Mid year cleanup - Githubissues

This issue tracks tasks for a mid-year package cleanup.

Supercharge your pkgdown website

[x] Verify that website URL is listed in _pkgdown.yml
[x] Verify pkgdown site is using epiversetheme
[x] Check for manual specification of Bootstrap version (currently 5)
[x] Add logo to epiverse-trace/hex-stickers
[x] Use svg version of logo
[x] Verify logo is properly detected by pkgdown & r-universe (path and name need to be exactly man/figures/logo.png or man/figures/logo.svg)
[x] Add a pkgdown reference index: https://pkgdown.r-lib.org/reference/build_reference.html#reference-index. Use selectors (e.g., starts_with() or contains()) to select functions rather than an explicit list. This serves the double purpose of checking that functions follow a coherent naming scheme.
[x] Verify intro vignette appears under 'Get started'
[x] Verify vignettes are ordered correctly (if applicable) ~- [ ] Verify all images include helpful alt-text~

[x] Update lintr, roxygen, usethis, testthat, devtools to the latest version on your local computer: pak::pak(c("lintr", "devtools"), dependencies = TRUE)
Copy from packagetemplate: ~- .lintr config file~ see #184
- [x] GitHub Actions worfklows
- [x] tools/ folder
- [x] tests/spelling.R
- [x] tests/testthat/helper-state.R
- [x] tests/testthat/setup-options.R
[x] Run spelling::spell_check_package()

[x] Change files ending in .r to .R in R/ and/or tests/testthat/"
[x] Review usage of # nolint comments. New versions of lintr may have squashed previous bugs
[x] Update year in license file

[x] Use roxygen2 markdown syntax (usethis::use_roxygen_md())
[x] Add a related project section at the end of the README
[x] Check that all URLs are working, up-to-date, and leading directly to the expected page: urlchecker::url_check()
[x] Add package-level documentation page: usethis::use_package_doc()
[x] Move package-level imports to the package-level documentation
[x] Verify that all @import and @importFrom import functions that are actually used in the relevant function
[x] Identify potential for reuse in documentation
[x] Run devtools::document()

[x] Verify if any package in Remotes is still necessary
[x] Check that package Description is still in line with the current scope
[x] Make sure links to GitHub repository and issue tracker are listed: usethis::use_github_links()
[x] Re-order and standardize DESCRIPTION with desc::desc_normalize()
[x] Submit a PR adding yourself as author to packagetemplate

[x] Run devtools::check() locally to catch NOTEs and WARNINGs that can still easily slip through continuous integration
[ ] devtools::check(remote = TRUE, manual = TRUE)
[ ] devtools::check_win_devel(): cannot complete due to curl issues

[ ] Check if issues are still relevant. If not, please close them, ideally with a link to the commit fixing them or a comment explaining why they no longer apply.
[ ] Check if discussions you started are still ongoing. If not, please close the thread.