* Attempt to inherit custom_sections parameter from asar::create_template()

* Changed remaining x's (former argument) into custom_sections (new argument), and removed the parameter definition

* Clarified argument definitions for add_child.R

* Clarified argument definitions for add_chunk.R

* Clarified argument definitions for add_section.R.

Note: The text previously referenced an argument that was missing from the function ('title'). In my update, I changed it to 'sec_names'. Please verify that this was an accurate assumption.

* Clarified argument definitions for create_citation.R

* Clarified argument definitions for create_figures_doc.R

* Clarified argument definitions for create_title.R

* Clarified argument definitions for export_object.R

* Clarified argument definitions for format_quarto.R

* Clarified argument definitions in create_template. Since associated scripts (add_section, create_title, format_quarto) used same parameters (but with different names), changed the parameter names in associated scripts to names in create_template, then inherited parameter names from create_template to reduce redundancy.

Questions for Sam:
Please check/edit the "parameters" parameter's definition. What does it mean, and how should it be defined? Is it ever false?

Please check/edit the "param_values" parameter's definition. What does it mean, and how should it be defined?

Please check/edit the "convert_output" parameter's definition for accuracy.

* Updated documentation

* Clarified argument definitions in convert_output.R and updated documentation.

* Update(affiliation_info.csv): add country

* update(create_figures_doc): add example of where caption will go

Integration of the other captions once written and alt. text will form adjustments to here

* Reorder skeleton (#59)

* update(template): add changes for debugging and issue

- Added options for english and removed the old czech lang the in-header doc
- changed the chunks for figs and tabs not to render while development is occurring

* update(template): add changes for debugging and issue

- Added options for english and removed the old czech lang the in-header doc
- changed the chunks for figs and tabs not to render while development is occurring

* Attempt to inherit custom_sections parameter from asar::create_template()

* Changed remaining x's (former argument) into custom_sections (new argument), and removed the parameter definition

* Clarified argument definitions for create_title.R

* Clarified argument definitions in create_template. Since associated scripts (add_section, create_title, format_quarto) used same parameters (but with different names), changed the parameter names in associated scripts to names in create_template, then inherited parameter names from create_template to reduce redundancy.

Questions for Sam:
Please check/edit the "parameters" parameter's definition. What does it mean, and how should it be defined? Is it ever false?

Please check/edit the "param_values" parameter's definition. What does it mean, and how should it be defined?

Please check/edit the "convert_output" parameter's definition for accuracy.

* Clarified argument definitions in convert_output.R and updated documentation.

* update(create_figures_doc): add example of where caption will go

Integration of the other captions once written and alt. text will form adjustments to here

* refactor: Changed names of sections in create_template to those voted on by steering committee (as of Sept 2024)

* deleted files with outdated names (i.e., without numbers before descriptions

* updated test-create_template.R to avoid merge conflict

* Remove test folder pushed to repo

* fix(custom section op): change base_section, add_section, and test

- changes in both naming of arguments and templates were fixed
- test-add_section was adjusted so expected values were correct

* fix(assessment spelling): change file name and will now pass test

* delete(assessment_gloassaries.tex)

* fix(test-add_section): spelling error in test

* deleted files with outdated names (i.e., without numbers before descriptions

* updated test-create_template.R to avoid merge conflict

* Remove test folder pushed to repo

* fix(assessment spelling): change file name and will now pass test

* fix(test-add_section): change file names in test and adjust fxns to meet test expectations

* fix(test-create_template): add to resdir to remove warning in test

* delete(utils): remove add_base_section from utils

* Attempt to inherit custom_sections parameter from asar::create_template()

* Changed remaining x's (former argument) into custom_sections (new argument), and removed the parameter definition

* Clarified argument definitions for add_child.R

* Clarified argument definitions for add_chunk.R

* Clarified argument definitions for add_section.R.

Note: The text previously referenced an argument that was missing from the function ('title'). In my update, I changed it to 'sec_names'. Please verify that this was an accurate assumption.

