From 5141eec3f77db39905615765833bb69b5bb9dae5 Mon Sep 17 00:00:00 2001 From: Simon Parker Date: Thu, 19 Dec 2024 09:45:13 +0000 Subject: [PATCH 1/4] chore: update paper.md --- paper/paper.md | 67 +++++++++++++++++++++++++++----------------------- 1 file changed, 36 insertions(+), 31 deletions(-) diff --git a/paper/paper.md b/paper/paper.md index 149085f..904c459 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -31,25 +31,21 @@ bibliography: paper.bib # Summary -Researchers studying newborn and child growth often want to assess how the size -of infants relative to their peers. To do this, researchers can use a growth -standard. A growth standard describes how infants *should* grow if provided -with the nutrition and support required to reach their growth potential. -``gigs`` makes a range of growth standards available in one R package: -the INTERGROWTH-21^st^ Fetal Standards -[@Papageorghiou2014AInternationalPregnancy; @Stirnemann2017InternationalProject; -@Papageorghiou2016InternationalCountries; -@Papageorghiou2014BInternationalPregnancy; -@Drukker2020InternationalProject; @Rodriguez-Sibaja2021FetalProject; -@Stirnemann2020IntergrowthWeight]; INTERGROWTH-21^st^ Newborn Size -and Very Preterm Newborn Size Standards [@Villar2014InternationalProject; -@Villar2016INTERGROWTH-21stCharts; @Villar2017BodyProject]; INTERGROWTH-21^st^ Postnatal Growth -of Preterm Infants Standards [@Villar2015PostnatalProject]; and the WHO Child Growth Standards -[@WHOMulticentreGrowthReferenceStudyGroup2006WHOAge; @WHO2006WHODevelopment; -@WHO2007WHODevelopment]. Also included are functions to classify growth for -indicators including size-for-gestational age, small vulnerable newborns -[@Ashorn2023SmallImpact; @Lawn2023SmallCounting], stunting, wasting, -weight-for-age (underweight), and micro/macrocephaly. +There is a gap for clear guidance and open access tools for assessing nutrition +and growth indicators as part of individual clinical care and population-based +epidemiology. To enable better identification of at-risk infants, a unifying +framework and clear guidance for how, when and for whom to use the existing +international newborn and child growth standards developed by the WHO and +INTERGROWTH-21^st^ is needed. Such guidance is essential to enable tracking of +progress towards Sustainable Development Goals and the WHO Global +Nutrition targets. This need is the motivation for ``gigs`` - a package for +researchers and policymakers that facilitates the appropriate use of growth +standards for the determination and assessment of growth outcomes at the +population level (e.g., stunting, wasting, underweight and trajectories over +time) among vulnerable infants. For clinicians, the ``gigs`` also provides +support in choosing which standards to use when assessing growth of individual +infants. + # Statement of need @@ -66,14 +62,13 @@ and local goals. Similarly, use of appropriate standards by clinicians will enable proper identification of at-risk infants and inform the clinical care management and decision-making. -Applying appropriate growth standards can be difficult - not all -research groups have the ability to implement growth standards in software, and -may make errors whilst doing so. Furthermore, researchers must pick and choose -the right growth standards for their work - which is not always achieved in -practice [@perumal_who_2015]. The ``gigs`` package makes these issues less -common. Firstly, extensive unit testing ensures that each growth standard in -``gigs`` is accurate to published charts, for every growth standard we've -implemented: +Applying appropriate growth standards can be difficult - not all research groups +have the ability to implement growth standards in software, and may make errors +whilst doing so. Furthermore, researchers must pick and choose the right growth +standards for their work - which is not always achieved in practice +[@perumal_who_2015]. The ``gigs`` package makes these issues less common. +Firstly, extensive unit testing ensures that each growth standard in ``gigs`` is +accurate to published charts, for every growth standard we've implemented: - The INTERGROWTH-21^st^ Fetal Standards [@Papageorghiou2014AInternationalPregnancy; @Stirnemann2017InternationalProject; @@ -99,6 +94,17 @@ Stata [@vidmar_standardizing_2013], and the R packages ``anthro`` [@r_anthro], However, only ``gigs`` implements the full set of INTERGROWTH-21^st^ Fetal standards and INTERGROWTH-21^st^ Postnatal Growth of Preterm Infants standards. +Next, ``gigs`` offers specific functions (``classify_growth()``, ``gigs_waz()``, +and friends) which select an appropriate growth standard to apply to each +observation in flat, tabular dataset. Growth standards are selected based on the +chronological and gestational age for each observation, and the specific +criteria can be found in the [package +documentation](https://docs.ropensci.org/gigs/reference/gigs_zscoring.html). +These functions can be used to investigate growth indicators including +size-for-gestational age, small vulnerable newborns +[@Ashorn2023SmallImpact; @Lawn2023SmallCounting], stunting, wasting, +weight-for-age (underweight), and micro/macrocephaly. + When benchmarked against each other, ``gigs`` for R outperforms almost all the packages mentioned above, or is at most a few milliseconds slower. It does this whilst checking inputs to ensure they are formatted correctly, to make life @@ -113,10 +119,9 @@ In addition to the R package, a these statistical softwares. All versions of ``gigs`` are already in use by researchers at LSHTM, Harvard, the [Small Vulnerable Newborn Collaboration](https://www.thelancet.com/series/small-vulnerable-newborns) and -an international collaboration investigating stillbirths, led by Eric Ohuma. -Thanks to its speed, input checking, and unit test-backed accuracy, we believe -``gigs`` will be used widely by those looking to assess newborn, infant, or -child growth in R. +an international collaboration investigating stillbirths. Thanks to its speed, +input checking, and unit test-backed accuracy, we believe ``gigs`` will be used +widely by those looking to assess newborn, infant, or child growth in R. # Acknowledgements From 824e7b9d236f0c3422ff039a111f498965d8cb52 Mon Sep 17 00:00:00 2001 From: Simon Parker Date: Thu, 19 Dec 2024 09:48:09 +0000 Subject: [PATCH 2/4] chore: update paper.md (again) --- paper/paper.md | 1 - 1 file changed, 1 deletion(-) diff --git a/paper/paper.md b/paper/paper.md index 904c459..4829f95 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -46,7 +46,6 @@ time) among vulnerable infants. For clinicians, the ``gigs`` also provides support in choosing which standards to use when assessing growth of individual infants. - # Statement of need Without accurate global data on newborn and child growth patterns using From 484cb3e2fdd465a8f68ef963f7084e65809efcf4 Mon Sep 17 00:00:00 2001 From: Simon Parker Date: Thu, 19 Dec 2024 09:49:36 +0000 Subject: [PATCH 3/4] docs: updated classify_growth() docs to include @seealso-style ref to gigs_waz() documentation --- R/growth_classify.R | 7 +++++-- man/classify_growth.Rd | 6 +++++- man/classify_headsize.Rd | 3 ++- man/classify_stunting.Rd | 3 ++- man/classify_wasting.Rd | 3 ++- man/classify_wfa.Rd | 3 ++- 6 files changed, 18 insertions(+), 7 deletions(-) diff --git a/R/growth_classify.R b/R/growth_classify.R index d21ba48..0f28ea3 100644 --- a/R/growth_classify.R +++ b/R/growth_classify.R @@ -215,7 +215,8 @@ classify_svn <- function(.data, #' gest_days = gestage, #' sex = sex) #' @seealso See [classify_growth()] to run this analysis and others at the same -#' time. +#' time. See [gigs_waz()] to learn which growth standard will be used for +#' different combinations of gestational/chronological age. #' @export classify_stunting <- function( .data, @@ -537,13 +538,15 @@ classify_headsize <- function(.data, #' @note For size-for-GA and small vulnerable newborn analyses, centiles and #' categorisations will only be applied for birth measurements. These are #' considered to be the observation per level of `id` where `age_days` is -#' smallest, provided that `age_days` is between `<3`. +#' smallest, provided that `age_days` is `<3`. #' #' Categorical (factor) columns produced here may contain unused factor #' levels. By default, gigs will inform you if these columns have unused #' factor levels. You can change this behaviour using the #' [GIGS package-level option][gigs_options] #' `.gigs_options$handle_unused_levels`. +#' @seealso See [gigs_waz()] to learn which growth standard will be used for +#' different combinations of gestational/chronological age. #' @examples #' # This dummy dataset contains data from two people, from birth (<3 days) to #' # 500 days of age. diff --git a/man/classify_growth.Rd b/man/classify_growth.Rd index b0bad07..81f67c1 100644 --- a/man/classify_growth.Rd +++ b/man/classify_growth.Rd @@ -105,7 +105,7 @@ wasting, weight-for-age, and more) at once in \code{data.frame}-like objects. For size-for-GA and small vulnerable newborn analyses, centiles and categorisations will only be applied for birth measurements. These are considered to be the observation per level of \code{id} where \code{age_days} is -smallest, provided that \code{age_days} is between \verb{<3}. +smallest, provided that \code{age_days} is \verb{<3}. Categorical (factor) columns produced here may contain unused factor levels. By default, gigs will inform you if these columns have unused @@ -204,3 +204,7 @@ Accogli A, Geraldo AF, Piccolo G, Riva A, Scala M, Balagura G, et al. \strong{Diagnostic Approach to Macrocephaly in Children}. \emph{Frontiers in Paediatrics} 2022, \emph{9:794069} \doi{10.3389/fped.2021.794069} } +\seealso{ +See \code{\link[=gigs_waz]{gigs_waz()}} to