From 0023df3c31fac29b5f9337ecd732a5dfd4d51a2d Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 19 Dec 2022 06:37:32 +0100 Subject: Template and spreadsheet for hierarchical kinetics The template only shows parent data evaluation without covariate models for now. The spreadsheet will also be useful for unit testing of the read_spreadsheet function. --- .gitignore | 3 +++ 1 file changed, 3 insertions(+) (limited to '.gitignore') diff --git a/.gitignore b/.gitignore index 75005f00..4f479259 100644 --- a/.gitignore +++ b/.gitignore @@ -1,5 +1,8 @@ docs/articles/*_cache/ install.log +inst/rmarkdown/templates/hier/skeleton/skeleton_cache +inst/rmarkdown/templates/hier/skeleton/skeleton_files +inst/rmarkdown/templates/hier/skeleton/skeleton.pdf mkin*.tar.gz mkin.tar mkin.Rcheck -- cgit v1.2.1 From 886c9ef013124aa954d960c655b349b5340ff154 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 19 Dec 2022 12:31:56 +0100 Subject: Rename template folder, create format Instead of rmarkdown::pdf_document, mkin::hierarchical_kinetics is used as a document format in the template. In this way, the template file can be freed from some R code and yaml options that the average user does not have to be aware of. --- .gitignore | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to '.gitignore') diff --git a/.gitignore b/.gitignore index 4f479259..9808896d 100644 --- a/.gitignore +++ b/.gitignore @@ -1,8 +1,8 @@ docs/articles/*_cache/ install.log -inst/rmarkdown/templates/hier/skeleton/skeleton_cache -inst/rmarkdown/templates/hier/skeleton/skeleton_files -inst/rmarkdown/templates/hier/skeleton/skeleton.pdf +inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton_cache +inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton_files +inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.pdf mkin*.tar.gz mkin.tar mkin.Rcheck -- cgit v1.2.1 From ed2ab7bba07e3cb036782227fe27943f4b5583fa Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 3 Jan 2023 09:31:48 +0100 Subject: Improved skeleton for hierarchical fits Now with working pathway fits using SFORB-SFO2 (only two parallel metabolites instead of three) as the data for compound Ia was not sufficient for a reliable fit. --- .gitignore | 1 + 1 file changed, 1 insertion(+) (limited to '.gitignore') diff --git a/.gitignore b/.gitignore index 9808896d..5416f8f0 100644 --- a/.gitignore +++ b/.gitignore @@ -3,6 +3,7 @@ install.log inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton_cache inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton_files inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.pdf +inst/rmarkdown/templates/hierarchical_kinetics/skeleton/*_dlls mkin*.tar.gz mkin.tar mkin.Rcheck -- cgit v1.2.1 From ae314cd8869765dd05f1ae44f4d73ae71f788c62 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 3 Jan 2023 17:42:15 +0100 Subject: Reflect changed name of dll directory in template --- .gitignore | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to '.gitignore') diff --git a/.gitignore b/.gitignore index 5416f8f0..a86197a1 100644 --- a/.gitignore +++ b/.gitignore @@ -3,7 +3,7 @@ install.log inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton_cache inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton_files inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.pdf -inst/rmarkdown/templates/hierarchical_kinetics/skeleton/*_dlls +inst/rmarkdown/templates/hierarchical_kinetics/skeleton/dlls mkin*.tar.gz mkin.tar mkin.Rcheck -- 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 --- .gitignore | 4 ++++ 1 file changed, 4 insertions(+) (limited to '.gitignore') diff --git a/.gitignore b/.gitignore index a86197a1..5bec45e6 100644 --- a/.gitignore +++ b/.gitignore @@ -28,3 +28,7 @@ vignettes/cache/ vignettes/figure/ vignettes/*_cache/ vignettes/*_files/ +vignettes/prebuilt/*_cache +vignettes/prebuilt/*_files +vignettes/prebuilt/*_dlls +vignettes/prebuilt/*.pdf -- cgit v1.2.1