* Clarified argument definitions for create_citation.R

* Clarified argument definitions for create_figures_doc.R

* Clarified argument definitions for create_title.R

* Clarified argument definitions for export_object.R

* Clarified argument definitions for format_quarto.R

* Clarified argument definitions in create_template. Since associated scripts (add_section, create_title, format_quarto) used same parameters (but with different names), changed the parameter names in associated scripts to names in create_template, then inherited parameter names from create_template to reduce redundancy.

Questions for Sam:
Please check/edit the "parameters" parameter's definition. What does it mean, and how should it be defined? Is it ever false?

Please check/edit the "param_values" parameter's definition. What does it mean, and how should it be defined?

Please check/edit the "convert_output" parameter's definition for accuracy.

* Updated documentation

* Clarified argument definitions in convert_output.R and updated documentation.

* Update(affiliation_info.csv): add country

* update(create_figures_doc): add example of where caption will go

Integration of the other captions once written and alt. text will form adjustments to here

* Attempt to inherit custom_sections parameter from asar::create_template()

* Changed remaining x's (former argument) into custom_sections (new argument), and removed the parameter definition

* Clarified argument definitions for create_title.R

* Clarified argument definitions in create_template. Since associated scripts (add_section, create_title, format_quarto) used same parameters (but with different names), changed the parameter names in associated scripts to names in create_template, then inherited parameter names from create_template to reduce redundancy.

Questions for Sam:
Please check/edit the "parameters" parameter's definition. What does it mean, and how should it be defined? Is it ever false?

Please check/edit the "param_values" parameter's definition. What does it mean, and how should it be defined?

Please check/edit the "convert_output" parameter's definition for accuracy.

* Clarified argument definitions in convert_output.R and updated documentation.

* refactor: Changed names of sections in create_template to those voted on by steering committee (as of Sept 2024)

* deleted files with outdated names (i.e., without numbers before descriptions

* updated test-create_template.R to avoid merge conflict

* Remove test folder pushed to repo

* fix(custom section op): change base_section, add_section, and test

- changes in both naming of arguments and templates were fixed
- test-add_section was adjusted so expected values were correct

* fix(assessment spelling): change file name and will now pass test

* delete(assessment_gloassaries.tex)

* fix(test-add_section): spelling error in test

* deleted files with outdated names (i.e., without numbers before descriptions

* updated test-create_template.R to avoid merge conflict

* Remove test folder pushed to repo

* fix(assessment spelling): change file name and will now pass test

* fix(test-add_section): change file names in test and adjust fxns to meet test expectations

* fix(test-create_template): add to resdir to remove warning in test

* delete(utils): remove add_base_section from utils

* Fix naming in create_template

---------

Co-authored-by: Schiano-NOAA <[email protected]>

* Updating ss3 variable names Excel file by highlighting variables that have been included in the ss3/BAM model variable name guide/key and updating some variable definitions (#61)

* fix: adjustments to pass checks/ghactions

* fix(std naming&convert_output): make changes to standard naming sheets and convert_output to pass tests

test-add_chunk commented out due to issues I can not find

* Update(wordlist): issues with spelling and names for species fixed

* feat(README): change example to petrale

Changing to a working example in read me that mimic that of a current stock assessment. The files resulting from the example and rendered report need to be added as their own example in a folder

* update(example): change README so users can run  petrale example

# Summary

- add raw and converted petrale output to data folder
- ran usethis::use_data() creating structure for the example
- updated documentation

* fix:(create_template): add preamble

- read in converted output in chunk
- create place for pre-loaded quantities to reference later in the document

