From a21c67dd75d23babc1059394b208ce53d25002a0 Mon Sep 17 00:00:00 2001 From: Simon Parker Date: Sat, 14 Dec 2024 14:51:48 +0000 Subject: [PATCH] chore: Write out JOSS paper and add relevant CI --- .Rbuildignore | 1 + .github/workflows/draft-joss-paper.yml | 28 +++ paper/paper.bib | 304 +++++++++++++++++++++++++ paper/paper.md | 115 ++++++++++ 4 files changed, 448 insertions(+) create mode 100644 .github/workflows/draft-joss-paper.yml create mode 100644 paper/paper.bib create mode 100644 paper/paper.md diff --git a/.Rbuildignore b/.Rbuildignore index d46d39b..c5c9f6e 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -18,3 +18,4 @@ ^codemeta\.json$ ^CODE_OF_CONDUCT\.md$ ^CITATION\.cff$ +^paper$ diff --git a/.github/workflows/draft-joss-paper.yml b/.github/workflows/draft-joss-paper.yml new file mode 100644 index 0000000..76c2b72 --- /dev/null +++ b/.github/workflows/draft-joss-paper.yml @@ -0,0 +1,28 @@ +name: Draft JOSS PDF +on: + push: + paths: + - paper/** + - .github/workflows/draft-pdf.yml + +jobs: + paper: + runs-on: ubuntu-latest + name: JOSS Paper Draft + steps: + - name: Checkout + uses: actions/checkout@v4 + - name: Build draft PDF + uses: openjournals/openjournals-draft-action@master + with: + journal: joss + # This should be the path to the paper within your repo. + paper-path: paper/paper.md + - name: Upload + uses: actions/upload-artifact@v4 + with: + name: paper + # This is the output path where Pandoc will write the compiled + # PDF. Note, this should be the same directory as the input + # paper.md + path: paper/paper.pdf \ No newline at end of file diff --git a/paper/paper.bib b/paper/paper.bib new file mode 100644 index 0000000..fef9ede --- /dev/null +++ b/paper/paper.bib @@ -0,0 +1,304 @@ +@article{perumal_who_2015, + title = {{WHO} {Child} {Growth} {Standards} {Are} {Often} {Incorrectly} {Applied} to {Children} {Born} {Preterm} in {Epidemiologic} {Research}}, + volume = {145}, + issn = {00223166}, + doi = {10.3945/jn.115.214064}, + number = {11}, + journal = {The Journal of Nutrition}, + author = {Perumal, Nandita and Gaffey, Michelle F and Bassani, Diego G and Roth, Daniel E}, + month = nov, + year = {2015}, + pages = {2429--2439}, +} + +@article{Vesel2022LowSettings, + title = {Low Birthweight Infant Feeding Practices and Growth Patterns in the First Six Months of Life in Resource-Limited Settings}, + volume = {6}, + ISSN = {2475-2991}, + url = {http://dx.doi.org/10.1093/cdn/nzac060.069}, + DOI = {10.1093/cdn/nzac060.069}, + journal = {Current Developments in Nutrition}, + publisher = {Elsevier BV}, + author = {Vesel, Linda and Kisenge, Rodrick and Koujalagi, Murugaraj and Kusagur, Varun and Manji, Karim and Mvalo, Tisungane and Nayak, Rashmita and Phiri, Melda and Saidi, Friday and Semrau, Katherine and Sudfeld, Christopher}, + year = {2022}, + month = jun, + pages = {611} +} + +@article{Vesel2023FeedingStudy, + title = {Feeding practices and growth patterns of moderately low birthweight infants in resource-limited settings: results from a multisite, longitudinal observational study}, + volume = {13}, + ISSN = {2044-6055}, + url = {http://dx.doi.org/10.1136/bmjopen-2022-067316}, + DOI = {10.1136/bmjopen-2022-067316}, + number = {2}, + journal = {BMJ Open}, + publisher = {BMJ}, + author = {Vesel, Linda and Bellad, Roopa M and Manji, Karim and Saidi, Friday and Velasquez, Esther and Sudfeld, Christopher R and Miller, Katharine and Bakari, Mohamed and Lugangira, Kristina and Kisenge, Rodrick and Salim, Nahya and Somji, Sarah and Hoffman, Irving and Msimuko, Kingsly and Mvalo, Tisungane and Nyirenda, Fadire and Phiri, Melda and Das, Leena and Dhaded, Sangappa and Goudar, Shivaprasad S and Herekar, Veena and Kumar, Yogesh and Koujalagi, M B and Guruprasad, Gowdar and Panda, Sanghamitra and Shamanur, Latha G and Somannavar, Manjunath and Vernekar, Sunil S and Misra, Sujata and Adair, Linda and Bell, Griffith and Caruso, Bethany A and Duggan, Christopher and Fleming, Katelyn and Israel-Ballard, Kiersten and Fishman, Eliza and Lee, Anne C C and Lipsitz, Stuart and Mansen, Kimberly L and Martin, Stephanie L and Mokhtar, Rana R and North, Krysten and Pote, Arthur and Spigel, Lauren and Tuller, Danielle E and Young, Melissa