><span class="r-pr">#></span> 2 deSolve_compiled 1.0 0.005</span> +<span class="r-out co"><span class="r-pr">#></span> 4 analytical 1.0 0.005</span> +<span class="r-out co"><span class="r-pr">#></span> 1 eigen 3.2 0.016</span> +<span class="r-out co"><span class="r-pr">#></span> 3 deSolve 24.4 0.122</span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># \dontrun{</span></span></span> <span class="r-in"><span> <span class="co"># Predict from a fitted model</span></span></span> diff --git a/docs/reference/mkinresplot-1.png b/docs/reference/mkinresplot-1.png Binary files differindex 7c64d0f0..97ccd762 100644 --- a/docs/reference/mkinresplot-1.png +++ b/docs/reference/mkinresplot-1.png diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index 8cdb55d0..4bfd033e 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -20,7 +20,7 @@ argument show_residuals = TRUE."><!-- mathjax --><script src="https://cdnjs.clou </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -57,6 +57,9 @@ argument show_residuals = TRUE."><!-- mathjax --><script src="https://cdnjs.clou <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/mmkin-1.png b/docs/reference/mmkin-1.png Binary files differindex 9642db70..2361d3dc 100644 --- a/docs/reference/mmkin-1.png +++ b/docs/reference/mmkin-1.png diff --git a/docs/reference/mmkin-2.png b/docs/reference/mmkin-2.png Binary files differindex d9aa755d..6ce2010f 100644 --- a/docs/reference/mmkin-2.png +++ b/docs/reference/mmkin-2.png diff --git a/docs/reference/mmkin-3.png b/docs/reference/mmkin-3.png Binary files differindex ed8e87e6..5d56da86 100644 --- a/docs/reference/mmkin-3.png +++ b/docs/reference/mmkin-3.png diff --git a/docs/reference/mmkin-4.png b/docs/reference/mmkin-4.png Binary files differindex 11eae1f9..132380a8 100644 --- a/docs/reference/mmkin-4.png +++ b/docs/reference/mmkin-4.png diff --git a/docs/reference/mmkin-5.png b/docs/reference/mmkin-5.png Binary files differindex e88bd59f..4bfcc55e 100644 --- a/docs/reference/mmkin-5.png +++ b/docs/reference/mmkin-5.png diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index e09dc469..57039604 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -20,7 +20,7 @@ datasets specified in its first two arguments."><!-- mathjax --><script src="htt </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -57,6 +57,9 @@ datasets specified in its first two arguments."><!-- mathjax --><script src="htt <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> @@ -206,10 +209,10 @@ plotting.</p></div> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="va">time_default</span></span></span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 1.502 0.665 0.624 </span> +<span class="r-out co"><span class="r-pr">#></span> 3.540 1.287 1.429 </span> <span class="r-in"><span><span class="va">time_1</span></span></span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 1.824 0.028 1.852 </span> +<span class="r-out co"><span class="r-pr">#></span> 4.074 0.037 4.142 </span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[[</span><span class="st">"SFO_lin"</span>, <span class="fl">2</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> $ff</span> diff --git a/docs/reference/multistart-1.png b/docs/reference/multistart-1.png Binary files differindex 8133170b..cf3cdca3 100644 --- a/docs/reference/multistart-1.png +++ b/docs/reference/multistart-1.png diff --git a/docs/reference/multistart-2.png b/docs/reference/multistart-2.png Binary files differindex 5cfdbd63..05a160d0 100644 --- a/docs/reference/multistart-2.png +++ b/docs/reference/multistart-2.png diff --git a/docs/reference/multistart.html b/docs/reference/multistart.html index 4da88d48..840f0e01 100644 --- a/docs/reference/multistart.html +++ b/docs/reference/multistart.html @@ -22,7 +22,7 @@ mixed-effects models by Duchesne et al (2021)."><!-- mathjax --><script src="htt </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -59,6 +59,9 @@ mixed-effects models by Duchesne et al (2021)."><!-- mathjax --><script src="htt <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/nafta-1.png b/docs/reference/nafta-1.png Binary files differindex 98d4246c..5d2d434b 100644 --- a/docs/reference/nafta-1.png +++ b/docs/reference/nafta-1.png diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html index 5e733f99..011b766a 100644 --- a/docs/reference/nafta.html +++ b/docs/reference/nafta.html @@ -21,7 +21,7 @@ order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP."><! </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -58,6 +58,9 @@ order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP."><! <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/nlme-1.png b/docs/reference/nlme-1.png Binary files differindex 9583da2a..0134107f 100644 --- a/docs/reference/nlme-1.png +++ b/docs/reference/nlme-1.png diff --git a/docs/reference/nlme-2.png b/docs/reference/nlme-2.png Binary files differindex 02aa0573..95739890 100644 --- a/docs/reference/nlme-2.png +++ b/docs/reference/nlme-2.png diff --git a/docs/reference/nlme.html b/docs/reference/nlme.html index 60095af6..26c56e54 100644 --- a/docs/reference/nlme.html +++ b/docs/reference/nlme.html @@ -20,7 +20,7 @@ datasets. They are used internally by the nlme.mmkin() method."><!-- mathjax --> </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -57,6 +57,9 @@ datasets. They are used internally by the nlme.mmkin() method."><!-- mathjax --> <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/nlme.mmkin-1.png b/docs/reference/nlme.mmkin-1.png Binary files differindex 762d5412..7cabb086 100644 --- a/docs/reference/nlme.mmkin-1.png +++ b/docs/reference/nlme.mmkin-1.png diff --git a/docs/reference/nlme.mmkin-2.png b/docs/reference/nlme.mmkin-2.png Binary files differindex 779adbdb..b9a68e92 100644 --- a/docs/reference/nlme.mmkin-2.png +++ b/docs/reference/nlme.mmkin-2.png diff --git a/docs/reference/nlme.mmkin-3.png b/docs/reference/nlme.mmkin-3.png Binary files differindex 046d0238..ce7999bd 100644 --- a/docs/reference/nlme.mmkin-3.png +++ b/docs/reference/nlme.mmkin-3.png diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html index d41f9abd..05fbac5c 100644 --- a/docs/reference/nlme.mmkin.html +++ b/docs/reference/nlme.mmkin.html @@ -19,7 +19,7 @@ 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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -56,6 +56,9 @@ have been obtained by fitting the same model to a list of datasets."><!-- mathja <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/nobs.mkinfit.html b/docs/reference/nobs.mkinfit.html index 5781c4dc..c3e24a08 100644 --- a/docs/reference/nobs.mkinfit.html +++ b/docs/reference/nobs.mkinfit.html @@ -17,7 +17,7 @@ </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -54,6 +54,9 @@ <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/parms.html b/docs/reference/parms.html index 345bb1bc..89831adb 100644 --- a/docs/reference/parms.html +++ b/docs/reference/parms.html @@ -19,7 +19,7 @@ without considering the error structure that was assumed for the fit."><!-- math </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -56,6 +56,9 @@ without considering the error structure that was assumed for the fit."><!-- math <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/parplot.html b/docs/reference/parplot.html index edefb059..2ae8d39f 100644 --- a/docs/reference/parplot.html +++ b/docs/reference/parplot.html @@ -19,7 +19,7 @@ or by their medians as proposed in the paper by Duchesne et al. (2021)."><!-- ma </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -56,6 +56,9 @@ or by their medians as proposed in the paper by Duchesne et al. (2021)."><!-- ma <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/plot.mixed.mmkin-1.png b/docs/reference/plot.mixed.mmkin-1.png Binary files differindex 2e145bb7..8a09a167 100644 --- a/docs/reference/plot.mixed.mmkin-1.png +++ b/docs/reference/plot.mixed.mmkin-1.png diff --git a/docs/reference/plot.mixed.mmkin-2.png b/docs/reference/plot.mixed.mmkin-2.png Binary files differindex 65f5593b..68a76b47 100644 --- a/docs/reference/plot.mixed.mmkin-2.png +++ b/docs/reference/plot.mixed.mmkin-2.png diff --git a/docs/reference/plot.mixed.mmkin-3.png b/docs/reference/plot.mixed.mmkin-3.png Binary files differindex ef4fa3a7..e18a0da1 100644 --- a/docs/reference/plot.mixed.mmkin-3.png +++ b/docs/reference/plot.mixed.mmkin-3.png diff --git a/docs/reference/plot.mixed.mmkin-4.png b/docs/reference/plot.mixed.mmkin-4.png Binary files differindex d7030dea..f574fdd9 100644 --- a/docs/reference/plot.mixed.mmkin-4.png +++ b/docs/reference/plot.mixed.mmkin-4.png diff --git a/docs/reference/plot.mixed.mmkin.html b/docs/reference/plot.mixed.mmkin.html index 507684a1..b0e0f159 100644 --- a/docs/reference/plot.mixed.mmkin.html +++ b/docs/reference/plot.mixed.mmkin.html @@ -17,7 +17,7 @@ </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -54,6 +54,9 @@ <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/plot.mkinfit-1.png b/docs/reference/plot.mkinfit-1.png Binary files differindex a48ea72b..ea1032fb 100644 --- a/docs/reference/plot.mkinfit-1.png +++ b/docs/reference/plot.mkinfit-1.png diff --git a/docs/reference/plot.mkinfit-2.png b/docs/reference/plot.mkinfit-2.png Binary files differindex 43184bcb..4a3ddf29 100644 --- a/docs/reference/plot.mkinfit-2.png +++ b/docs/reference/plot.mkinfit-2.png diff --git a/docs/reference/plot.mkinfit-3.png