gigs 0.5.0

What's Changed

• The new version of the package includes many changes recommended by the good folks at rOpenSci, who have reviewed (and now host!) the package.
• BREAKING CHANGES:
  • Conversion between anthropometric values and z-scores/centiles is now done with value2zscore(), value2centile(), zscore2value(), and centile2value().
    • The family and acronym arguments are used to select a specific growth standard.
  • The classify_*() family of functions no longer take vectors as input, but instead take data.frame-like objects.
• NEW FEATURES:
  • Use classify_growth() to get data on multiple growth indicators at the same time. It will try to compute as many growth outcomes (i.e. size-for-GA, SVN, stunting, wasting, weight-for-age and head size) as possible based on the data you provide, and will tell you which analyses were performed.
  • The GIGS z-scoring functions are now explicitly user-facing. Check out gigs_waz() and friends for easy z-scoring using growth standards suggested by GIGS.
  • An id parameter for classify_growth() and friends, as well as the gigs z-scoring functions. This parameter informs the functions about who each data point is from, so that birth measurements for each individual can be identified and assessed appropriately.
  • The compute_*() functions for growth analysis. These functions take several vectors containing anthropometric measurements, age, and sex; they return a factor of growth categories. They are equivalent to the classify_*() functions from v0.4.1 and earlier.
  • The categorise_*() functions for growth analysis. These functions take vectors of growth centiles/z-scores as input, and return a factor of growth categories.
  • Added the INTERGROWTH-21st standard for estimated fetal weight based on the Hadlock formula. The is available through value2zscore() and friends provided that family = "ig_fet" and acronym = "hefwfga".
  • Added a new package-level option - "handle_unused_levels". This option matters when you're categorising growth data, but want gigs to drop unused levels in your newly-made factors.
    • By default, .gigs_options$handle_unused_levels is "keep_warn". So gigs will tell you that there are unused factor levels, but not drop them. Change it to "drop_warn" or "drop_silent"to drop the unused factor levels automatically.
  • Added extended versions of the INTERGROWTH-21^st Newborn Size standards for weight-for-GA, length-for-GA, and head circumference-for-GA. These extended versions have a GA range from 154 days (22⁺⁰ to 44⁺⁶ weeks). You can access these extended standards by setting family = "ig_nbs_ext" in GIGS conversion functions.
  • You can now set all gigs input-checking options at once with gigs_input_options_set().
• FIXES:
  • Z-scoring based on GIGS-recommended standards now accounts for measurements from different individuals, whereas in earlier versions the z-scoring logic treated data as if it all came from the same individual.
  • .gigs_options is now actively exported by gigs and available to end-users.
• INTERNAL/DOCS CHANGES:
  • Errors, warnings, and messages from GIGS are now handled with cli::cli_abort() and friends, and look much prettier.
  • Updates to the 'Getting Started' vignette and 'Benchmarking' article, and an article on how we extrapolated the INTERGROWTH-21^st Newborn Size standards for weight/length/HC-for-GA.
  • Other non-breaking changes to documentation and test suite.

Full Changelog: v0.4.1...v0.5.0