* update(test-add_chunk): correct notes in test

* Fix(readme): example needed csv file

* Update(readme): adjust for new section names

* update(website): change set up of pkgdown website

* Update(pkgdown.yml): include tutorial

* feature(add tutorial): demo in shiny app

Might need to move folders - pushing now in order to switch branches ok

* remove(tutorial): move materials to asar-demo repo and host there

* update(pkgdown): add tutorial link to site

* update(README): add link for tutorial in examples

* add(species images): more images for title page

added in most of AK stocks and changed NE stocks to png

* feature(create_template): add output R chunk and space for bib file

- Also add in renaming of file when skeleton is rendered

* fix: fixed small typo

* Add in bib_file arg

* add(spp_images): hawaiian big7 species images

* update(create_figures_doc): add in chunk options for cap and alt text

Also add space to read in sheet containing labels, fig caps, and alt-text

*Uncomment for implementation*

* Make adjustments to BAM names

* fix(references): method so .bib file is read in with the quarto file and not at the end of the doc

* uncomment the add_chunk() tests (#63)

* update: decription and create_template documentation

Add in place for bib file if added

* fix(create_template): replace example with previous one developed by … (#64)

* fix(create_template): replace example with previous one developed by @sbreitbart-NOAA

* update(rd): update create_template documentation

* build: started building functionality to add captions and alt text to figures by adding to create_figures_doc.R and adding .csv with pre-populated captions and alt text templates (captions_alttext.csv).

* build: developed capability to caption tables.

* Update(pkgdown yml): Reorder top nav bar and have a drop down manual for all vignettes instead

* Remove example data - moved to asar-demo

* Create working example and resources for users (#54)

* feat(README): change example to petrale

Changing to a working example in read me that mimic that of a current stock assessment. The files resulting from the example and rendered report need to be added as their own example in a folder

* update(example): change README so users can run  petrale example

# Summary

- add raw and converted petrale output to data folder
- ran usethis::use_data() creating structure for the example
- updated documentation

* fix:(create_template): add preamble

- read in converted output in chunk
- create place for pre-loaded quantities to reference later in the document

* update(test-add_chunk): correct notes in test

* Fix(readme): example needed csv file

* Update(readme): adjust for new section names

* update(website): change set up of pkgdown website

* Update(pkgdown.yml): include tutorial

* feature(add tutorial): demo in shiny app

Might need to move folders - pushing now in order to switch branches ok

* remove(tutorial): move materials to asar-demo repo and host there

* update(pkgdown): add tutorial link to site

* update(README): add link for tutorial in examples

* Update(pkgdown yml): Reorder top nav bar and have a drop down manual for all vignettes instead

* Remove example data - moved to asar-demo

* fix(create_template): replaced params_chunk with preamble

* build: created first outline and basic files for new accessibility vignette

* fix(author order): add line so order of authors follows that input by the user

* Update(WORDLIST)

* feature(_titlepage); add dynamic alt text to cover image

* feature(create_tempalte): change pdf engine to lualatex when format is pdf

* Update(tex): documentation

* feature(create_template): add quanitites to preamble chunk

Most of these still need to be looked up and adjusted so they are read from the output file - then they can be uncommented

* update(create_template): reflect changes to create_titlepage_tex in fxn

* build: finished first full draft of accessibility vignette

* build: adding some files associated with building the accessibility vignette

* fix(create_template): reference to converted output correction

* Revert "Pkgdown vignettes"

* fix: to resolve call-workflow / spell-check error, added words to the WORDLIST that R didn't recognize and added language to the DESCRIPTION file

* fix(site): remove unncessary folders and files

Add accessibility article into site and add in references.bib file

* Update(description): authorship

* fix(description): authorship structure

* Fix description...again

* Update(authorship)

Works with site

* build: added alt text to cover page's US Dept of Commerce seal

* fix: Changed the NOAA logo classification to an artifact and removed alt text

* Fix(create_template): change save for convert_output to remove extra underscore and paste spp name together with underscore

* fix(create_template.R): updated definition of model_results argument.

