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@dan-knight dan-knight commented Jun 4, 2025

Description

Checklist

  • This PR does NOT contain Protected Health Information (PHI). A repo may need to be deleted if such data is uploaded.
    Disclosing PHI is a major problem1 - Even a small leak can be costly2.

  • This PR does NOT contain germline genetic data3, RNA-Seq, DNA methylation, microbiome or other molecular data4.

  • This PR does NOT contain other non-plain text files, such as: compressed files, images (e.g. .png, .jpeg), .pdf, .RData, .xlsx, .doc, .ppt, or other output files.

  To automatically exclude such files using a .gitignore file, see here for example.

  • I have read the code review guidelines and the code review best practice on GitHub check-list.

  • I have set up or verified the main branch protection rule following the github standards before opening this pull request.

  • The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].

  • I have added the major changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.

Footnotes

  1. UCLA Health reaches $7.5m settlement over 2015 breach of 4.5m patient records

  2. The average healthcare data breach costs $2.2 million, despite the majority of breaches releasing fewer than 500 records.

  3. Genetic information is considered PHI.
    Forensic assays can identify patients with as few as 21 SNPs

  4. RNA-Seq, DNA methylation, microbiome, or other molecular data can be used to predict genotypes (PHI) and reveal a patient's identity.

@dan-knight dan-knight added the testing Limited to test cases or test methods label Jun 4, 2025
@whelena
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whelena commented Jun 9, 2025

I've tested it by generating some randomized plot. For my purposes I replaced the SRCGrob call with create.phylogenetic.tree so that each function call can automatically save the plot. Do you have strong preference for keeping SRCGrob, for example for testing or working with the grob objects?

@whelena whelena self-requested a review July 17, 2025 22:43
@whelena whelena merged commit 8053203 into main Jul 17, 2025
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@whelena whelena deleted the danknight-fuzz branch July 17, 2025 22:43
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3 participants