gigs 0.0.7

README.md

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+![gigs](./logoSAS.png)
+---
+
+*Assess Fetal, Newborn, and Child Growth with International Standards* 
+
+### Version information:
+
+- Package: gigs
+- Version: 0.0.7
+- Generated: 2024-05-16T17:17:08
+- Author(s): Bartosz Jablonski ([email protected]), Simon Parker ([email protected]), Linda Vesel, Eric Ohuma ([email protected])
+- Maintainer(s): Bartosz Jablonski ([email protected])
+- License: GNU General Public License v3.0
+- File SHA256: `F*9B3B83F9CE523633159727EED8688851AC1DBDC0B7EE492DF90BFD6448933D4C` for this version
+- Content SHA256: `C*A3084D73E2B717E303A1F97AEE11E8D43E5C07738C2B0EB3C59BB741DB84B6FF` for this version
+
+---
+
+# `gigs` version: `0.0.7`;
+
+---
+
+
+# `gigs` SAS Package
+
+## Overview
+
+Produced as part of the Guidance for International Growth Standards (GIGS)
+project at the London School of Hygiene & Tropical Medicine,
+`gigs` provides a single, simple interface for working with
+the WHO Child Growth standards and outputs from the
+INTERGROWTH-21<sup>st</sup> project. You will find functions for
+converting from anthropometric measures (e.g. weight or length) to
+z-scores and centiles, and the inverse. Also included are functions for
+classifying newborn and infant growth according to literature-based
+cut-offs.
+
+`gigs` is of use to anyone interested in fetal and child growth, including
+child health researchers, policymakers, and clinicians. This package is best
+suited to growth data where the gestational age (GA) of each child is known, as
+the use of the growth standards included in `gigs` is GA-dependent.
+We recommend you check out the
+[available standards](#available-international-growth-standards) section to
+see if your anthropometric measurements can be converted to z-scores/centiles by
+`gigs`. We recommend using `gigs` to generate continuous or categorical
+measures of fetal/newborn/child growth, which can then be used in downstream
+analyses.
+
+## Installation
+
+### Installing the SAS packages framework
+
+`gigs` works with the SAS Packages Framework (SPF), so installing `gigs` requires
+that the SPF is installed. First, create a directory where the SPF and 
+packages will be stored. This can be at any directory you choose, for example:
+- `D:\SAS_Packages`
+- `/home/myuser/myPackages`
+
+SPF is designed in such a way that this directory you've made **must** be refered 
+to by fileref `packages`. In your SAS session (preferably at the beginning), you 
+should run the following code:
+
+```sas
+filename packages "/path/to/packages/directory";
+```
+
+Installing an SPF package, "in a nutshell", means copying `SPFinit.sas` (from 
+`packagename.zip`) file into the packages directory. This can be done 
+automatically or manually.
+
+### Installing `gigs` - automatic
+
+To install `gigs` automatically, your SAS session must have access to the 
+internet.
+
+The following code will install the SAS Packages Framework, `gigs`, 
+and `macroArray` (required for `gigs` to work). You only need to execute
+this code *once*:
+
+```sas
+filename packages "/path/to/packages/directory";
+filename SPFinit url 
+ "https://raw.githubusercontent.com/yabwon/SAS_PACKAGES/main/SPF/SPFinit.sas"; 
+%include SPFinit; 
+
+%installPackage(SPFinit gigs macroArray)
+
+filename SPFinit clear;
+```
+
+After running this code, check the log to see if the process was successful.
+
+### Installing `gigs` - manual
+
+If your SAS session *does not* have access to the internet but you can copy 
+files manually to your packages directory, you can install `gigs` like so:
+
+- Download `SPFinit.sas` from [here](https://github.com/yabwon/SAS_PACKAGES/tree/main/SPF)
+- Download `gigs.zip` from [here](https://github.com/SASPAC/gigs)
+- Download `macroarray.zip` from [here](https://github.com/SASPAC/macroarray)
+
+Once downloaded, copy these files manually to your SAS packages directory.