* Automatically identify fleet names in BAM output (#72)

* feature(find BAM fleet names)

Fix standard naming conventions sheet

* fix(convert_output):change age to numeric for converting purposes

* Update(documentation): fleet names documentation

Update create_template to reflect changes to convert_output

* Update(convert_output): fleet names not kept in D.release/Dosed.release

* Deprecate fleet_names parameter in create_template

* Update documentation for PR

* Fix(create_template): species naming in converted output within create_template

* fix(convert_output): add nsim factor

Nsim factor in BAM for eq.series and pr.series - might need further adjustment for naming (unsure if nsim)

* fix(convert_output test): reflect the new factor added to the output file

* fix(convert_output): aging error matrix for BAM incorrectly transformed

Reflect the changes and addition of another factor into the test

* style(create_template): shortened chunk labels by removing preceding numbers

---------

Co-authored-by: Schiano-NOAA <[email protected]>
Co-authored-by: Bai Li - NOAA <[email protected]>
Co-authored-by: Sam Schiano <[email protected]>

Please see release notes v0.3 for more succinct changes

* Inherit custom_sections parameter from asar::create_template()

*Clarified argument definitions for multiple functions

* Clarified argument definitions in create_template. Since associated scripts (add_section, create_title, format_quarto) used same parameters (but with different names), changed the parameter names in associated scripts to names in create_template, then inherited parameter names from create_template to reduce redundancy.

* Updated documentation

* Update(affiliation_info.csv): add country

* Reorder skeleton (#59)

- Added options for english and removed the old czech lang the in-header doc

* refactor: Changed names of sections in create_template to those voted on by steering committee (as of Sept 2024)

* deleted files with outdated names (i.e., without numbers before descriptions

* delete(utils): remove add_base_section from utils

* Updated documentation

* Clarified argument definitions in convert_output.R and updated documentation.

* Update(affiliation_info.csv): add country

* update(create_figures_doc): add example of where caption will go

Integration of the other captions once written and alt. text will form adjustments to here

* Attempt to inherit custom_sections parameter from asar::create_template()

* Changed remaining x's (former argument) into custom_sections (new argument), and removed the parameter definition

* Clarified argument definitions for create_title.R

* Clarified argument definitions in create_template. Since associated scripts (add_section, create_title, format_quarto) used same parameters (but with different names), changed the parameter names in associated scripts to names in create_template, then inherited parameter names from create_template to reduce redundancy.

Questions for Sam:
Please check/edit the "parameters" parameter's definition. What does it mean, and how should it be defined? Is it ever false?

Please check/edit the "param_values" parameter's definition. What does it mean, and how should it be defined?

Please check/edit the "convert_output" parameter's definition for accuracy.

* Clarified argument definitions in convert_output.R and updated documentation.

* refactor: Changed names of sections in create_template to those voted on by steering committee (as of Sept 2024)

* deleted files with outdated names (i.e., without numbers before descriptions

* updated test-create_template.R to avoid merge conflict

* Remove test folder pushed to repo

* fix(custom section op): change base_section, add_section, and test

- changes in both naming of arguments and templates were fixed
- test-add_section was adjusted so expected values were correct

* fix(assessment spelling): change file name and will now pass test

* delete(assessment_gloassaries.tex)

* fix(test-add_section): spelling error in test

* deleted files with outdated names (i.e., without numbers before descriptions

* updated test-create_template.R to avoid merge conflict

* Remove test folder pushed to repo

* fix(assessment spelling): change file name and will now pass test

* fix(test-add_section): change file names in test and adjust fxns to meet test expectations

* fix(test-create_template): add to resdir to remove warning in test

* delete(utils): remove add_base_section from utils

* Fix naming in create_template

---------

Co-authored-by: Schiano-NOAA <[email protected]>

* Updating ss3 variable names Excel file by highlighting variables that have been included in the ss3/BAM model variable name guide/key and updating some variable definitions (#61)

* fix: adjustments to pass checks/ghactions

* fix(std naming&convert_output): make changes to standard naming sheets and convert_output to pass tests

test-add_chunk commented out due to issues I can not find

* Update(wordlist): issues with spelling and names for species fixed

* feat(README): change example to petrale

Changing to a working example in read me that mimic that of a current stock assessment. The files resulting from the example and rendered report need to be added as their own example in a folder

