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SomaDataIO 6.0.0
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@stufield stufield released this 15 Mar 15:49
· 136 commits to main since this release
v6.0.0
f7d41c3

We are now on CRAN! 🥳

New changes

  • New clinical data merge CLI tool (#25)
    • Rscript --vanilla merge_clin.R for merging clinical variables
      into existing *.adat SomaScan data files
    • added 2 new example meta.csv and meta2.csv files
      to run examples with random data but with valid index keys
    • see dir(system.file("cli", "merge", package = "SomaDataIO"))

Package data objects

  • general reorganization of package objects, trimming
    and slimming, renaming, and file structure (#32)
  • example_data.adat was reduced in size to n = 10 samples (from 192)
    to conform to CRAN size requirements (< 5MB)
  • the current file was renamed example_data10.adat to reflect this change
  • this likely has far-reaching consequences for users who access
    this flat file via system.file()
  • the example_data object itself however remains true to its original
    file (https://github.com/SomaLogic/SomaLogic-Data/blob/master/example_data.adat)
  • the directory location inst/example/ was renamed inst/extdata/
    to conform to CRAN package standard naming conventions
  • the file single_sample.adat was removed from package data
    as it is now redundant (however still used in unit testing)
  • SomaDataObjects was renamed and is now SomaScanObjects

Gradual deprecation

  • read.adat() is now soft-deprecated; please use read_adat() instead
  • lifecycle for soft-deprecated warn() -> stop() for functions
    that have been been soft deprecated since v5.0.0
    • getSomamers()
    • getSomamerData()
    • meltExpressionSet()

S3 Methods

  • New S3 print method default
    • tibble has new max_extra_cols = argument, which
      is set to 6 for the print.soma_adat method
  • New S3 merge method (#31)
    • calling base::merge() on a soma_adat is strongly discouraged
    • we now redirect users to use dplyr::*_join() alternatives
      which are designed to preserve soma_adat attributes

Internal upgrades

  • Code hardening for prepHeaderMeta()

    • some ADATs do not have CreatedDate and CreatedBy
      in the HEADER entry. This currently breaks the writer
    • simplified to make more robust but also refactor
      to be more convenient (for abnormal ADATs not generated
      by standard SomaScan processing)
    • CreatedDateHistory was removed as an entry from written ADATs
    • CreatedByHistory was combined and dated for written ADATs
    • NULL behavior remains if keys are missing
    • CreatedBy and CreatedDate will be generated either
      as new entries or over-written as appropriate

  • Numerous non-user-facing (API) changes internal package
    maintenance, efficiency, and structural upgrades were included

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