From 9aa186eaf43d3c86a99fd08c310cefbc5dfe0612 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 28 Jan 2023 17:40:31 +0100 Subject: Build online HTML versions of prebuilt vignettes Also, give some structure to the menu for selecting articles --- _pkgdown.yml | 32 +- docs/dev/articles/index.html | 41 +- docs/dev/articles/prebuilt/2022_cyan_pathway.html | 5623 ++++++++++++++++++++ .../figure-html/unnamed-chunk-11-1.png | Bin 0 -> 363943 bytes .../figure-html/unnamed-chunk-12-1.png | Bin 0 -> 365867 bytes .../figure-html/unnamed-chunk-13-1.png | Bin 0 -> 363662 bytes .../figure-html/unnamed-chunk-17-1.png | Bin 0 -> 378667 bytes .../figure-html/unnamed-chunk-18-1.png | Bin 0 -> 372548 bytes .../figure-html/unnamed-chunk-19-1.png | Bin 0 -> 373913 bytes .../figure-html/unnamed-chunk-6-1.png | Bin 0 -> 373737 bytes .../figure-html/unnamed-chunk-7-1.png | Bin 0 -> 373913 bytes docs/dev/articles/prebuilt/2022_dmta_parent.html | 2204 ++++++++ .../figure-html/convergence-saem-dfop-const-1.png | Bin 0 -> 130847 bytes .../figure-html/convergence-saem-dfop-tc-1.png | Bin 0 -> 116026 bytes .../convergence-saem-dfop-tc-no-ranef-k2-1.png | Bin 0 -> 128564 bytes .../figure-html/convergence-saem-fomc-const-1.png | Bin 0 -> 101690 bytes .../figure-html/convergence-saem-fomc-tc-1.png | Bin 0 -> 97397 bytes .../figure-html/convergence-saem-hs-const-1.png | Bin 0 -> 132456 bytes .../figure-html/convergence-saem-hs-tc-1.png | Bin 0 -> 102390 bytes .../figure-html/convergence-saem-sfo-const-1.png | Bin 0 -> 76259 bytes .../figure-html/convergence-saem-sfo-tc-1.png | Bin 0 -> 64271 bytes .../figure-html/multistart-full-par-1.png | Bin 0 -> 72048 bytes .../figure-html/multistart-reduced-par-1.png | Bin 0 -> 66652 bytes .../multistart-reduced-par-llquant-1.png | Bin 0 -> 59486 bytes .../plot-saem-dfop-tc-no-ranef-k2-1.png | Bin 0 -> 158323 bytes docs/dev/articles/prebuilt/2022_dmta_pathway.html | 2022 +++++++ .../saem-sforb-path-1-tc-reduced-convergence-1.png | Bin 0 -> 160921 bytes .../figure-html/unnamed-chunk-2-1.png | Bin 0 -> 108560 bytes .../figure-html/unnamed-chunk-3-1.png | Bin 0 -> 403164 bytes .../figure-html/unnamed-chunk-4-1.png | Bin 0 -> 403636 bytes .../figure-html/unnamed-chunk-5-1.png | Bin 0 -> 393985 bytes .../figure-html/unnamed-chunk-6-1.png | Bin 0 -> 400319 bytes .../figure-html/unnamed-chunk-7-1.png | Bin 0 -> 403164 bytes docs/dev/authors.html | 31 +- docs/dev/index.html | 36 +- docs/dev/news/index.html | 31 +- docs/dev/pkgdown.yml | 6 +- docs/dev/reference/index.html | 31 +- docs/dev/sitemap.xml | 9 + 39 files changed, 10017 insertions(+), 49 deletions(-) create mode 100644 docs/dev/articles/prebuilt/2022_cyan_pathway.html create mode 100644 docs/dev/articles/prebuilt/2022_cyan_pathway_files/figure-html/unnamed-chunk-11-1.png create mode 100644 docs/dev/articles/prebuilt/2022_cyan_pathway_files/figure-html/unnamed-chunk-12-1.png create mode 100644 docs/dev/articles/prebuilt/2022_cyan_pathway_files/figure-html/unnamed-chunk-13-1.png create mode 100644 docs/dev/articles/prebuilt/2022_cyan_pathway_files/figure-html/unnamed-chunk-17-1.png create mode 100644 docs/dev/articles/prebuilt/2022_cyan_pathway_files/figure-html/unnamed-chunk-18-1.png create mode 100644 docs/dev/articles/prebuilt/2022_cyan_pathway_files/figure-html/unnamed-chunk-19-1.png create mode 100644 docs/dev/articles/prebuilt/2022_cyan_pathway_files/figure-html/unnamed-chunk-6-1.png create mode 100644 docs/dev/articles/prebuilt/2022_cyan_pathway_files/figure-html/unnamed-chunk-7-1.png create mode 100644 docs/dev/articles/prebuilt/2022_dmta_parent.html create mode 100644 docs/dev/articles/prebuilt/2022_dmta_parent_files/figure-html/convergence-saem-dfop-const-1.png create mode 100644 docs/dev/articles/prebuilt/2022_dmta_parent_files/figure-html/convergence-saem-dfop-tc-1.png create mode 100644 docs/dev/articles/prebuilt/2022_dmta_parent_files/figure-html/convergence-saem-dfop-tc-no-ranef-k2-1.png create mode 100644 docs/dev/articles/prebuilt/2022_dmta_parent_files/figure-html/convergence-saem-fomc-const-1.png create mode 100644 docs/dev/articles/prebuilt/2022_dmta_parent_files/figure-html/convergence-saem-fomc-tc-1.png create mode 100644 docs/dev/articles/prebuilt/2022_dmta_parent_files/figure-html/convergence-saem-hs-const-1.png