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  • This is a new release.

Resubmission 2023-04-31

This is a resubmission. In this version I have:

  • Removed the use of the package name BREADR in the description part of DESCRIPTION to avoid spell-checker errors.

  • Wrapped the example for saveSlices in \dontrun{} to avoid excess execution time.

Resubmission 2023-04-05

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) doi:... authors (year) arXiv:... authors (year, ISBN:...) or if those are not available: https:... 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")

  • Added a link to the preprint manuscript into the DESCRIPTION file.

\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{}.

  • Changed to donttest{}.

You write information messages to the console that cannot be easily suppressed. It is more R like to generate objects that can be used to extract the information a user is interested in, and then print() that object. Instead of print()/cat() rather use message()/warning() or if(verbose)cat(..) (or maybe stop()) if you really have to write text to the console. (except for print, summary, interactive functions)

  • Changed the output from test_degree to print to screen only if verbose is set to TRUE.

Resubmission 2023-04-06

Please write references in the description of the DESCRIPTION file in the form authors (year) doi:... authors (year) arXiv:... authors (year, ISBN:...) or if those are not available: authors (year) https:... 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")

  • Added author and year - used et al. as four authors.

You still write information messages to the console that cannot be easily suppressed. It is more R like to generate objects that can be used to extract the information a user is interested in, and then print() that object. Instead of print()/cat() rather use message()/warning() or if(verbose)cat(..) (or maybe stop()) if you really have to write text to the console. (except for print, summary, interactive functions) e.g.: R/plotLOAF.R

  • Changed all output to be wrapped in verbose and added verbose as parameter.

Resubmission 2023-04-07

Please also add the verbose argument to all functions with cat() as you correctly did for R/plotLOAF.R

-> e.g.: R/processEigenstrat.R, R/saveSLICES.R...

  • All cat functions wrapped in verbose if condition.

Patch 2023-04-12

  • Found an error in read functions that causing error in PMR. Fixed.

Patch 2024-09-09

  • Fixed processEigenstrat so that works on windows machines.

Resubmission 2024-09-09

Mistakenly left repdev checking in folder - now removed.

Patch 2025-04-14

Submitting paper to JOSS. Reviewer could only install if R4.4, so changed to this from their recommendation.