Clean-up epireview

[sangeetabhatia03]

This PR follows on Tristan's PR that cleans up the vignettes. This PR:

• fixes all examples in the documentation (many of them didn't work);
• removes examples from functions that add data as this functionality needs more thinking about;
• updates tests so that they all pass now;
• updates documentation to deal with all notes and warnings issued during the build process.

The package now builds without any errors and all tests pass. Bumping up version number is not needed because we are not adding any new functionality.

To test this PR, clone the repository or pull the latest changes from this branch if already have a clone. Then in an R session, run

devtools::check()

Expect 0 errors

[sangeetabhatia03]

For your attention @CosmoNaught

[CosmoNaught]

Happy in principle to approve pending advice on the following;

Issues found

• get_parameter is now correctly exported and documented. Have pushed fix to branch.
• Ensuring correct linkage in Rd files, especially for load_epidata(), to resolve the documentation warning. The warning clearly arises from this double commenting @sangeetabhatia03 can we enable this function please? https://github.com/mrc-ide/epireview/blob/a150eb0c90af347053b34d8d4256fda992d9abcc/R/prep_data_forest_plots.R#L43-L67
• Please advise on handling the meta package in Suggests. Unsure if necessary for package but I would suggest moving to Imports if possible.

Please advise on how to proceed. Other than this the branch passes all checks now (bar the following)

── R CMD check results ───────────────────────────────────────────── epireview 1.1.3 ────
Duration: 3m 28.3s

❯ checking Rd cross-references ... WARNING
  Missing link or links in documentation object 'get_parameter.Rd':
    ‘load_epidata()’

  See section 'Cross-references' in the 'Writing R Extensions' manual.

0 errors ✔ | 1 warning ✖ | 0 notes ✔

System Information

• R version 4.3.3 (2024-02-29)
• Platform: x86_64-redhat-linux-gnu (64-bit)
• Using R under: Fedora Linux 39