Co-authored-by: Schiano-NOAA <Schiano-NOAA@users.noreply.github.com>

Co-authored-by: Schiano-NOAA <Schiano-NOAA@users.noreply.github.com>

Adding back section tagging

…ta Barbara office in offices (#159)

* Feat(vignettes):
-added tables of contents to vignettes
-added tip for how to edit rda files to a11y vignette
-added link to faqs vignette to a11y vignette re: how to edit alt text and captions

* fix to incorrect reference in .bib file (#149)

* fix incorrect reference

* add url to reference fix

* remove replicate nmfs palette and add_theme

* remove files

* Custom template fixes (#143)

* update(create_template): comment out skeleton pop up at the end

* update(add_section): add functionality for putting new subsection into section

* Update(add_section): fix pathing for locating section to place code and change from add_chunk to add_child

* update(create_template): select only custom_sections when user wants to make a different outline of report

custom must = TRUE otherwise copies all files

* Fix(create_template): adjust if statement argument for custom_sections

* Add nmfspalette package back in

* removed add_theme and associated test and documentation

* remove static NOAA Fishies in authorship

* update NOAA fisheries affiliations

Co-authored-by: Schiano-NOAA <Schiano-NOAA@users.noreply.github.com>

---------

Co-authored-by: sbreitbart-NOAA <sophie.breitbart@noaa.gov>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Schiano-NOAA <Schiano-NOAA@users.noreply.github.com>

* Fix(create_template):
-Fix so that rda files can be added as input, if already created, OR generated if model results are included as an argument.
-Update documentation

* update(format_quarto): add functionality for html formatting with associated files and changes to create_template (#152)

* small comment update

* update(create_template): custom_sections adds all selected plus refs, acknow, and tables and figs if desired

* Custom template fixes (#143)

* update(create_template): comment out skeleton pop up at the end

* update(add_section): add functionality for putting new subsection into section

* Update(add_section): fix pathing for locating section to place code and change from add_chunk to add_child

* update(create_template): select only custom_sections when user wants to make a different outline of report

custom must = TRUE otherwise copies all files

* Fix(create_template): adjust if statement argument for custom_sections

* Add nmfspalette package back in

* removed add_theme and associated test and documentation

* remove static NOAA Fishies in authorship

* update NOAA fisheries affiliations

Co-authored-by: sbreitbart-NOAA <sophie.breitbart@noaa.gov>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Schiano-NOAA <Schiano-NOAA@users.noreply.github.com>

* Inject accessibility (#124)

* Custom template fixes (#143)

* update(create_template): comment out skeleton pop up at the end

* update(add_section): add functionality for putting new subsection into section

* Update(add_section): fix pathing for locating section to place code and change from add_chunk to add_child

* update(create_template): select only custom_sections when user wants to make a different outline of report

custom must = TRUE otherwise copies all files

* Fix(create_template): adjust if statement argument for custom_sections



* Removed captions_alt_text_template.csv because it's not used in asar... only satf. Then updated a11y vignette to reflect where users should look for the file.

* changed eval for first chunk to true, and eval for indices table setup chunk to false, re: #102 . Will change eval to true for all chunks once indices table fxn is completed.

* feature(add new template partial for accessibility and add fxn)

* Update(add_tagging): ability to add alternative text to tex file from rdas

* fix(add_taggig): change directory for rda files to arg

* fix(add_tagging): change pathing to rda_dir

* fix(add-tagging): rename accessibility tex for output

* feature(add_accessibility): rename function and load documentation

* Initial commit for add_accessibility test - commented out bc unfinished

* update(test-add_accessibility): add snapshot for tex file and add proper code for testing

* feature(alter accessibility fxns): split up funxtion into two and called both using the add_accessibility function

Also adjusted testing function for add_alttext and removed old snapshot - was not working properly

* Remove nmfspallete from dependencies temporarily (#139)

* Remove nmfs-pallete from dependencies temporarily

* Comment out reference to nmfs pallete in add_theme and tests

* style and docs: run devtools::document() and styler::style_pkg() (#140)

Co-authored-by: Schiano-NOAA <Schiano-NOAA@users.noreply.github.com>

* Add nmfspalette back into package

* Merge newer dev branch into old (#148)

* Minor grammatical changes just to set up new dev-1.1 branch (changed quarto --> Quarto)

* Feat(vignettes):
-added tables of contents to vignettes
-added tip for how to edit rda files to a11y vignette
-added link to faqs vignette to a11y vignette re: how to edit alt text and captions

* remove old package from namespace and add in new

* add notes for new alttext test

* Removed captions_alt_text_template.csv because it's not used in asar... only satf. Then updated a11y vignette to reflect where users should look for the file.

