NEWS

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gigs 0.5.2.9000

• Documentation updates due to JOSS publication.
• Other docs updates to fix minor errors.

gigs 0.5.2

• More changes to online articles to facilitate rOpenSci website building.
• Improved .gigs_options docs to mention the "handle_missing_levels".
• Minor docs updates.
• Now cached with Zenodo.

gigs 0.5.1

• Update package installation instructions.
• Minor changes to benchmarking vignette to facilitate docs building.

gigs 0.5.0

• 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.
  • Other non-breaking changes to documentation and test suite.

gigs 0.4.1

• Changes to documentation to facilitate autotest::autotest_package() pass.
• Minor changes to vignettes for new patched version.

gigs 0.4.0

• BREAKING CHANGES:
  • Changed name of classify_sga() to classify_sfga()
• NEW FEATURES:
  • Added INTERGROWTH-21^st Fetal standards, including the Fetal Growth standards, Fetal Doppler standards, Brain Development, and more!
  • The INTERGROWTH-21^st Postnatal Growth (ig_png) conversion functions now accept post-menstrual age in weeks (pma_weeks) as either whole weeks or decimals, e.g. 37 or 37.142857, where 37.142857 is equal to 37 weeks + 1 day, so 37 + 1/7 weeks.
  • Added checkmate-based verification of inputs, with customised warning() and stop() mechanisms to exported functions. See documentation for allowed data types/lengths in each function argument.
  • gigs package options via .gigs_options, which lets you customise warning and error behaviour as you see fit.
• INTERNAL/DOCS CHANGES:
  • Added statistical review roclets tags.
  • Better documentation, for compliance with SRR tags.
  • Internal, non-breaking changes to test suite and documentation.

gigs 0.3.1

• Internal, non-breaking changes to test suite and documentation.
• Classification functions now use gigs_**z() functions internally for z-scoring. These z-scoring functions, found in gigs-zscoring.R, will be made user-facing once the GIGS guidance documentation is made public.

gigs 0.3.0

• This update includes several large changes to the GIGS interface, including changed argument names for some classification and conversion functions. We have only not used a major release as the package may still change with the release of the GIGS guidance document.
• BREAKING CHANGES:
  • Replaced gest_age parameter with gest_days in all circumstances, including ig_nbs growth curve/coefficient tables.
  • classify_wasting() now takes in gestational age/age data, and uses this to apply the INTERGROWTH-21^st Postnatal Growth standard for weight-for-length where appropriate.
  • Changed out percentile for centile in function names and documentation. Argument names left unchanged, so centiles are still passed into functions as p.
• NEW FEATURES:
  • Added classify_svn() function, which classifies newborns into the categories used in the Lancet's 2023 Small Vulnerable Newborn (SVN) Series.
• INTERNAL/DOCS CHANGES:
  • Updated coefficient retrieval functions to run ~ 2 times as fast as in version 0.2.3.
  • Added type checking functions to conversion functions, along with additional unit tests to make sure they work.
  • Extensive changes to documentation structure. These changes appear internally, where the roxygen documentation uses more @inherit/@inheritParams tags.
  • Added vignette displaying performance differences between gigs and other, similar R packages, as well as Stata implementations.

gigs 0.2.3

• Updated regression equations for the normative body composition standards in ig_nbs, namely fmfga, ffmfga, and bfpfga. These functions give outputs much closer to the published centiles, though a degree of error is still present.
• Updated and improved body composition vignette to include the new derivation process.
• The coefficient-based ig_nbs/who_gs functions are now 30 to 10x quicker depending on the length of the function inputs (more inputs = slower).
  • This comes from removal of the data.table dependency - all coefficient retrieval/interpolation now occurs using matrices. The move from using data.table.merge() to subsetting operators has sped up the code significantly.
• More consistent subsetting operators and terminology in package source code.

gigs 0.2.2

• Optimised interpolation for coefficient-based who_gs_...()/ig_nbs_...() functions. No more for-loops with rbind - instead, the approx() function for interpolation is called on vectors.
• Began using data.table for retrieving/merging coefficient tables, in a new helper function named retrive_coefficients(). This approach is slower for smaller inputs than the old data.frame approach, but maintains a much lower time as the number of inputs are increased. It also concentrates all the coefficient-retrieval logic in one group of common functions.
• Minor changes to README.md and small refactors for readability.

gigs 0.2.1

• Renamed coarse parameter in classify_sga() to severe to better reflect its function; now setting severe to FALSE will cause classify_sga() to specify which SGA cases are below the 3rd percentile.
• Documentation updates:
  • Full use of <sup> tags for pkgdown website
  • Standardised titles in documentation for conversion + classification functions
  • Updated "Introduction to gigs" article to include all available classification functions
  • Extra docs changes which can be viewed in the diffs for this commit (e.g., replacing all @returns Roxygen tags with @return)

gigs 0.2.0

• Added INTERGROWTH-21st Postnatal Growth tables + functions for a new weight-for-length standard. These include ig_png_wfl_value2zscore() and ig_png_wfl_percentile2value().
• Refactored check_params.R to be more standard-specific. Added some comments as the purpose of this code was unclear. May refactor later to make more self-evidently important.

gigs 0.1.2

• classify_sga() now uses < and >, not <= and >= to determine LGA/SGA cut-offs. This aligns this function with the 'correct' methodology for calculating size for GA.

gigs 0.1.1

• Major documentation updates
• Added life6mo dataset
• Added 'Getting Started' vignette

gigs 0.1.0

• Created package
• Added a NEWS.md file to track changes to the package.
• Added conversion functions (e.g. who_gs_value2zscore()/ig_png_value2percentile())
• Added classification functions (e.g. classify_sga())
• Added reference datasets (e.g. ig_nbs, who_gs, who_gs_coeffs)