Fix CRAN issues

[richelbilderbeek]

If there are references describing the methods in your package, please add these in the description field of your DESCRIPTION file in the form authors (year) authors (year) authors (year, ISBN:...) or if those are not available: with no space after 'doi:', 'arXiv:', 'https:' and angle brackets for auto-linking. (If you want to add a title as well please put it in quotes: "Title")

Done!

Please add \value to .Rd files regarding exported methods and explain the functions results in the documentation. Please write > about the structure of the output (class) and also what the output means. (If a function does not return a value, please document > that too, e.g. \value{No return value, called for side effects} or similar) Missing Rd-tags in up to 84 .Rd files, e.g.: check_alignment.Rd: \value check_beast2_installed.Rd: \value check_candidates_save_to_same_files.Rd: \value check_error_fun.Rd: \value check_experiments_all_inference_models_are_unique.Rd: \value check_experiments_candidates_have_same_mcmcs.Rd: \value ...

Done!

\dontrun{} should only be used if the example really cannot be executed (e.g. because of missing additional software, missing API keys, ...) by the user. That's why wrapping examples in \dontrun{} adds the comment ("# Not run:") as a warning for the user. Does not seem necessary. Please unwrap the examples if they are executable in < 5 sec, or replace \dontrun{} with \donttest{}.

Done!

Please ensure that your functions do not write by default or in your examples/vignettes/tests in the user's home filespace (including the package directory and getwd()). This is not allowed by CRAN policies. Please omit any default path in writing functions. In your examples/vignettes/tests you can write to tempdir().

Done! That is, in est_evidences, a writing function, I did so. In the create_test_ functions, I leave these, as these allow for convenient testing and are not be used by the user. In the reading functions, I kept this.

[richelbilderbeek]

Dear CRAN,

Thanks for the previous feedback, I followed it all:

• I added a reference to the methods
• I added the description of the return value (\value) to all functions' documentation
• I only run code that takes less than 5 secs on CRAN infrastructure
• There are no default paths in this package's functions

Thanks and cheers, Richel Bilderbeek