Address Review Comments (#40)

* Initial commit for 'manuscript' branch.

* Update draft-pdf.yml

* Updated 'paper.md'.

* (auto) Paper PDF Draft

* Updated 'paper.md'.

* (auto) Paper PDF Draft

* Updated 'paper.md'.

* (auto) Paper PDF Draft

* Updated 'paper.md'.

* (auto) Paper PDF Draft

* Updated 'paper.md'.

* (auto) Paper PDF Draft

* Updated 'paper.md'.

* (auto) Paper PDF Draft

* Updated  'paper.bib' with DOIs.

* (auto) Paper PDF Draft

* Add RStudio link to README

* Updated and renumbered vignettes.

* Updated _pkgdown.yml

* Updated vignette '02_details.Rmd' to conform with styler.

* Renamed vignettes.

* Inlcude link to issues and contact email (will need to be filled in). Also include link to GNU General Public License (future LICENSE file).

* typo in markdown heading

* Include GPL 3.0 license and appropriate link in README

* Added new vignette 'details.Rmd'.

* Updated vignette 'details.Rmd' using styler.

* Updated vignettes.

* Used styler to update 'details.Rmd'.

* (auto) Paper PDF Draft

* Added vignette 'pbpk_demo.Rmd' to provide an example involving a PBPK model.

* Updated '_pkgdown.yml' to include the new vignette 'pbpk_demo.Rmd'.

* Modified description file to add URL for documentation web page.

* Remove one section from 'pbpk_demo.Rmd'.

* Removed documentation URL from DESCRIPTION file.

* Added some lines back to 'pbpk_demo.Rmd'.

* Added some more lines back to 'pbpk_demo.Rmd'.

* Removed line with 'loadModel()' from 'pbpk_demo.Rmd'.

* Modified 'compileModel.R' for more complete logging of the model translation step. Added all lines back to 'pbpk_demo.Rmd'.

* Ran styler::style_pkg().

* Updated 'main.yml' to use 'windows-2025' instead of 'windows-2022'.

* Added debug script to 'main.yml'.

* Updated 'main.yml' to modify testing.

* Simplified 'pbpk_simple.model' for debugging/testing.

* Ran styler::style_pkg().

* Removed some lines from 'pbpk_demo.Rmd' for debugging.

* Removed lines from 'pbpk_simple.model' for debugging.

* Updated 'pbpk_demo.Rmd' and 'pbpk_simple.model'.

* Modified 'main.yml' so that continuous integration checks are only performed on Unix (not on Windows).

* Updated 'paper.md' to explain why users might choose MCSimMod over existing R packages for solving ODE IVPs.

* (auto) Paper PDF Draft

* Edited 'pbpk_demo.Rmd' so that R code chunks are not evaluated. Tranlsating and compiling 'pbpk_simple.model' seems to require so much time that it causes devtools::build() to time out.

* Ran styler::style_pkg().

* Add R plot figures to vignette 'pbpk_demo.Rmd'.

* Updated 'paper.md' and 'README.md' with new text.

* (auto) Paper PDF Draft

* Updated 'paper.md' and 'paper.bib'.

* (auto) Paper PDF Draft

* Updated 'DESCRIPTION' file.

* Formatted 'DESCRIPTION' file.

* Corrected typographical error in 'details.Rmd'.

* Corrected a typographical error in 'pbpk_demo.Rmd' and made minor format changes.

* Corrected typographical error in 'newt_cool_demo.Rmd'.

* Minor modifications to three vignettes.

* Updated badges in 'README' file.

* Corrected typographical error in 'pbpk_demo.Rmd'.

* Updated version number to 1.0.

* Made minor changes in response to Copilot review.

* (auto) Paper PDF Draft

* Made minor changes in response to Copilot review.

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Co-authored-by: dkapraun <kapraun.dustin@epa.gov>
Co-authored-by: Andy Shapiro <shapiro.andy@epa.gov>
Co-authored-by: dfkapraun <dfkapraun@users.noreply.github.com>