From e5d1df9a9b1f0951d7dfbaf24eee4294470b73e2 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 17 Nov 2022 14:54:20 +0100 Subject: Complete update of online docs for v1.2.0 --- _pkgdown.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to '_pkgdown.yml') diff --git a/_pkgdown.yml b/_pkgdown.yml index bb1ad052..8aa44ed4 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,8 +1,8 @@ url: https://pkgdown.jrwb.de/mkin development: - mode: devel - version_label: info + mode: release + version_label: default template: bootswatch: spacelab -- cgit v1.2.1 From 5364f037a72863ef5ba81e14ba4417f68fd389f9 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 18 Nov 2022 19:14:47 +0100 Subject: Make mixed model test data permanent to ensure reproducibility To ensure that tests on different platforms work on the same data, the mixed modelling test data previosly generated in tests/testthat/setup_script.R were generated once using the script in inst/dataset/generation/ds_mixed.R, and are now distributed with the package. --- _pkgdown.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to '_pkgdown.yml') diff --git a/_pkgdown.yml b/_pkgdown.yml index 8aa44ed4..98ed84f2 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -67,7 +67,7 @@ reference: - parplot - title: Datasets and known results contents: - - focus_soil_moisture + - ds_mixed - D24_2014 - dimethenamid_2018 - FOCUS_2006_A @@ -82,6 +82,7 @@ reference: - synthetic_data_for_UBA_2014 - experimental_data_for_UBA_2019 - test_data_from_UBA_2014 + - focus_soil_moisture - mkinds - mkindsg - title: NAFTA guidance -- cgit v1.2.1 From e99b46a2020a6b6578b0c3c88c17d5980e4d921a Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 22 Nov 2022 13:49:02 +0100 Subject: Start new development version --- _pkgdown.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to '_pkgdown.yml') diff --git a/_pkgdown.yml b/_pkgdown.yml index 98ed84f2..ca5ea6e0 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,8 +1,8 @@ url: https://pkgdown.jrwb.de/mkin development: - mode: release - version_label: default + mode: devel + version_label: info template: bootswatch: spacelab -- cgit v1.2.1 From 24eb77216700cf8b2f2bde3abad84c1f83f9e32a Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 9 Jan 2023 06:22:04 +0100 Subject: Prebuilt PDF vignettes, summary_listing --- _pkgdown.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) (limited to '_pkgdown.yml') diff --git a/_pkgdown.yml b/_pkgdown.yml index ca5ea6e0..5d7fdbf4 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -47,6 +47,7 @@ reference: - title: Mixed models desc: Create and work with nonlinear hierarchical models contents: + - hierarchical_kinetics - read_spreadsheet - nlme.mmkin - saem.mmkin @@ -92,7 +93,7 @@ reference: - plot.nafta - title: Utility functions contents: - - tex_listing + - summary_listing - f_time_norm_focus - set_nd_nq - max_twa_parent -- cgit v1.2.1 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 +++++++++++++++++++++++--------- 1 file changed, 23 insertions(+), 9 deletions(-) (limited to '_pkgdown.yml') 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 -- cgit v1.2.1