+
+### Using `gigs` in a SAS session
+To use `gigs` in a new SAS session, you must enable the SAS Packages Framework, then
+load `gigs` with `%loadPackage`:
+
+```sas
+filename packages "/path/to/packages/directory";
+%include packages(SPFinit.sas);
+%loadPackage(gigs)
+```
+
+The `macroArray` package will be loaded automatically when `gigs` is loaded.
+
+If using `gigs` often in your work, the most convenient/practical way to load `gigs` is
+to put those three lines of code in your `autoexec.sas` file.
+
+### Links to SAS Package Framework materials
+
+The [**SAS Packages Framework (SPF)**](https://github.com/yabwon/SAS_PACKAGES)
+
+Location of the [**SAS Packages Repository**](https://github.com/SASPAC)
+
+[**Workshop materials**](https://github.com/yabwon/HoW-SASPackages)
+
+---
+
+## Documentation
+
+### [Package Documentation](./gigs.md)
+
+### [Introductory Examples](./examples/gigs_examples.md)
+
+## Terminology
+
+`gigs` operates with anthropometric measurements, and can convert between these and
+*z-scores*/*centiles*. Z-scores and centiles represent the location of a
+measurement within a normal distribution of values, such that:
+
+* A *z-score* is the number of standard deviations from the mean for a given
+ anthropometric measurement (e.g. height or weight).
+* A *centile* represents the proportion of measurements in some distribution
+ which we would expect to be lower than a measurement we've taken. In `gigs`,
+ these are represented as a value between `0` and `1`. For example, `0.5`
+ corresponds to the 50<sup>th</sup> centile (i.e. the mean), whereas `0.75`
+ corresponds to the 75<sup>th</sup> centile.
+
+In growth data, z-scores and centiles represent the size a fetus, newborn, or
+child relative to its peers. Its size is considered relative to some
+standardising variable, which is usually age but could also be another variable
+such as their length. By tracking a child's relative size as they
+grow, you can see if they are achieving their growth potential or not. If not,
+this may indicate underlying issues such as ill health or undernutrition.
+
+### Available international growth standards
+`gigs` facilitates the proper use of international growth standards, which
+are growth charts developed using international samples of healthy singleton
+children born to mothers that had their health needs met during pregnancy.
+They represent an international standard of 'optimal' growth. `gigs` implements
+international growth standards from the WHO and INTERGROWTH-21<sup>st</sup>
+project:
+
+* `ig_nbs` - INTERGROWTH-21<sup>st</sup> Newborn Size standards (including very preterm)
+ <details><summary>Component standards</summary>
+
+ | Acronym | Description | Unit | `gest_days` range |
+ |----------|-------------------------------|-------|-------------------|
+ | `wfga` | weight-for-GA | kg | 168 to 300 days |
+ | `lfga` | length-for-GA | cm | 168 to 300 days |
+ | `hcfga` | head circumference-for-GA | cm | 168 to 300 days |
+ | `wlrfga` | weight-to-length ratio-for-GA | kg/cm | 168 to 300 days |
+ | `ffmfga` | fat-free mass-for-GA | kg | 266 to 294 days |
+ | `bfpfga` | body fat percentage-for-GA | % | 266 to 294 days |
+ | `fmfga` | fat mass-for-GA | kg | 266 to 294 days |
+
+ </details>
+* `ig_png` - INTERGROWTH-21<sup>st</sup> Postnatal Growth of Preterm Infants standards