b/docs/reference/plot.mkinfit-3.png Binary files differindex 8de1babc..8a9dbd13 100644 --- a/docs/reference/plot.mkinfit-3.png +++ b/docs/reference/plot.mkinfit-3.png diff --git a/docs/reference/plot.mkinfit-4.png b/docs/reference/plot.mkinfit-4.png Binary files differindex 4b7a5f27..a7164caa 100644 --- a/docs/reference/plot.mkinfit-4.png +++ b/docs/reference/plot.mkinfit-4.png diff --git a/docs/reference/plot.mkinfit-5.png b/docs/reference/plot.mkinfit-5.png Binary files differindex 50c13686..3545b8d8 100644 --- a/docs/reference/plot.mkinfit-5.png +++ b/docs/reference/plot.mkinfit-5.png diff --git a/docs/reference/plot.mkinfit-6.png b/docs/reference/plot.mkinfit-6.png Binary files differindex 878e3dd6..3d0fb25e 100644 --- a/docs/reference/plot.mkinfit-6.png +++ b/docs/reference/plot.mkinfit-6.png diff --git a/docs/reference/plot.mkinfit-7.png b/docs/reference/plot.mkinfit-7.png Binary files differindex e81d2737..85045bc3 100644 --- a/docs/reference/plot.mkinfit-7.png +++ b/docs/reference/plot.mkinfit-7.png diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 3cd677be..bc4c743f 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -19,7 +19,7 @@ observed data together with the solution of the fitted model."><!-- mathjax -->< </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -56,6 +56,9 @@ observed data together with the solution of the fitted model."><!-- mathjax -->< <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/plot.mmkin-1.png b/docs/reference/plot.mmkin-1.png Binary files differindex c4fcb9ac..235e33a7 100644 --- a/docs/reference/plot.mmkin-1.png +++ b/docs/reference/plot.mmkin-1.png diff --git a/docs/reference/plot.mmkin-2.png b/docs/reference/plot.mmkin-2.png Binary files differindex 8cc727c3..7af84edf 100644 --- a/docs/reference/plot.mmkin-2.png +++ b/docs/reference/plot.mmkin-2.png diff --git a/docs/reference/plot.mmkin-3.png b/docs/reference/plot.mmkin-3.png Binary files differindex 066958c9..56bfac50 100644 --- a/docs/reference/plot.mmkin-3.png +++ b/docs/reference/plot.mmkin-3.png diff --git a/docs/reference/plot.mmkin-4.png b/docs/reference/plot.mmkin-4.png Binary files differindex 09caa509..29439156 100644 --- a/docs/reference/plot.mmkin-4.png +++ b/docs/reference/plot.mmkin-4.png diff --git a/docs/reference/plot.mmkin-5.png b/docs/reference/plot.mmkin-5.png Binary files differindex c35f7c80..77aa611d 100644 --- a/docs/reference/plot.mmkin-5.png +++ b/docs/reference/plot.mmkin-5.png diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index 455a67f3..f3d56cd2 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -21,7 +21,7 @@ the fit of at least one model to the same dataset is shown."><!-- mathjax --><sc </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -58,6 +58,9 @@ the fit of at least one model to the same dataset is shown."><!-- mathjax --><sc <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/plot.nafta.html b/docs/reference/plot.nafta.html index 0d5a0940..81cfd7b2 100644 --- a/docs/reference/plot.nafta.html +++ b/docs/reference/plot.nafta.html @@ -18,7 +18,7 @@ function (SFO, then IORE, then DFOP)."><!-- mathjax --><script src="https://cdnj </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -55,6 +55,9 @@ function (SFO, then IORE, then DFOP)."><!-- mathjax --><script src="https://cdnj <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html index a50ee30f..847be2cb 100644 --- a/docs/reference/reexports.html +++ b/docs/reference/reexports.html @@ -28,7 +28,7 @@ intervals, nlme </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -65,6 +65,9 @@ intervals, nlme <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/residuals.mkinfit.html b/docs/reference/residuals.mkinfit.html index f4516026..0115cc3f 100644 --- a/docs/reference/residuals.mkinfit.html +++ b/docs/reference/residuals.mkinfit.html @@ -17,7 +17,7 @@ </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -54,6 +54,9 @@ <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/saem-1.png b/docs/reference/saem-1.png Binary files differindex 1fa206c4..9e310252 100644 --- a/docs/reference/saem-1.png +++ b/docs/reference/saem-1.png diff --git a/docs/reference/saem-2.png b/docs/reference/saem-2.png Binary files differindex e5c62c35..de1bcf57 100644 --- a/docs/reference/saem-2.png +++ b/docs/reference/saem-2.png diff --git a/docs/reference/saem-3.png b/docs/reference/saem-3.png Binary files differindex f191ad3a..8667ef06 100644 --- a/docs/reference/saem-3.png +++ b/docs/reference/saem-3.png diff --git a/docs/reference/saem-4.png b/docs/reference/saem-4.png Binary files differindex 36deeada..cd464533 100644 --- a/docs/reference/saem-4.png +++ b/docs/reference/saem-4.png diff --git a/docs/reference/saem.html b/docs/reference/saem.html index 9c367984..527718ef 100644 --- a/docs/reference/saem.html +++ b/docs/reference/saem.html @@ -19,7 +19,7 @@ Expectation Maximisation algorithm (SAEM)."