* update(example): change README so users can run  petrale example

# Summary

- add raw and converted petrale output to data folder
- ran usethis::use_data() creating structure for the example
- updated documentation

* fix:(create_template): add preamble

- read in converted output in chunk
- create place for pre-loaded quantities to reference later in the document

* update(test-add_chunk): correct notes in test

* Fix(readme): example needed csv file

* Update(readme): adjust for new section names

* update(website): change set up of pkgdown website

* Update(pkgdown.yml): include tutorial

* feature(add tutorial): demo in shiny app

Might need to move folders - pushing now in order to switch branches ok

* remove(tutorial): move materials to asar-demo repo and host there

* update(pkgdown): add tutorial link to site

* update(README): add link for tutorial in examples

* add(species images): more images for title page

added in most of AK stocks and changed NE stocks to png

* feature(create_template): add output R chunk and space for bib file

- Also add in renaming of file when skeleton is rendered

* fix: fixed small typo

* Add in bib_file arg

* add(spp_images): hawaiian big7 species images

* update(create_figures_doc): add in chunk options for cap and alt text

Also add space to read in sheet containing labels, fig caps, and alt-text

*Uncomment for implementation*

* Make adjustments to BAM names

* fix(references): method so .bib file is read in with the quarto file and not at the end of the doc

* uncomment the add_chunk() tests (#63)

* update: decription and create_template documentation

Add in place for bib file if added

* fix(create_template): replace example with previous one developed by … (#64)

* fix(create_template): replace example with previous one developed by @sbreitbart-NOAA

* update(rd): update create_template documentation

* build: started building functionality to add captions and alt text to figures by adding to create_figures_doc.R and adding .csv with pre-populated captions and alt text templates (captions_alttext.csv).

* build: developed capability to caption tables.

* Update(pkgdown yml): Reorder top nav bar and have a drop down manual for all vignettes instead

* Remove example data - moved to asar-demo

* Create working example and resources for users (#54)

* feat(README): change example to petrale

Changing to a working example in read me that mimic that of a current stock assessment. The files resulting from the example and rendered report need to be added as their own example in a folder

* update(example): change README so users can run  petrale example

# Summary

- add raw and converted petrale output to data folder
- ran usethis::use_data() creating structure for the example
- updated documentation

* fix:(create_template): add preamble

- read in converted output in chunk
- create place for pre-loaded quantities to reference later in the document

* update(test-add_chunk): correct notes in test

* Fix(readme): example needed csv file

* Update(readme): adjust for new section names

* update(website): change set up of pkgdown website

* Update(pkgdown.yml): include tutorial

* feature(add tutorial): demo in shiny app

Might need to move folders - pushing now in order to switch branches ok

* remove(tutorial): move materials to asar-demo repo and host there

* update(pkgdown): add tutorial link to site

* update(README): add link for tutorial in examples

* Update(pkgdown yml): Reorder top nav bar and have a drop down manual for all vignettes instead

* Remove example data - moved to asar-demo

* fix(create_template): replaced params_chunk with preamble

* build: created first outline and basic files for new accessibility vignette

* fix(author order): add line so order of authors follows that input by the user

* Update(WORDLIST)

* feature(_titlepage); add dynamic alt text to cover image

* feature(create_tempalte): change pdf engine to lualatex when format is pdf

* Update(tex): documentation

* feature(create_template): add quanitites to preamble chunk

Most of these still need to be looked up and adjusted so they are read from the output file - then they can be uncommented

* update(create_template): reflect changes to create_titlepage_tex in fxn

* build: finished first full draft of accessibility vignette

* build: adding some files associated with building the accessibility vignette

* fix(create_template): reference to converted output correction

* Revert "Pkgdown vignettes"

* fix: to resolve call-workflow / spell-check error, added words to the WORDLIST that R didn't recognize and added language to the DESCRIPTION file

* fix(site): remove unncessary folders and files

Add accessibility article into site and add in references.bib file

* Update(description): authorship

* fix(description): authorship structure

* Fix description...again

* Update(authorship)

Works with site

* build: added alt text to cover page's US Dept of Commerce seal

* fix: Changed the NOAA logo classification to an artifact and removed alt text

* Fix(create_template): change save for convert_output to remove extra underscore and paste spp name together with underscore

* fix(create_template.R): updated definition of model_results argument.