learn which growth standard will be used for +different combinations of gestational/chronological age. +} diff --git a/man/classify_headsize.Rd b/man/classify_headsize.Rd index 8debac7..9f45905 100644 --- a/man/classify_headsize.Rd +++ b/man/classify_headsize.Rd @@ -124,5 +124,6 @@ Paediatrics} 2022, \emph{9:794069} \doi{10.3389/fped.2021.794069} } \seealso{ See \code{\link[=classify_growth]{classify_growth()}} to run this analysis and others at the same -time. +time. See \code{\link[=gigs_waz]{gigs_waz()}} to learn which growth standard will be used for +different combinations of gestational/chronological age. } diff --git a/man/classify_stunting.Rd b/man/classify_stunting.Rd index aa215a5..6b15189 100644 --- a/man/classify_stunting.Rd +++ b/man/classify_stunting.Rd @@ -126,5 +126,6 @@ Rockville, Maryland, USA: ICF (2020). pp. 431-435. } \seealso{ See \code{\link[=classify_growth]{classify_growth()}} to run this analysis and others at the same -time. +time. See \code{\link[=gigs_waz]{gigs_waz()}} to learn which growth standard will be used for +different combinations of gestational/chronological age. } diff --git a/man/classify_wasting.Rd b/man/classify_wasting.Rd index b3d4540..baa306a 100644 --- a/man/classify_wasting.Rd +++ b/man/classify_wasting.Rd @@ -136,5 +136,6 @@ Rockville, Maryland, USA: ICF (2020). pp. 431-435. } \seealso{ See \code{\link[=classify_growth]{classify_growth()}} to run this analysis and others at the same -time. +time. See \code{\link[=gigs_waz]{gigs_waz()}} to learn which growth standard will be used for +different combinations of gestational/chronological age. } diff --git a/man/classify_wfa.Rd b/man/classify_wfa.Rd index 453f3f2..a9bc6b7 100644 --- a/man/classify_wfa.Rd +++ b/man/classify_wfa.Rd @@ -130,5 +130,6 @@ Rockville, Maryland, USA: ICF (2020). pp. 431-435. } \seealso{ See \code{\link[=classify_growth]{classify_growth()}} to run this analysis and others at the same -time. +time. See \code{\link[=gigs_waz]{gigs_waz()}} to learn which growth standard will be used for +different combinations of gestational/chronological age. } From bcfdbfb775be0e22988d0af6b8a51449b4fba2d9 Mon Sep 17 00:00:00 2001 From: Simon Parker <65285181+simpar1471@users.noreply.github.com> Date: Fri, 10 Jan 2025 19:11:40 +0000 Subject: [PATCH 4/4] chore: update joss paper.md --- paper/paper.md | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/paper/paper.md b/paper/paper.md index 4829f95..c2d4b9e 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -1,6 +1,6 @@ --- title: | - 'gigs: A package for standardising fetal, neonatal, and child growth assessment' + `gigs: A package for standardising fetal, neonatal, and child growth assessment` tags: - R - intergrowth @@ -19,13 +19,13 @@ authors: affiliation: '1' affiliations: - index: 1 - name: Maternal, Adolescent, Reproductive and Child Health Centre, London School of Hygiene & Tropical Medicine, London, UK + name: Maternal, Adolescent, Reproductive and Child Health Centre, London School of Hygiene & Tropical Medicine, London, United Kingdom ror: 00a0jsq62 - index: 2 - name: Ariadne Labs, Brigham and Women’s Hospital, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, U.S.A. + name: Ariadne Labs, Brigham and Women’s Hospital, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America ror: 03vek6s52 -date: 14 December 2024 +date: 10 January 2024 bibliography: paper.bib --- @@ -41,7 +41,7 @@ progress towards Sustainable Development Goals and the WHO Global Nutrition targets. This need is the motivation for ``gigs`` - a package for researchers and policymakers that facilitates the appropriate use of growth standards for the determination and assessment of growth outcomes at the -population level (e.g., stunting, wasting, underweight and trajectories over +population level (e.g. stunting, wasting, underweight and trajectories over time) among vulnerable infants. For clinicians, the ``gigs`` also provides support in choosing which standards to use when assessing growth of individual infants. @@ -115,7 +115,7 @@ website](https://docs.ropensci.org/gigs/articles/benchmarking.html). In addition to the R package, a [Stata package](https://www.github.com/lshtm-gigs/gigs-stata/) and [SAS package](https://www.github.com/SASPAC/gigs/) are available for users of -these statistical softwares. All versions of ``gigs`` are already in use by +these statistical software. All versions of ``gigs`` are already in use by researchers at LSHTM, Harvard, the [Small Vulnerable Newborn Collaboration](https://www.thelancet.com/series/small-vulnerable-newborns) and an international collaboration investigating stillbirths. Thanks to its speed, @@ -131,4 +131,4 @@ Ordu and Chitra Saraswati - and handling editor Rebecca Killick, whose feedback and guidance through the rOpenSci software review process has been extremely useful. -# References \ No newline at end of file +# References