CRAN Compliance Issue: Broken and Redirected URLs in PEcAn's `data.atmosphere `

[Sweetdevil144]

Bug Description

When I access specific URLs within the PEcAn Project's data.atmosphere module documentation, I expect to be redirected to the correct and functioning pages (AmeriFlux site list, equations reference, NEON site list, and Package Documentation) but observe broken links, redirected URLs, and a 404 error.

To Reproduce

Steps to reproduce the behavior:

1. Go to the data.atmosphere module documentation on the PEcAn Project website.
2. Click on the AmeriFlux site list link (http://fluxnet.fluxdata.org//sites/site-list-and-pages/), which incorrectly redirects to https://fluxnet.org/sites/site-list-and-pages/.
3. Click on the reference for equations link (http://www.eol.ucar.edu/projects/ceop/dm/documents/refdata_report/eqns.html), which incorrectly redirects to https://archive.eol.ucar.edu/projects/ceop/dm/documents/refdata_report/eqns.html.
4. Click on the NEON site list link (http://www.neonscience.org/science-design/field-sites/list), which incorrectly redirects to https://www.neonscience.org/science-design/field-sites/list.
5. Attempt to access the Package Documentation at https://pecanproject.github.io/pecan/modules/data.atmosphere/inst/web/index.html and observe a 404 Not Found error.

Expected behavior

I expected the documentation to contain accurate, functioning links to the AmeriFlux site list, equations reference, NEON site list, and the Package Documentation. These resources are crucial for users seeking detailed information and proper navigation within the data.atmosphere module documentation.

Screenshots

[Not applicable]

Machine (please complete the following information):

• Server: [e.g., NCSA]
• OS: [e.g., Linux]
• Browser (if applicable): [e.g., Chrome]
• Version: [e.g., 98]

Additional context

These issues with broken links, incorrect redirections, and a missing documentation page significantly hinder the user experience and accessibility of the PEcAn Project's data.atmosphere module documentation. It's important to address these problems to maintain the reliability and usability of this resource for researchers and users. Moreover, if we run these tests on a large scale, we'll get to find even more broken links and problems.

CRAN is picky about URLs—can you run urlchecker::url_check("modules/data.atmosphere") to check that this is OK?

Originally posted by @Aariq in https://github.com/PecanProject/pecan/pull/3120#discussion_r1119056677

Checkout his comments in #3120 for more information

[Sweetdevil144]

Let's complete this. Can you assign this to me @dlebauer

[kutumia]

Fixed in PR #3493.

Replaced or commented out broken and redirected URLs in README.md, .Rmd, and .Rd files

Updated Ameriflux, NEON, and PEcAn doc links

Included inline comments for traceability