* Automatically identify fleet names in BAM output (#72)

* feature(find BAM fleet names)

Fix standard naming conventions sheet

* fix(convert_output):change age to numeric for converting purposes

* Update(documentation): fleet names documentation

Update create_template to reflect changes to convert_output

* Update(convert_output): fleet names not kept in D.release/Dosed.release

* Deprecate fleet_names parameter in create_template

* Update documentation for PR

* Fix(create_template): species naming in converted output within create_template

* fix(convert_output): add nsim factor

Nsim factor in BAM for eq.series and pr.series - might need further adjustment for naming (unsure if nsim)

* fix(convert_output test): reflect the new factor added to the output file

* fix(convert_output): aging error matrix for BAM incorrectly transformed

Reflect the changes and addition of another factor into the test

* style(create_template): shortened chunk labels by removing preceding numbers

* fix: updated syntax for cover USDC logo. It should contain no alt text since it's an artifact.

* Create excel spreadsheet showing which accessibility-related criteria our report is meeting

* Adding Ross' proposed changes to Latex files through comments

* Adding (more of) Ross' proposed changes to Latex files through comments

* feature(add_chunk): new argument to add rmarkdown chunk options

* Update fxn documentation

* fix(add_chunk): features to add Rmarkdown or quarto formatted options in the chunk

* Adding (even more of) Ross' proposed changes to Latex files through comments

* Enhanced accessibility vignette (incl. minor edits, added to-do list for user, and added prompts to help the user expand upon prewritten alt text)

* update .gitignore

* updated labels to fig-__ and tbl-__ in create_figures/tables_docs; updated gitignore

* added FAQs vignette (placeholder)

* added new chunks for plot-generating fxns in create_figures_doc; changed eval to T for fxns

* update .gitignore

* Preamble key quantities (#75)

* update(preamble quanities): add in new coding for pulling quantities from std otuput

* Update(create_template): update preamble quantities and formatting

* feature(finish preamble): add h and R0 quantities to fxn and finish formatting

* fix(minor changes to create template)

- Impacts the naming structure of the converted output file and supdir
- Add back in mutating the estimate and uncertainty to numeric
- Adding in fixes to the preamble quanitties after testing

* feature(check for results files): commented out check added for renaming results file if the output is converted

* update(preamble in create_template): add in comments as suggested by @sbreitbart-NOAA

* update .gitignore

* started reorganizing create_figures_doc and create_template to intake rdas
-first chunk in create_figures_doc states location of rda folder
-added new argument to create_template (rda_dir) with location of rda folder

* continued reorganizing create_figures_doc:
-updated first rda chunk
-added 2 chunks for first plot: recruitment

* continued reorganizing create_figures_doc:
-added chunks for other remaining plots
-made captions, alt text part of strings instead pasting in as objects
-added argument for rda_dir
-updated rda directory call

* Update documentation and fix end fxn bracket for create_tables_doc

* reorganized create_tables_doc in the style of create_figures_doc

* editing create_template
-added arguments to function setup

* updated documentation and create_template; troubleshooting the latter

* Update(WORDLIST)

* troubleshooting new if statement for making rda files if not present

* update(create_template): change files directory to single folder names report

* update .gitignore

* started reorganizing create_figures_doc and create_template to intake rdas
-first chunk in create_figures_doc states location of rda folder
-added new argument to create_template (rda_dir) with location of rda folder

* continued reorganizing create_figures_doc:
-updated first rda chunk
-added 2 chunks for first plot: recruitment

* continued reorganizing create_figures_doc:
-added chunks for other remaining plots
-made captions, alt text part of strings instead pasting in as objects
-added argument for rda_dir
-updated rda directory call