and Semrau, Katherine E A}, + year = {2023}, + month = feb, + pages = {e067316} +} + +@article{Papageorghiou2014AInternationalPregnancy, + title = {International standards for fetal growth based on serial ultrasound measurements: the {Fetal} {Growth} {Longitudinal} {Study} of the {INTERGROWTH}-21st {Project}}, + volume = {384}, + issn = {0140-6736, 1474-547X}, + shorttitle = {International standards for fetal growth based on serial ultrasound measurements}, + doi = {10.1016/S0140-6736(14)61490-2}, + language = {English}, + number = {9946}, + urldate = {2024-01-16}, + journal = {The Lancet}, + author = {Papageorghiou, Aris T. and Ohuma, Eric O. and Altman, Douglas G. and Todros, Tullia and Cheikh Ismail, Leila and Lambert, Ann and Jaffer, Yasmin A. and Bertino, Enrico and Gravett, Michael G. and Purwar, Manorama and Noble, J. Alison and Pang, Ruyan and Victora, Cesar G. and Barros, Fernando C. and Carvalho, Maria and Salomon, Laurent J. and Bhutta, Zulfiqar A. and Kennedy, Stephen H. and Villar, José}, + month = sep, + year = {2014}, + pmid = {25209488}, + pages = {869--879}, +} + +@article{Stirnemann2017InternationalProject, + title = {International estimated fetal weight standards of the {INTERGROWTH}-21st {Project}}, + volume = {49}, + copyright = {© 2016 The Authors. Ultrasound in Obstetrics \& Gynecology published by John Wiley \& Sons Ltd on behalf of the International Society of Ultrasound in Obstetrics and Gynecology.}, + issn = {1469-0705}, + doi = {10.1002/uog.17347}, + abstract = {Objective Estimated fetal weight (EFW) and fetal biometry are complementary measures used to screen for fetal growth disturbances. Our aim was to provide international EFW standards to complement the INTERGROWTH-21st Fetal Growth Standards that are available for use worldwide. Methods Women with an accurate gestational-age assessment, who were enrolled in the prospective, international, multicenter, population-based Fetal Growth Longitudinal Study (FGLS) and INTERBIO-21st Fetal Study (FS), two components of the INTERGROWTH-21st Project, had ultrasound scans every 5 weeks from 9–14 weeks' until 40 weeks' gestation. At each visit, measurements of fetal head circumference (HC), biparietal diameter, occipitofrontal diameter, abdominal circumference (AC) and femur length (FL) were obtained blindly by dedicated research sonographers using standardized methods and identical ultrasound machines. Birth weight was measured within 12 h of delivery by dedicated research anthropometrists using standardized methods and identical electronic scales. Live babies without any congenital abnormality, who were born within 14 days of the last ultrasound scan, were selected for inclusion. As most births occurred at around 40 weeks' gestation, we constructed a bootstrap model selection and estimation procedure based on resampling of the complete dataset under an approximately uniform distribution of birth weight, thus enriching the sample size at extremes of fetal sizes, to achieve consistent estimates across the full range of fetal weight. We constructed reference centiles using second-degree fractional polynomial models. Results Of the overall population, 2404 babies were born within 14 days of the last ultrasound scan. Mean time between the last scan and birth was 7.7 (range, 0–14) days and was uniformly distributed. Birth weight was best estimated as a function of AC and HC (without FL) as log(EFW) = 5.084820 − 54.06633 × (AC/100)3 − 95.80076 × (AC/100)3 × log(AC/100) + 3.136370 × (HC/100), where EFW is in g and AC and HC are in cm. All other measures, gestational age, symphysis–fundus height, amniotic fluid indices and interactions between biometric measures and gestational age, were not retained in the selection process because they did not improve the prediction of EFW. Applying the formula to FGLS biometric data (n = 4231) enabled gestational age-specific EFW tables to be constructed. At term, the EFW centiles matched those of the INTERGROWTH-21st Newborn Size Standards but, at {\textless} 37 weeks' gestation, the EFW centiles were, as expected, higher than those of babies born preterm. Comparing EFW cross-sectional values with the INTERGROWTH-21st Preterm Postnatal Growth Standards confirmed that preterm postnatal growth is a different biological process from intrauterine growth. Conclusions We provide an assessment of EFW, as an adjunct to routine ultrasound biometry, from 22 to 40 weeks' gestation. However, we strongly encourage clinicians to evaluate fetal growth using separate biometric measures such as HC and AC, as well as EFW, to avoid the minimalist approach of focusing on a single value. © 2016 Authors. Ultrasound in Obstetrics \& Gynecology published by John Wiley \& Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.