Manuscript to do list

[Gian77]

Things to check and/or improve

• Go through the manuscript and add commends edit, probably using track changes would help.

• Figure 1 ( the only figure we have) should reflect the package content

• the main steps of the BRCore pipeilien would be: preprocessing, identify core, fit neutral model

Novel implementation that the package do compared to old code

• implement parallelized multiple rarefaction
• regenerate the phyloseq object with the rarefied otu_table (phyloseq, per se, does not implement multiple rarefaction)
• put the whole core identification pipeline in 1 function
• organize results in lists
• provide useful visualizations of the calculated statistics for interpretation

Other points to consider

• The vignette - which was giving us trouble with Mac test on github
• Do we want Windows user to be able to run this package

Contributions

• We think we should include Shade and Stopnisek ( Nico will reach out)

[jibarozzo]

From MRA Journal:

Accessibility and usability of code:

• The code should be available within a publicly accessible repository with version control (e.g. GitHub, gitlab, bitbucket, subversion).
• The repository should include a copy of the license, a README document, and installation instructions.
• As part of the repository containing the code, the author should provide a test suite and example data with corresponding outputs to confirm code correctness.
• If possible, the code should be available for downloading and cloning without registration.
• An issue tracker should be available to read without registration.
• Users must be able to open issues/propose code changes at the repository without manual approval or a paid account.
• Authors should provide support/maintenance for at least 3 years after publication.

[Gian77]

@jibarozzo Do you want me to work on redoing the blocks diagram to add to figure 1?

[jibarozzo]

Give it a go. I think we need to make that a huge figure with big resolution so then online people can zoom in better