* reorganized create_tables_doc in the style of create_figures_doc

* editing create_template
-added arguments to function setup

* updated documentation and create_template; troubleshooting the latter

* troubleshooting new if statement for making rda files if not present

* Fix(create_template test): change final paths for testing to report

* update .gitignore

* started reorganizing create_figures_doc and create_template to intake rdas
-first chunk in create_figures_doc states location of rda folder
-added new argument to create_template (rda_dir) with location of rda folder

* continued reorganizing create_figures_doc:
-updated first rda chunk
-added 2 chunks for first plot: recruitment

* continued reorganizing create_figures_doc:
-added chunks for other remaining plots
-made captions, alt text part of strings instead pasting in as objects
-added argument for rda_dir
-updated rda directory call

* reorganized create_tables_doc in the style of create_figures_doc

* editing create_template
-added arguments to function setup

* updated documentation and create_template; troubleshooting the latter

* troubleshooting new if statement for making rda files if not present

* -differentiated first chunk labels for figures and tables docs
-added make_rda param definition to create_template and moved code that runs satf::exp_all_figs_tables below code that converts files if convert_output = T

* Fix(create_template test): change path

* fixed bug in #93 (comment)

* fix - had extra s in the test smh

* feature(create_template): reports and associated files are now exported to a single folder named report

Also fixes error in testing where (due to new folder structure), the files are overwritten but the skeleton remained; this is now fixed

* fix(test-create_template): folder name changes to report rather than reports

* Updated accessibility vignette to explain how to edit alt text and captions

* update wordlist

* started reorganizing create_figures_doc and create_template to intake rdas
-first chunk in create_figures_doc states location of rda folder
-added new argument to create_template (rda_dir) with location of rda folder

* continued reorganizing create_figures_doc:
-updated first rda chunk
-added 2 chunks for first plot: recruitment

* continued reorganizing create_figures_doc:
-added chunks for other remaining plots
-made captions, alt text part of strings instead pasting in as objects
-added argument for rda_dir
-updated rda directory call

* reorganized create_tables_doc in the style of create_figures_doc

* editing create_template
-added arguments to function setup

* updated documentation and create_template; troubleshooting the latter

* troubleshooting new if statement for making rda files if not present

* -differentiated first chunk labels for figures and tables docs
-added make_rda param definition to create_template and moved code that runs satf::exp_all_figs_tables below code that converts files if convert_output = T

* started reorganizing create_figures_doc and create_template to intake rdas
-first chunk in create_figures_doc states location of rda folder
-added new argument to create_template (rda_dir) with location of rda folder

* reorganized create_tables_doc in the style of create_figures_doc

* updated documentation and create_template; troubleshooting the latter

* troubleshooting new if statement for making rda files if not present

* update(create_template):
-remove exp_all_figs_tables() code that occurred before model conversion (second time doing this- maybe a rebase error?)
-allow conditions for user to use create_template without any arguments
-add checks so that if rda_dir or end_year are NULL, then figures and tables docs will be structured appropriately and with warnings in console

* feature(new AK spp images)

* update WORDLIST

* Fix errors in convert_output (#92)

* fix(convert_output): exp and obs labels are properly indicated whether the source is from indices or catch

- ss3 and bam naming conventions are now merged by module_name as well
- module_name is not an essential and non-changeable column

* feature(convert_output): add progress messages for each module as fxn words

Mimics the messages generated from SS3 conversion

* feature(convert_output): add 'Finished!' message

* Fix(convert_output): age series in BAM keeps ages

* Add codespaces setup

* Feature(add package rd): adds documentation for package and removes global variables in checks

* -replaced alt text/caps csv
-updated a11y and manual vignettes

* feature(default bib file): created into the template to solve issue #70

* Remove legacy template files

---------

Co-authored-by: sbreitbart-NOAA <[email protected]>
Co-authored-by: Bai Li - NOAA <[email protected]>