><!-- mathjax --><script src="https:/ </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -56,6 +56,9 @@ Expectation Maximisation algorithm (SAEM)."><!-- mathjax --><script src="https:/ <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> @@ -365,6 +368,8 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="saem-1.png" alt="" width="700" height="433"></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"individual.fit"</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Simulating data using nsim = 1000 simulated datasets</span> +<span class="r-out co"><span class="r-pr">#></span> Computing WRES and npde .</span> <span class="r-plt img"><img src="saem-2.png" alt="" width="700" height="433"></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_saem_fomc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"npde"</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Simulating data using nsim = 1000 simulated datasets</span> @@ -439,10 +444,10 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-plt img"><img src="saem-4.png" alt="" width="700" height="433"></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_saem_dfop_sfo</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> saemix version used for fitting: 3.2 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.4 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.0 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri May 19 09:17:55 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri May 19 09:17:55 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.6 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.1 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Oct 30 09:34:35 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Oct 30 09:34:35 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 = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> @@ -457,7 +462,7 @@ using <a href="mmkin.html">mmkin</a>.</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 4.02 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 8.745 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 10 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: Constant variance </span> diff --git a/docs/reference/schaefer07_complex_case-1.png b/docs/reference/schaefer07_complex_case-1.png Binary files differindex 41665b13..a1d7d2f2 100644 --- a/docs/reference/schaefer07_complex_case-1.png +++ b/docs/reference/schaefer07_complex_case-1.png diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index 075f22c0..abef385d 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -19,7 +19,7 @@ </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -56,6 +56,9 @@ <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/set_nd_nq.html b/docs/reference/set_nd_nq.html index 662779ca..249a7600 100644 --- a/docs/reference/set_nd_nq.html +++ b/docs/reference/set_nd_nq.html @@ -21,7 +21,7 @@ it automates the proposal of Boesten et al (2015)."><!-- mathjax --><script src= </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -58,6 +58,9 @@ it automates the proposal of Boesten et al (2015)."><!-- mathjax --><script src= <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/sigma_twocomp-1.png b/docs/reference/sigma_twocomp-1.png Binary files differindex 3671c658..0353b72c 100644 --- a/docs/reference/sigma_twocomp-1.png +++ b/docs/reference/sigma_twocomp-1.png diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html index 24593d2c..06bae61f 100644 --- a/docs/reference/sigma_twocomp.html +++ b/docs/reference/sigma_twocomp.html @@ -18,7 +18,7 @@ dependence of the measured value \(y\):"><!-- mathjax --><script src="https://cd </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -55,6 +55,9 @@ dependence of the measured value \(y\):"><!-- mathjax --><script src="https://cd <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/status.html b/docs/reference/status.html index 1acb7c2e..2ff35423 100644 --- a/docs/reference/status.html +++ b/docs/reference/status.html @@ -17,7 +17,7 @@ </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -54,6 +54,9 @@ <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 5bd1db76..fe24f3a4 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -21,7 +21,7 @@ values."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mat </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -58,6 +58,9 @@ values."