[docs]: Create README files for all folders

.github/README.md

@@ -0,0 +1,8 @@
+# GitHub Workflows and Templates
+
+This folder contains the workflows to initiate:
+
+* the pull request template (`pull_request_template.md`)
+* checks for the repository and code (e.g., code coverage check, code styling and adjustment, CMD check, spell check) (`workflows` folder)
+* issue templates which translate to pre-made 
+templates that are shown when a user opens an issue in the repository (`ISSUE_TEMPLATE` folder)

.github/pull_request_template.md

@@ -3,10 +3,10 @@ Thanks for opening a PR. This commented text will **NOT** appear in the final PR
 -->
 
 # What is the feature?
-*
+* 
 
 # How have you implemented the solution?
-*
+* 
 
 # Does the PR impact any other area of the project, maybe another repo?
-*
+* 

R/README.md

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+# Functions
+
+This folder is composed of all the exported and utility functions used in {asar}. These utility functions are typically used to perform intermediary tasks in the process of making a report, and are run within the other functions.
+Each script depicts the specific function within the file. The utility file functions include
+
+* `utils_tex.R`: utility functions that output LaTeX to modify asar reports
+* `utils.R`: general helpful utility functions

README.md

@@ -73,7 +73,7 @@ output <- stockplotr::convert_output(
 ```
 
 In this function, the users have the option to convert output files to a standardized 
-framework from either SS3 (Report.sso) or BAM (.rdat) output files. `asar` uses this 
+framework from either SS3 (Report.sso), BAM (.rdat), FIMS, or Rceattle output files. `asar` uses this 
 converted output from the environment to calculate quantities in the preamble and 
 it is also used for creating plots and tables from [`stockplotr`](https://github.com/nmfs-ost/stockplotr).
 

inst/README.md

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+# Inst
+
+This folder contains various files which support the creation of materials for running functions in {asar}.
+
+* WORDLIST contains a list of words that are used in the spell check workflow. It is a plain text file with one word per line. The words in this list are considered correct and will not be flagged as spelling errors during the spell check process.
+
+## Sub-folders
+
+* The `extdata` sub-folder contains an example of an SS3 report file that can be input into `convert_output()`.
+* The `glossary` sub-folder contains the materials used to create the {asar} glossary (`report_glossary.tex`).
+* The `resources` sub-folder contains files used in the development of {asar} reports. This includes:
+  * author affiliation information (`affiliation_info.csv`)
+  * citations for use in the report bibliography (`citations.bib`)
+  * citation formatting file in the style of the Canadian Journal of Fisheries and Aquatic Sciences (CJFAS) (`cjfas.csl`)
+  * LaTeX partials used to format the Quarto-based report (`formatting_files` folder)
+  * NOAA logo placed on report title page (`NOAA_Transparent_Logo.png`)
+  * `preamble` R file used to extract key quantities from model results file used in asar report (`preamble.R`)
+  * Images of species used for asar report cover pages (`spp_img` folder)
+  * US Dept of Commerce logo placed on report title page (`us_doc_logo.png`)
+* The `templates` sub-folder contains the child documents used for each report "type": Northeast management track (nemt); Pacific Fisheries Marine Council (pfmc); Stock Assessment and Fishery Evaluation (safe); standard report format (skeleton)

inst/WORDLIST

@@ -16,6 +16,7 @@ Drs
 ECOMON
 EcoMon
 Fabio
+FIMS
 Flextable
 Gertseva
 Hardcoding
@@ -39,6 +40,7 @@ Pandoc
 Pomatomus
 Pre
 Quillback
+Rceattle
 README
 RStudio
 RTF
@@ -78,6 +80,7 @@ frac
 gls
 goa
 hardcoding
+href
 is’
 jpg
 knitr

tests/README.md

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+# Tests
+
+This folder contains tests for the functions in {asar}. The tests are located in the sub-folder "testthat". We follow the testing structure and approach found using {testthat} R package. Each function should have its own test. If a new function is made, you can create a new testing script by running the following in the console:
+
+```
+usethis::use_test()
+```
+
+The above function references whatever function is currently open. From there, use the options for testing in the testthat package, make your own testing function, or reference the current tests in this folder.

vignettes/README.md

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+# Vignettes
+
+The `articles` sub-folder contains the articles (a special type of vignette) found in the [asar website](https://nmfs-ost.github.io/asar/) under the 
+"Articles" drop-down tab.
+
+Note that these files are "articles", rather than "vignettes". We chose articles over vignettes because these documents benefited from having features available to Quarto documents (like a floating table of contents) but not simple markdown documents. As a result, these articles appear on the package website but are not included in the user-facing package.
+
+To create a new article, create a new quarto file then add this information as the yaml:
+
+```
+title: "My Title"
+format:
+  html:
+    toc: true
+    toc-depth: 3
+    anchor-sections: true
+    other-links:
+      - text: stockplotr
+        href: https://nmfs-ost.github.io/stockplotr/
+knitr:
+  opts_chunk:
+    collapse: true
+    comment: '#>'
+bibliography: references.bib
+```
+
+Afterwards, edit the `_pkgdown.yml` file located in the `pkgdown` folder. The new article can be added under the "articles:" then "menu:" lines. Please include:
+
+* text -- the title that's presented to the site visitor when looking at the drop-down menu
+* href -- the path to the vignette file. It should be "articles/{name_of_file}.qmd"
+