}, + language = {en}, + number = {4}, + urldate = {2024-01-16}, + journal = {Ultrasound in Obstetrics \& Gynecology}, + author = {Stirnemann, J. and Villar, J. and Salomon, L. J. and Ohuma, E. and Ruyan, P. and Altman, D. G. and Nosten, F. and Craik, R. and Munim, S. and Cheikh Ismail, L. and Barros, F. C. and Lambert, A. and Norris, S. and Carvalho, M. and Jaffer, Y. A. and Noble, J. A. and Bertino, E. and Gravett, M. G. and Purwar, M. and Victora, C. G. and Uauy, R. and Bhutta, Z. and Kennedy, S. and Papageorghiou, A. T.}, + year = {2017}, + keywords = {birth weight, fetal growth, gestational age, screening, ultrasound}, + pages = {478--486}, +} + +@article{Papageorghiou2016InternationalCountries, + title = {International standards for symphysis-fundal height based on serial measurements from the {Fetal} {Growth} {Longitudinal} {Study} of the {INTERGROWTH}-21st {Project}: prospective cohort study in eight countries}, + volume = {355}, + copyright = {Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions. This is an Open Access article distributed in accordance with the terms of the Creative Commons Attribution (CC BY 3.0) license, which permits others to distribute, remix, adapt and build upon this work, for commercial use, provided the original work is properly cited. See: http://creativecommons.org/licenses/by/3.0/.}, + issn = {1756-1833}, + shorttitle = {International standards for symphysis-fundal height based on serial measurements from the {Fetal} {Growth} {Longitudinal} {Study} of the {INTERGROWTH}-21st {Project}}, + doi = {10.1136/bmj.i5662}, + abstract = {Objective To create international symphysis-fundal height standards derived from pregnancies of healthy women with good maternal and perinatal outcomes. +Design Prospective longitudinal observational study. +Setting Eight geographically diverse urban regions in Brazil, China, India, Italy, Kenya, Oman, United Kingdom, and United States. +Participants Healthy, well nourished pregnant women enrolled into the Fetal Growth Longitudinal Study component of the INTERGROWTH-21st Project at 9-14 weeks’ gestation, and followed up until birth. +Main outcome measures Symphysis-fundal height was measured every five weeks from 14 weeks’ gestation until birth using standardised methods and dedicated research staff who were blinded to the symphysis-fundal height measurements by turning the tape measure so that numbers were not visible during examination. The best fitting curve was selected using second degree fractional polynomials and further modelled in a multilevel framework to account for the longitudinal design of the study. +Results Of 13 108 women screened in the first trimester, 4607 (35.1\%) met the study entry criteria. Of the eligible women, 4321 (93.8\%) had pregnancies without major complications and delivered live singletons without congenital malformations. The median number of symphysis-fundal height measurements was 5.0 (range 1-7); 3976 (92.0\%) women had four or more measurements. Symphysis-fundal height measurements increased almost linearly with gestational age; data were used to determine fitted 3rd, 50th, and 97th centile curves, which showed excellent agreement with observed values. +Conclusions This study presents international standards to measure symphysis-fundal height as a first level screening tool for fetal growth disturbances.