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mat <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> @@ -231,17 +234,17 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <h2>Examples</h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></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="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_A</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.4 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.0 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri May 19 09:19:51 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri May 19 09:19:51 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.6 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.1 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Oct 30 09:39:49 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Oct 30 09:39:49 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> <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 using 131 model solutions performed in 0.008 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 131 model solutions performed in 0.02 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Error model: Constant variance </span> <span class="r-out co"><span class="r-pr">#></span> </span> diff --git a/docs/reference/summary.mmkin.html b/docs/reference/summary.mmkin.html index b5f17839..9b10a415 100644 --- a/docs/reference/summary.mmkin.html +++ b/docs/reference/summary.mmkin.html @@ -18,7 +18,7 @@ and gives an overview of ill-defined parameters calculated by illparms."><!-- ma </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -55,6 +55,9 @@ and gives an overview of ill-defined parameters calculated by illparms."><!-- ma <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> @@ -154,7 +157,7 @@ and gives an overview of ill-defined parameters calculated by <a href="illparms. <span class="r-wrn co"><span class="r-pr">#></span> 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">fits</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Error model: Constant variance </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.433 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.705 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Status:</span> <span class="r-out co"><span class="r-pr">#></span> dataset</span> diff --git a/docs/reference/summary.nlme.mmkin.html b/docs/reference/summary.nlme.mmkin.html index 33d8c01d..58eb3e21 100644 --- a/docs/reference/summary.nlme.mmkin.html +++ b/docs/reference/summary.nlme.mmkin.html @@ -21,7 +21,7 @@ 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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -58,6 +58,9 @@ endpoints such as formation fractions and DT50 values. Optionally <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> @@ -251,11 +254,11 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <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-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: 3.1.162 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.4 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.0 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri May 19 09:19:53 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri May 19 09:19:53 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> nlme version used for fitting: 3.1.163 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.6 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.1 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Oct 30 09:39:53 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Oct 30 09:39:53 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> @@ -265,7 +268,7 @@ 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 0.175 s using 4 iterations</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.451 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> diff --git a/docs/reference/summary.saem.mmkin.html b/docs/reference/summary.saem.mmkin.html index d9049ce5..54e5260b 100644 --- a/docs/reference/summary.saem.mmkin.html +++ b/docs/reference/summary.saem.mmkin.html @@ -21,7 +21,7 @@ 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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -58,6 +58,9 @@ endpoints such as formation fractions and DT50 values. Optionally <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> @@ -330,10 +333,10 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> b.1 0.06401324 0.07920531 0.09439739</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_saem_dfop_sfo_2</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> saemix version used for fitting: 3.2 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.4 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.0 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri May 19 09:20:09 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri May 19 09:20:09 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.6 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.1 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Oct 30 09:40:27 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Oct 30 09:40:27 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 = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> @@ -348,7 +351,7 @@ saemix authors for the parts inherited from saemix.