Releases | Open Source Science

gigs - gigs 0.5.2

What's changed

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.

Full Changelog: https://github.com/ropensci/gigs/compare/v0.5.1...v0.5.2

Scientific Software - Peer-reviewed - R
Published by simpar1471 about 1 year ago

gigs - gigs 0.5.1

What's new

Nothing internally has changed from 0.5.0 - this minor release is to get the docs website building.
Update package installation instructions in README.
Minor changes to benchmarking vignette to facilitate docs building.

Full Changelog: https://github.com/ropensci/gigs/compare/v0.5.0...v0.5.1

Scientific Software - Peer-reviewed - R
Published by simpar1471 about 1 year ago

gigs - 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: https://github.com/ropensci/gigs/compare/v0.4.1...v0.5.0

Scientific Software - Peer-reviewed - R
Published by simpar1471 about 1 year ago

gigs - gigs 0.5.0

What's Changed (from NEWS.md)

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.

Full Changelog: https://github.com/ropensci/gigs/compare/v0.4.1...v0.5.0

Scientific Software - Peer-reviewed - R
Published by simpar1471 about 1 year ago

gigs - gigs 0.4.1

What's Changed

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

Full Changelog: https://github.com/lshtm-gigs/gigs/compare/v0.4.0...v0.4.1

Scientific Software - Peer-reviewed - R
Published by simpar1471 about 2 years ago

gigs - gigs 0.4.0

What's Changed

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.

Full Changelog: https://github.com/lshtm-gigs/gigs/compare/v0.3.1...v0.4.0

Scientific Software - Peer-reviewed - R
Published by simpar1471 about 2 years ago