}, + language = {en}, + urldate = {2024-01-16}, + journal = {BMJ}, + author = {Papageorghiou, Aris T. and Ohuma, Eric O. and Gravett, Michael G. and Hirst, Jane and Silveira, Mariangela F. da and Lambert, Ann and Carvalho, Maria and Jaffer, Yasmin A. and Altman, Douglas G. and Noble, Julia A. and Bertino, Enrico and Purwar, Manorama and Pang, Ruyan and Cheikh Ismail, Leila and Victora, Cesar and Bhutta, Zulfiqar A. and Kennedy, Stephen H. and Villar, José}, + month = nov, + year = {2016}, + pages = {i5662}, +} + +@article{Papageorghiou2014BInternationalPregnancy, + title = {International standards for early fetal size and pregnancy dating based on ultrasound measurement of crown–rump length in the first trimester of pregnancy}, + volume = {44}, + copyright = {© 2014 Authors. Ultrasound in Obstetrics \& Gynecology published by John Wiley \& Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.}, + issn = {1469-0705}, + doi = {10.1002/uog.13448}, + abstract = {Objectives There are no international standards for relating fetal crown–rump length (CRL) to gestational age (GA), and most existing charts have considerable methodological limitations. The INTERGROWTH-21st Project aimed to produce the first international standards for early fetal size and ultrasound dating of pregnancy based on CRL measurement. Methods Urban areas in eight geographically diverse countries that met strict eligibility criteria were selected for the prospective, population-based recruitment, between 9 + 0 and 13 + 6 weeks' gestation, of healthy well-nourished women with singleton pregnancies at low risk of fetal growth impairment. GA was calculated on the basis of a certain last menstrual period, regular menstrual cycle and lack of hormonal medication or breastfeeding in the preceding 2 months. CRL was measured using strict protocols and quality-control measures. All women were followed up throughout pregnancy until delivery and hospital discharge. Cases of neonatal and fetal death, severe pregnancy complications and congenital abnormalities were excluded from the study. Results A total of 4607 women were enrolled in the Fetal Growth Longitudinal Study, one of the three main components of the INTERGROWTH-21st Project, of whom 4321 had a live singleton birth in the absence of severe maternal conditions or congenital abnormalities detected by ultrasound or at birth. The CRL was measured in 56 women at {\textless} 9 + 0 weeks' gestation; these were excluded, resulting in 4265 women who contributed data to the final analysis. The mean CRL and SD increased with GA almost linearly, and their relationship to GA is given by the following two equations (in which GA is in days and CRL in mm): mean CRL = −50.6562 + (0.815118 × GA) + (0.00535302 × GA2); and SD of CRL = −2.21626 + (0.0984894 × GA). GA estimation is carried out according to the two equations: GA = 40.9041 + (3.21585 × CRL0.5) + (0.348956 × CRL); and SD of GA = 2.39102 + (0.0193474 × CRL). Conclusions We have produced international prescriptive standards for early fetal linear size and ultrasound dating of pregnancy in the first trimester that can be used throughout the world. © 2014 Authors. Ultrasound in Obstetrics \& Gynecology published by John Wiley \& Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.}, + language = {en}, + number = {6}, + urldate = {2024-01-16}, + journal = {Ultrasound in Obstetrics \& Gynecology}, + author = {Papageorghiou, A. T. and Kennedy, S. H. and Salomon, L. J. and Ohuma, E. O. and Cheikh Ismail, L. and Barros, F. C. and Lambert, A. and Carvalho, M. and Jaffer, Y. A. and Bertino, E. and Gravett, M. G. and Altman, D. G. and Purwar, M. and Noble, J. A. and Pang, R. and Victora, C. G. and Bhutta, Z. A. and Villar, J. and {International Fetal and Newborn Growth Consortium for the 21st Century (INTERGROWTH-21st)}}, + year = {2014}, + keywords = {crown–rump length, dating, gestational age, global health, growth, pregnancy}, + pages = {641--648}, +} + +@article{Drukker2020InternationalProject, + title = {International gestational age-specific centiles for umbilical artery {Doppler} indices: a longitudinal prospective cohort study of the {INTERGROWTH}-21st {Project}}, + volume = {222}, + issn = {0002-9378, 1097-6868}, + shorttitle = {International gestational age-specific centiles for umbilical artery {Doppler} indices}, + doi = {10.1016/j.ajog.2020.01.012}, + language = {English}, + number = {6}, + urldate = {2024-01-16}, + journal = {American Journal of Obstetrics \& Gynecology}, + author = {Drukker, Lior and Staines-Urias, Eleonora and Villar, José and Barros, Fernando C. and Carvalho, Maria and Munim, Shama and McGready, Rose and Nosten, Francois and Berkley, James A. and Norris, Shane A. and Uauy, Ricardo and Kennedy, Stephen H. and Papageorghiou, Aris T.