lshtm-gigs/gigs

Convert between measurements and z-scores/percentiles for INTERGROWTH-21st and WHO Child Growth Standards, and classify growth patterns.

gigs's Issues

Extra INTERGROWTH-21st Fetal Standards

Symphysis-fundal height (sfhfga)

• Data objects (centile tables)
• Code
• Tests

Early pregnancy dating (crown-rump length; crlfga/gafcrl)

• Data objects (centile tables)
• Code
• Tests

Late pregnancy dating (headcirc/femurlen to GA function)

• Data objects (centile tables ?)
• Code
• Tests

Gestational/maternal weight gain (gwgfga)

• Data objects (centile tables)
• Code
• Tests

Fetal doppler (pifga/rifga/sdrfga)

• Data objects (centile tables)
• Code
• Tests

Brain development (poffga/sffga/ahlvfga/aphlvfga/cmfga)

• Data objects (centile tables)
• Code
• Tests

Cerebellar growth (tcdfga/gaftcd)

• Data objects (centile tables)
• Code
• Tests

pkgcheck results - v0.4.1

Checks for gigs (v0.4.1)

git hash: a9d9654a

• ✔️ Package name is available
• ✔️ has a 'codemeta.json' file.
• ✔️ has a 'contributing' file.
• ✔️ uses 'roxygen2'.
• ✔️ 'DESCRIPTION' has a URL field.
• ✔️ 'DESCRIPTION' has a BugReports field.
• ✔️ Package has at least one HTML vignette
• ✔️ All functions have examples.
• ✔️ Package has continuous integration checks.
• ✔️ Package coverage is 100%.
• ✔️ R CMD check found no errors.
• ✔️ R CMD check found no warnings.

Package License: GPL (>= 3)

Add gigs_*() functions

The GIGS project is offering guidance on which standards should be used for different combinations of gestational age + chronological age. We should offer functions which wrap the existing ig_nbs_*()/ig_png_*()/who_gs_*() functions to use the 'right' function at each time point.

pkgcheck results - v0.4.0

Checks for gigs (v0.4.0)

git hash: f6b04c1e

• ✔️ Package name is available
• ✔️ has a 'codemeta.json' file.
• ✔️ has a 'contributing' file.
• ✔️ uses 'roxygen2'.
• ✔️ 'DESCRIPTION' has a URL field.
• ✔️ 'DESCRIPTION' has a BugReports field.
• ✔️ Package has at least one HTML vignette
• ✔️ All functions have examples.
• ✔️ Package has continuous integration checks.
• ✔️ Package coverage is 100%.
• ✔️ R CMD check found no errors.
• ✔️ R CMD check found no warnings.

Package License: GPL (>= 3)

pkgcheck results - master

Checks for gigs (v0.4.1)

git hash: a9d9654a

• ✔️ Package name is available
• ✔️ has a 'codemeta.json' file.
• ✔️ has a 'contributing' file.
• ✔️ uses 'roxygen2'.
• ✔️ 'DESCRIPTION' has a URL field.
• ✔️ 'DESCRIPTION' has a BugReports field.
• ✔️ Package has at least one HTML vignette
• ✔️ All functions have examples.
• ✔️ Package has continuous integration checks.
• ✔️ Package coverage is 100%.
• ✔️ R CMD check found no errors.
• ✔️ R CMD check found no warnings.

Package License: GPL (>= 3)

pkgcheck results - master

Checks for gigs (v0.4.0)

git hash: f6b04c1e

• ✔️ Package name is available
• ✔️ has a 'codemeta.json' file.
• ✔️ has a 'contributing' file.
• ✔️ uses 'roxygen2'.
• ✔️ 'DESCRIPTION' has a URL field.
• ✔️ 'DESCRIPTION' has a BugReports field.
• ✔️ Package has at least one HTML vignette
• ✔️ All functions have examples.
• ✔️ Package has continuous integration checks.
• ✔️ Package coverage is 100%.
• ✔️ R CMD check found no errors.
• ✔️ R CMD check found no warnings.

Package License: GPL (>= 3)

Re-work body composition equations

The current approach for getting the standard deviation is to get the standard deviation for the 90^th centile and work with that for all values. Instead, we should work out the standard deviation at all possible GAs and fit a linear model to this as well.

Add classify_svn() function

The Lancet's Small Vulnerable Newborn Series introduced different markers of smallness and vulnerability for newborns/infants. We could add a classification function for these markers called classify_svn().

Better error and warning messages.

Errors are currently unique and helpful, but not as much as possible.

For example consider this error for zero-length input:

ig_nbs_value2centile(y = numeric(), gest_days = 270, sex = "M", acronym = "ffmfga")

Output:
Error: Variable 'y': Input had length 0, but must have length 1 or greater.

This is fine - we know which of our inputs is causing the error, and how this looks.

When we do this in the standard-specific function, we get the same error:

ig_nbs_ffmfga_value2centile(fat_free_mass_g = numeric(), gest_days = 270, sex = "M")

Output:
Error: Variable 'y': Input had length 0, but must have length 1 or greater.

This tells us our y variable is the culprit, but the actual argument name is fatfree_mass_g, not y. This needs changing, probably through changes to how each standard-specific conversion function interfaces with the validate_ig_nbs()-style input checking functions.

pkgcheck results - master

Checks for gigs (v0.4.0)

git hash: 5ebd7c14

• ✔️ Package name is available
• ✔️ has a 'codemeta.json' file.
• ✔️ has a 'contributing' file.
• ✔️ uses 'roxygen2'.
• ✔️ 'DESCRIPTION' has a URL field.
• ✔️ 'DESCRIPTION' has a BugReports field.
• ✔️ Package has at least one HTML vignette
• ✔️ All functions have examples.
• ✔️ Package has continuous integration checks.
• ✔️ Package coverage is 100%.
• ✔️ R CMD check found no errors.
• ✔️ R CMD check found no warnings.

Package License: GPL (>= 3)

Investigate using `pBCCG()`/`qPCCG()` from `gamlss.dist` package

These functions implement the LMS method in R, but use mu/sigma/nu terminology. They may run quicker than the current GIGS implementations, so should be tested.

Actions before CRAN submission

See the CRAN release section in Hadley's R Packages (2e) for a good list of actions to take before CRAN submission. These include:

• usethis actions
  • usethis::use_news_md()
  • usethis::use_cran_comments()
  • usethis::use_release_issue()
• Documentation
  • Full check through documentation. Ensure units, bounds, and descriptions are accurate and concise.
  • Freshen up README.md (incl adding CRAN install instructions)
  • Freshen up NEWS.md --> revert to a 0.1.0 version
  • Add @returns and @examples for each exported function
  • Check that DESCRIPTION fits advice in this section of R packages
  • Add a copyright holder in DESCRIPTION
• Extra admin
  • Check licensing in included files
  • Dennis Vaughan's extrachecks
  • This collaborative list of extra actions
• Software
  • devtools::check() working
  • urlchecker::url_check()
  • devtools::build_readme()
• Finally
  • devtools::check(remote = TRUE, manual = TRUE)
  • devtools::check_win_devel()
  • devtools::release(pkg = ".", check = TRUE, args = NULL)