create mode 100644 docs/dev/articles/prebuilt/2022_dmta_parent_files/figure-html/convergence-saem-hs-tc-1.png create mode 100644 docs/dev/articles/prebuilt/2022_dmta_parent_files/figure-html/convergence-saem-sfo-const-1.png create mode 100644 docs/dev/articles/prebuilt/2022_dmta_parent_files/figure-html/convergence-saem-sfo-tc-1.png create mode 100644 docs/dev/articles/prebuilt/2022_dmta_parent_files/figure-html/multistart-full-par-1.png create mode 100644 docs/dev/articles/prebuilt/2022_dmta_parent_files/figure-html/multistart-reduced-par-1.png create mode 100644 docs/dev/articles/prebuilt/2022_dmta_parent_files/figure-html/multistart-reduced-par-llquant-1.png create mode 100644 docs/dev/articles/prebuilt/2022_dmta_parent_files/figure-html/plot-saem-dfop-tc-no-ranef-k2-1.png create mode 100644 docs/dev/articles/prebuilt/2022_dmta_pathway.html create mode 100644 docs/dev/articles/prebuilt/2022_dmta_pathway_files/figure-html/saem-sforb-path-1-tc-reduced-convergence-1.png create mode 100644 docs/dev/articles/prebuilt/2022_dmta_pathway_files/figure-html/unnamed-chunk-2-1.png create mode 100644 docs/dev/articles/prebuilt/2022_dmta_pathway_files/figure-html/unnamed-chunk-3-1.png create mode 100644 docs/dev/articles/prebuilt/2022_dmta_pathway_files/figure-html/unnamed-chunk-4-1.png create mode 100644 docs/dev/articles/prebuilt/2022_dmta_pathway_files/figure-html/unnamed-chunk-5-1.png create mode 100644 docs/dev/articles/prebuilt/2022_dmta_pathway_files/figure-html/unnamed-chunk-6-1.png create mode 100644 docs/dev/articles/prebuilt/2022_dmta_pathway_files/figure-html/unnamed-chunk-7-1.png diff --git a/_pkgdown.yml b/_pkgdown.yml index 5d7fdbf4..5c67d88f 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,7 +1,7 @@ url: https://pkgdown.jrwb.de/mkin development: - mode: devel + mode: devel version_label: info template: @@ -135,31 +135,45 @@ navbar: title: ~ type: default left: - - text: Functions and data + - text: Reference href: reference/index.html - text: Articles menu: - text: Introduction to mkin href: articles/mkin.html + - text: "-------" + - text: Example evaluations with (generalised) nonlinear least squares - text: Example evaluation of FOCUS Example Dataset D href: articles/FOCUS_D.html - text: Example evaluation of FOCUS Laboratory Data L1 to L3 href: articles/FOCUS_L.html - - text: Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models + - text: Example evaluation of FOCUS Example Dataset Z + href: articles/web_only/FOCUS_Z.html + - text: "-------" + - text: Example evaluations with hierarchical models (nonlinear mixed-effects models) + - text: Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P + href: articles/prebuilt/2022_dmta_parent.html + - text: Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P + href: articles/prebuilt/2022_dmta_pathway.html + - text: Testing hierarchical pathway kinetics with residue data on cyantraniliprole + href: articles/prebuilt/2022_cyan_pathway.html + - text: Comparison of saemix and nlme evaluations of dimethenamid data from 2018 href: articles/web_only/dimethenamid_2018.html - text: Short demo of the multistart method href: articles/web_only/multistart.html + - text: "-------" + - text: Performance - text: Performance benefit by using compiled model definitions in mkin href: articles/web_only/compiled_models.html - - text: Example evaluation of FOCUS Example Dataset Z - href: articles/web_only/FOCUS_Z.html - - text: Calculation of time weighted average concentrations with mkin - href: articles/twa.html - - text: Example evaluation of NAFTA SOP Attachment examples - href: articles/web_only/NAFTA_examples.html - text: Benchmark timings for mkin href: articles/web_only/benchmarks.html - text: Benchmark timings for saem.mmkin href: articles/web_only/saem_benchmarks.html + - text: "-------" + - text: Miscellaneous + - text: Calculation of time weighted average concentrations with mkin + href: articles/twa.html + - text: Example evaluation of NAFTA SOP Attachment examples + href: articles/web_only/NAFTA_examples.html - text: News href: news/index.html diff --git a/docs/dev/articles/index.html b/docs/dev/articles/index.html index cd0e315f..b9571a60 100644 --- a/docs/dev/articles/index.html +++ b/docs/dev/articles/index.html @@ -23,7 +23,7 @@