</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 9.513 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 19.763 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 10 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> @@ -619,25 +622,25 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Fixed effects:</span> <span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 98.32277831 101.40841461 104.49405092</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1 0.01510464 0.01667815 0.01841557</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.20195605 0.27597108 0.36471512</span> -<span class="r-out co"><span class="r-pr">#></span> k1 0.07321367 0.10121120 0.13991523</span> -<span class="r-out co"><span class="r-pr">#></span> k2 0.01466928 0.01766483 0.02127208</span> -<span class="r-out co"><span class="r-pr">#></span> g 0.35098400 0.46314412 0.57916193</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 98.42519529 101.51623115 104.60726702</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.01505059 0.01662123 0.01835577</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.20100222 0.27477835 0.36332008</span> +<span class="r-out co"><span class="r-pr">#></span> k1 0.07347479 0.10139028 0.13991179</span> +<span class="r-out co"><span class="r-pr">#></span> k2 0.01469861 0.01771120 0.02134125</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.35506898 0.46263682 0.57379888</span> <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> lower est. upper</span> -<span class="r-out co"><span class="r-pr">#></span> sd(f_parent_qlogis) 0.3832326 0.4435601 0.5038876</span> -<span class="r-out co"><span class="r-pr">#></span> sd(log_k1) 0.1181772 0.2996192 0.4810613</span> -<span class="r-out co"><span class="r-pr">#></span> sd(log_k2) -0.6281964 0.1898692 1.0079349</span> -<span class="r-out co"><span class="r-pr">#></span> sd(g_qlogis) 0.1885523 0.4250717 0.6615911</span> -<span class="r-out co"><span class="r-pr">#></span> corr(log_k2,g_qlogis) -0.8453380 -0.5695240 -0.2937099</span> +<span class="r-out co"><span class="r-pr">#></span> sd(f_parent_qlogis) 0.3827416 0.4435866 0.5044315</span> +<span class="r-out co"><span class="r-pr">#></span> sd(log_k1) 0.1226277 0.2981783 0.4737289</span> +<span class="r-out co"><span class="r-pr">#></span> sd(log_k2) -0.5457764 0.1912531 0.9282825</span> +<span class="r-out co"><span class="r-pr">#></span> sd(g_qlogis) 0.1483976 0.3997298 0.6510619</span> +<span class="r-out co"><span class="r-pr">#></span> corr(log_k2,g_qlogis) -0.8537145 -0.5845703 -0.3154261</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 0.67302582 0.87410123 1.07517663</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.06403679 0.07925211 0.09446744</span> +<span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.6732869 0.87421677 1.0751467</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.0640392 0.07925135 0.0944635</span> <span class="r-in"><span><span class="co"># The correlation does not improve the fit judged by AIC and BIC, although</span></span></span> <span class="r-in"><span><span class="co"># the likelihood is higher with the additional parameter</span></span></span> <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_saem_dfop_sfo</span>, <span class="va">f_saem_dfop_sfo_2</span>, <span class="va">f_saem_dfop_sfo_3</span><span class="op">)</span></span></span> @@ -645,7 +648,7 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> npar AIC BIC Lik</span> <span class="r-out co"><span class="r-pr">#></span> f_saem_dfop_sfo_2 12 806.91 802.23 -391.46</span> -<span class="r-out co"><span class="r-pr">#></span> f_saem_dfop_sfo_3 13 807.91 802.83 -390.95</span> +<span class="r-out co"><span class="r-pr">#></span> f_saem_dfop_sfo_3 13 807.96 802.88 -390.98</span> <span class="r-out co"><span class="r-pr">#></span> f_saem_dfop_sfo 14 810.83 805.36 -391.41</span> <span class="r-in"><span><span class="co"># }</span></span></span> <span class="r-in"><span></span></span> diff --git a/docs/reference/summary_listing.html b/docs/reference/summary_listing.html index 9869e2e6..315f7192 100644 --- a/docs/reference/summary_listing.html +++ b/docs/reference/summary_listing.html @@ -18,7 +18,7 @@ option results = "asis".'