}, + month = jun, + year = {2020}, + pmid = {31954701}, + keywords = {Doppler, INTERBIO, INTERGROWTH-21st ultrasound, antepartum testing, fetal growth restriction, fetal well-being, longitudinal study, multinational study, perinatal morbidity, perinatal mortality, placenta, pulsatility index, reference ranges, resistance index, systolic/diastolic ratio, umbilical artery}, + pages = {602.e1--602.e15}, +} + +@article{Rodriguez-Sibaja2021FetalProject, + title = {Fetal cerebellar growth and {Sylvian} fissure maturation: international standards from {Fetal} {Growth} {Longitudinal} {Study} of {INTERGROWTH}-21st {Project}}, + volume = {57}, + copyright = {© 2020 The Authors. Ultrasound in Obstetrics \& Gynecology published by John Wiley \& Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.}, + issn = {1469-0705}, + shorttitle = {Fetal cerebellar growth and {Sylvian} fissure maturation}, + doi = {10.1002/uog.22017}, + abstract = {Objective To construct international ultrasound-based standards for fetal cerebellar growth and Sylvian fissure maturation. Methods Healthy, well nourished pregnant women, enrolled at {\textless} 14 weeks' gestation in the Fetal Growth Longitudinal Study (FGLS) of INTERGROWTH-21st, an international multicenter, population-based project, underwent serial three-dimensional (3D) fetal ultrasound scans every 5 ± 1 weeks until delivery in study sites located in Brazil, India, Italy, Kenya and the UK. In the present analysis, only those fetuses that underwent developmental assessment at 2 years of age were included. We measured the transcerebellar diameter and assessed Sylvian fissure maturation using two-dimensional ultrasound images extracted from available 3D fetal head volumes. The appropriateness of pooling data from the five sites was assessed using variance component analysis and standardized site differences. For each Sylvian fissure maturation score (left or right side), mean gestational age and 95\% CI were calculated. Transcerebellar diameter was modeled using fractional polynomial regression, and goodness of fit was assessed. Results Of those children in the original FGLS cohort who had developmental assessment at 2 years of age, 1130 also had an available 3D ultrasound fetal head volume. The sociodemographic characteristics and pregnancy/perinatal outcomes of the study sample confirmed the health and low-risk status of the population studied. In addition, the fetuses had low morbidity and adequate growth and development at 2 years of age. In total, 3016 and 2359 individual volumes were available for transcerebellar-diameter and Sylvian-fissure analysis, respectively. Variance component analysis and standardized site differences showed that the five study populations were sufficiently similar on the basis of predefined criteria for the data to be pooled to produce international standards. A second-degree fractional polynomial provided the best fit for modeling transcerebellar diameter; we then estimated gestational-age-specific 3rd, 50th and 97th smoothed centiles. Goodness-of-fit analysis comparing empirical centiles with smoothed centile curves showed good agreement. The Sylvian fissure increased in maturation with advancing gestation, with complete overlap of the mean gestational age and 95\% CIs between the sexes for each development score. No differences in Sylvian fissure maturation between the right and left hemispheres were observed. Conclusion We present, for the first time, international standards for fetal cerebellar growth and Sylvian fissure maturation throughout pregnancy based on a healthy fetal population that exhibited adequate growth and development at 2 years of age. © 2020 The Authors. Ultrasound in Obstetrics \& Gynecology published by John Wiley \& Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.