* feature(alter accessibility fxns): split up funxtion into two and called both using the add_accessibility function

Also adjusted testing function for add_alttext and removed old snapshot - was not working properly

* update(create_template): custom_sections adds all selected plus refs, acknow, and tables and figs if desired

* add spp_conout.csv to gitignore during testing

* feature(add_alttext): add accessibility for user to add alt text to figures inserted into the outline (png)

* fix(add_alttext): improve fxning for adding alt text to custom figs either from images or code chunks

* feature(add_alttext): add example to function

* comment out alttext fxn test

* clean up fxns and add examples

* add in support_file/accessibilit.tex

* fix(create_tables_doc): remove incorrect and duplicate indices table code

* update(accessibility fxns): update to fix minor issues with functions and documentation as mentioned by @sbreitbart-NOAA

* update documentation

* update(test-alttext): change test for alttext to mimic changes to the function - sdoes not work still

* update(a11y fxns): improvements to functions as well as tests

* update(add_alttext): update example to show to to use rename arg

* minor updates and changes to fix test failures and checks

* Feat(create_tables_doc): automatically test if tables are wide enough to require changing page orientation from portrait to landscape. Alter the Tables qmd to allow orientation changes for each table, if necessary.

* Update orientation-related code for still-in-dev landings table

* Extend landscape table width from 7.5 to 8.5"; add page breaks between tables

* bug fixes

* Started coding new function to handle super wide tables and split into smaller ones

* Finished first full draft of function that will render large tables by splitting into multiple tables

* Added essential_columns arg to render_lg_table()

* Move orientation-detecting code into own function in utils, then update create_tables_doc

* Moved render_lg_table fxn to own R script, then updated documentation

* Update tests to remove temporary files upon test completion

* Add more params to render_lg_table() and ID_pg_orientation(), then update documentation and usage in create_tables_doc()

* Added code into create_tables_doc that splits extra-wide tables into multiple smaller tables, but still a bug in render_lg_table (producing "Error" as part of output when testing)

* Found a solution for sourcing render_lg_table in 08_tables.qmd and successfully rendering extra-wide table with new solution, but need to check if this will work in other circumstances

* found a successful workflow and applied it to indices table. Next step: apply to other tables, and simplify/clarify the new functions

* Copied new changes to bnc table, but referencing a chunk with multiple tables will only reference the last table in the chunk, not the first. So next step: make a chunk for each table.
Also removed now irrelevant function: ID_split_tbls

* Redesigned create_tables_doc so that each table has its own chunk and can be referenced.

* Updated landings table code

* Removed "-plot" from create_figures/tables_doc chunks

* Add note to create_tables_doc explaining why new rda with split tables is made; update documentation

* First draft of render_lg_table test; update documentation

* Remove code from create_tables_doc that reduces row height in tables

* update terminal sb naming to match other conventions

* Added Q&A about figure/table order to FAQs vignette

* Updated create_tables_doc so that split tables include header values in parentheses after caption (example: <indices caption> (Fleet 6, Fleet 7))

* Updated examples

* Clarified comments; renamed some variables to be unique and more clear; removed unnecessary and repetitious code

* Add vignette for convert_output fxn (#161)

* feature(convert output vignette): initial commit for article describing the convert output function

* feature(conout vignette): add in more information including example dataframe (needs adjustment to code chunk)

* minor improvements to convert_output vignette

* update(convert output vignette): add links to function and parts of code; add useful functions outside of asar used in function

* finish(convert output vignette): add in flowchart and final details

* add(conout-vignette): update chunk displatying example data

* Update vignettes/convert_output_details.Rmd

Co-authored-by: Sophie Breitbart <sophie.breitbart@noaa.gov>

* Update vignettes/convert_output_details.Rmd

Co-authored-by: Sophie Breitbart <sophie.breitbart@noaa.gov>

* Update vignettes/convert_output_details.Rmd

Co-authored-by: Sophie Breitbart <sophie.breitbart@noaa.gov>

* Update vignettes/convert_output_details.Rmd

Co-authored-by: Sophie Breitbart <sophie.breitbart@noaa.gov>

* fix(conout vignette): clarity to the text per comments made from @sbreitbart-NOAA

* update(conout vignette): add finishing touches to convert output vignette

* Fix translation of R0 parameter from BAM in convert_output (#163)

* fix(convert_output): fix error when parameters containing a number were incorrectly labelled in the final df

* First full draft of vignette re: #156

* fix(dev): remove add_accessibility and add_tagging functions since they are still in development until we can make the change to work alt text and tagging together

* Converting vignette's option comparison table to flextable

* update(add_alttext): change search name for figures to reflect change to rendering naming convention

* update(add_alttext): additional line to find old naming conventions from figures processed from quarto

* note(add_alttext): add TODO in fxn for rendering to html or docx if applicable down the line

---------

Co-authored-by: sbreitbart-NOAA <sophie.breitbart@noaa.gov>
Co-authored-by: Ian Taylor <4992918+iantaylor-NOAA@users.noreply.github.com>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Schiano-NOAA <Schiano-NOAA@users.noreply.github.com>

Co-authored-by: Schiano-NOAA <125507018+Schiano-NOAA@users.noreply.github.com>

* Updating create_template's exp_all_figs_tables to include new args

* Replace all instances of satf with stockplotr

* removed satf from wordlist per @Schiano-NOAA 's suggestion

Co-authored-by: sbreitbart-NOAA <181890943+sbreitbart-NOAA@users.noreply.github.com>