+ <details><summary>Component standards</summary>
+
+ | Acronym | Description | Unit | `x` range |
+ |---------|----------------------------|------|-----------------------|
+ | `wfa` | weight-for-age | kg | 27 to ≤64 exact weeks |
+ | `lfa` | length-for-age | cm | 27 to ≤64 exact weeks |
+ | `hcfa` | head circumference-for-age | cm | 27 to ≤64 exact weeks |
+ | `wfl` | weight-for-length | kg | 35 to 65 cm |
+
+ </details>
+* `ig_fet` - INTERGROWTH-21<sup>st</sup> Fetal standards
+ <details><summary>Component standards</summary>
+
+ | Acronym | Description | Unit | `x` range |
+ |-----------|--------------------------------------------------------------|------|-----------------|
+ | `hcfga` | head circumference-for-GA | mm | 98 to 280 days |
+ | `bpdfga` | biparietal diameter-for-GA | mm | 98 to 280 days |
+ | `acfga` | abdominal circumference-for-GA | mm | 98 to 280 days |
+ | `flfga` | femur length-for-GA | mm | 98 to 280 days |
+ | `ofdfga` | occipito-frontal diameter for-GA | mm | 98 to 280 days |
+ | `efwfga` | estimated fetal weight-for-GA | g | 154 to 280 days |
+ | `sfhfga` | symphisis-fundal height-for-GA | mm | 112 to 294 days |
+ | `crlfga` | crown-rump length-for-GA | mm | 58 to 105 days |
+ | `gafcrl` | GA-for-crown-rump length | days | 15 to 95 mm |
+ | `gwgfga` | gestational weight gain-for-GA | kg | 98 to 280 days |
+ | `pifga` | pulsatility index-for-GA | | 168 to 280 days |
+ | `rifga` | resistance index-for-GA | | 168 to 280 days |
+ | `sdrfga` | systolic/diastolic ratio-for-GA | | 168 to 280 days |
+ | `tcdfga` | transcerebellar diameter-for-GA | mm | 98 to 280 days |
+ | `tcdfga` | GA-for-transcerebellar diameter | mm | 98 to 280 days |
+ | `poffga` | parietal-occipital fissure-for-GA | mm | 105 to 252 days |
+ | `sffga` | Sylvian fissue-for-GA | mm | 105 to 252 days |
+ | `avfga` | anterior horn of the lateral ventricle-for-GA | mm | 105 to 252 days |
+ | `pvfga` | atrium of the posterior horn of the lateral ventricle-for-GA | mm | 105 to 252 days |
+ | `cmfga` | cisterna magna-for-GA | mm | 105 to 252 days |
+ | `hefwfga` | Hadlock estimated fetal weight-for-GA | g | 126 to 287 days |
+
+
+ </details>
+* `who_gs` - WHO Child Growth Standards for term infants
+ <details><summary>Component standards</summary>
+
+ | Acronym | Description | Unit | `x` range |
+ |---------|------------------------------|------------------|-----------------|
+ | `wfa` | weight-for-age | kg | 0 to 1856 days |
+ | `bfa` | BMI-for-age | kg/m<sup>2</sup> | 0 to 1856 days |
+ | `lhfa` | length/height-for-age | cm | 0 to 1856 days |
+ | `hcfa` | head circumference-for-age | cm | 0 to 1856 days |
+ | `wfl` | weight-for-height | kg | 45 to 110 cm |
+ | `wfh` | weight-for-length | kg | 65 to 120 cm |
+ | `acfa` | arm circumference-for-age | cm | 91 to 1856 days |
+ | `ssfa` | subscapular skinfold-for-age | mm | 91 to 1856 days |
+ | `tsfa` | triceps skinfold-for-age | mm | 91 to 1856 days |
+
+ </details>
+
+## Funding
+
+Bill & Melinda Gates Foundation
+
+---
+
+
+---
+
+
+---
+
+Required SAS Components: 
+ - Base SAS Software
+
+---
+
+Required SAS Packages: 
+ - macroArray (1.2.6)
+
+---
+
+
+--------------------------------------------------------------------
+
+*SAS package generated by SAS Package Framework, version `20240423`*
+
+--------------------------------------------------------------------
+
+---