><!-- mathjax --><script src="https://cdnjs.cloudflare. </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -55,6 +55,9 @@ option results = "asis".'><!-- mathjax --><script src="https://cdnjs.cloudflare. <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/synthetic_data_for_UBA_2014-1.png b/docs/reference/synthetic_data_for_UBA_2014-1.png Binary files differindex 11eae1f9..132380a8 100644 --- a/docs/reference/synthetic_data_for_UBA_2014-1.png +++ b/docs/reference/synthetic_data_for_UBA_2014-1.png diff --git a/docs/reference/synthetic_data_for_UBA_2014.html b/docs/reference/synthetic_data_for_UBA_2014.html index 91d7f6a6..ee71a4dd 100644 --- a/docs/reference/synthetic_data_for_UBA_2014.html +++ b/docs/reference/synthetic_data_for_UBA_2014.html @@ -32,7 +32,7 @@ Compare also the code in the example section to see the degradation models."><!- </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -69,6 +69,9 @@ Compare also the code in the example section to see the degradation models."><!- <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> @@ -269,10 +272,10 @@ Compare also the code in the example section to see the degradation models."><!- <span class="r-in"><span> <span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="synthetic_data_for_UBA_2014-1.png" alt="" width="700" height="433"></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">fit</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.4 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.0 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri May 19 09:20:19 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri May 19 09:20:19 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.6 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.1 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Oct 30 09:40:49 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Oct 30 09:40:49 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> @@ -281,7 +284,7 @@ Compare also the code in the example section to see the degradation models."><!- <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 using 848 model solutions performed in 0.154 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 848 model solutions performed in 0.408 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Error model: Constant variance </span> <span class="r-out co"><span class="r-pr">#></span> </span> diff --git a/docs/reference/test_data_from_UBA_2014-1.png b/docs/reference/test_data_from_UBA_2014-1.png Binary files differindex a007a102..e4fc2a4c 100644 --- a/docs/reference/test_data_from_UBA_2014-1.png +++ b/docs/reference/test_data_from_UBA_2014-1.png diff --git a/docs/reference/test_data_from_UBA_2014-2.png b/docs/reference/test_data_from_UBA_2014-2.png Binary files differindex f460ac83..4ce36561 100644 --- a/docs/reference/test_data_from_UBA_2014-2.png +++ b/docs/reference/test_data_from_UBA_2014-2.png diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html index b53b5de2..67acdb54 100644 --- a/docs/reference/test_data_from_UBA_2014.html +++ b/docs/reference/test_data_from_UBA_2014.html @@ -18,7 +18,7 @@ </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -55,6 +55,9 @@ <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 2cfe6df7..aade8415 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -22,7 +22,7 @@ the ilr transformation is used."><!-- mathjax --><script src="https://cdnjs.clou </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -59,6 +59,9 @@ the ilr transformation is used."><!-- mathjax --><script src="https://cdnjs.clou <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/reference/update.mkinfit-1.png b/docs/reference/update.mkinfit-1.png Binary files differindex 9278aefd..12fe1f5b 100644 --- a/docs/reference/update.mkinfit-1.png +++ b/docs/reference/update.mkinfit-1.png diff --git a/docs/reference/update.mkinfit-2.png b/docs/reference/update.mkinfit-2.png Binary files differindex f73a6180..21817f94 100644 --- a/docs/reference/update.mkinfit-2.png +++ b/docs/reference/update.mkinfit-2.png diff --git a/docs/reference/update.mkinfit.html b/docs/reference/update.mkinfit.html index c1e5edfc..10f9e8a2 100644 --- a/docs/reference/update.mkinfit.html +++ b/docs/reference/update.mkinfit.html @@ -20,7 +20,7 @@ override these starting values."><!-- mathjax --><script src="https://cdnjs.clou </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">1.2.4</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> </span> </div> @@ -57,6 +57,9 @@ override these starting values."><!-- mathjax --><script src="https://cdnjs.clou <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/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> |
