Fix and standardize @examples (\dontrun{})

[S1DDHEY]

Description

fixes #3797
This WIP PR starts cleaning up Roxygen @examples across PEcAn packages.

So far this includes:

• Fixing syntactic errors that cause pkgdown example parse failures
• Making examples self-contained (no undefined symbols)
• Converting non-R commands inside @examples to comments
• Standardizing use of \dontrun{} vs \donttest{} based on side effects

Motivation and Context

Review Time Estimate

• Immediately
• Within one week
• When possible

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)

Checklist:

• My change requires a change to the documentation.
• My name is in the list of CITATION.cff
• I agree that PEcAn Project may distribute my contribution under any or all of
  • the same license as the existing code,
  • and/or the BSD 3-clause license.
• I have updated the CHANGELOG.md.
• I have updated the documentation accordingly.
• I have read the CONTRIBUTING document.
• I have added tests to cover my changes.
• All new and existing tests passed.

[S1DDHEY]

I've added most of changes to @examples here, only the make document step remains to update the .Rd files which I'll do after this is reviewed.

There are also a few functions whose examples require specific inputs or domain knowledge that I don’t currently have. For those, I plan to open a separate issue.

[infotroph]

Thanks for working through this! Overall this looks great. I left some minor suggestions inline.

[S1DDHEY]

@infotroph Thank You for the review, as mentioned earlier there are a few places where specific inputs are needed for which I don't have that domain specific knowledge (for this one I'll open an issue mentioning all of them).

If someone wanted to spend more time on this they could come up with a minimal settings that can be loaded for an example with no \dontrun needed, then store it in a path like base/settings/inst/settings_example.xml and call it in the example using system.file(). But meanwhile for thie PR let's just cut the whole section down to one example and move on.

Also I can look forward to implement something similar to this one as well.