}, + language = {en}, + number = {4}, + urldate = {2024-01-16}, + journal = {Ultrasound in Obstetrics \& Gynecology}, + author = {Rodriguez-Sibaja, M. J. and Villar, J. and Ohuma, E. O. and Napolitano, R. and Heyl, S. and Carvalho, M. and Jaffer, Y. A. and Noble, J. A. and Oberto, M. and Purwar, M. and Pang, R. and Cheikh Ismail, L. and Lambert, A. and Gravett, M. G. and Salomon, L. J. and Drukker, L. and Barros, F. C. and Kennedy, S. H. and Bhutta, Z. A. and Papageorghiou, A. T.}, + year = {2021}, + keywords = {cerebellum, cerebral cortex, cortical development, cortical maturation, fetal brain, fissures, gyration, neurodevelopment, neurosonography, operculization, ultrasound}, + pages = {614--623}, +} + +@article{Stirnemann2020IntergrowthWeight, + title = {{INTERGROWTH}‐21st standards for {Hadlock}’s estimation of fetal weight}, + volume = {56}, + ISSN = {1469-0705}, + url = {http://dx.doi.org/10.1002/uog.22000}, + DOI = {10.1002/uog.22000}, + number = {6}, + journal = {Ultrasound in Obstetrics & Gynecology}, + publisher = {Wiley}, + author = {Stirnemann, J. and Salomon, L. J. and Papageorghiou, A. T.}, + year = {2020}, + month = dec, + pages = {946–948} +} + +@article{Villar2014InternationalProject, + title = {{International standards for newborn weight, length, and head circumference by gestational age and sex: The Newborn Cross-Sectional Study of the INTERGROWTH-21st Project}}, + year = {2014}, + journal = {The Lancet}, + author = {Villar, José and Ismail, Leila Cheikh and Victora, Cesar G. and Ohuma, Eric O. and Bertino, Enrico and Altman, Doug G. and Lambert, Ann and Papageorghiou, Aris T. and Carvalho, Maria and Jaffer, Yasmin A. and Gravett, Michael G. and Purwar, Manorama and Frederick, Ihunnaya O. and Noble, Alison J. and Pang, Ruyan and Barros, Fernando C. and Chumlea, Cameron and Bhutta, Zulfiqar A. and Kennedy, Stephen H. and Katz, M. and Bhan, M. K. and Garza, C. and Zaidi, S. and Langer, A. and Rothwell, P. M. and Weatherall, D. and Burton, F. and Er, Y. A.Jaff and Lumbiganon, P. and Rivera, J. and Shorten, M. and Hoch, L. and Knight, H. E. and Cosgrove, C. and Blakey, I. and Roseman, F. and Kunnawar, N. and Gu, S. H. and Wang, J. H. and Wu, M. H. and Domingues, M. and Gilli, P. and Juodvirsiene, L. and Musee, N. and Al-Jabri, H. and Waller, S. and Muninzwa, D. and Yellappan, D. and Carter, A. and Reade, D. and Miller, R. and Salomon, L. and Leston, A. and Mitidieri, A. and Al-Aamri, F. and Paulsene, W. and Sande, J. and Al-Zadjali, W. K.S. and Batiuk, C. and Bornemeier, S. and Dighe, M. and Gaglioti, P. and Jacinta, N. and Jaiswal, S. and Oas, K. and Oberto, M. and Olearo, E. and Owende, M. G. and Shah, J. and Sohoni, S. and Todros, T. and Venkataraman, M. and Vinayak, S. and Wang, L. and Wilson, D. and Wu, Q. Q. and Zhang, Y. and Chamberlain, P. and Danelon, D. and Sarris, I. and Dhami, J. and Ioannou, C. and Knight, C. L. and Napolitano, R. and Wanyonyi, S. and Pace, C. and Mkrtychyan, V. and Al-Habsi, F. and Alija, M. and Jimenez-Bustos, J. M. and Kizidio, J. and Puglia, F. and Liu, H. and Lloyd, S. and Mota, D. and Ochieng, R. and Rossi, C. and Luna, M. Sanchez and Shen, Y. J. and Rocco, D. A. and Albernaz, E. and Batra, M. and Bhat, B. A. and Di Nicola, P. and Giuliani, F. and Rovelli, I. and McCormick, K. and Paul, V. and Rajan, V. and Wilkinson, A. and Varalda, A. and Eskenazi, B. and Corra, L. A. and Dolk, H. and Golding, J. and Matijasevich, A. and De Wet, T. and Zhang, J. J. and Bradman, A. and Finkton, D. and Burnham, O. and Farhi, F. and Fonseca, S. and Sclowitz, I. K. and Da Silveira, M. and He, Y. P. and Pan, Y. and Yuan, Y. and Choudhary, A. and Choudhary, S. and Deshmukh, S. and Dongaonkar, D. and Ketkar, M. and Khedikar, V. and Mahorkar, C. and Mulik, I. and Saboo, K. and Shembekar, C. and Singh, A. and Taori, V. and Tayade, K. and Somani, A. and Frigerio, M. and Gilli, G. and Giolito, M. and Occhi, L. and Signorile, F. and Stones, T. and Todros, W. and Kisiang'ani, C. and Al-Abri, J. and Al-Abduwani, J. and Al-Lawatiya, H. and Al-Rashidiya, B. and Juangco, F. R. and Andersen, H. F. and Abbott, S. E. and Algren, H. and Sorensen, T. K. and Enquobahrie, D.}, + number = {9946}, + month = {9}, + pages = {857--868}, + volume = {384}, + publisher = {Elsevier B.V.}, + doi = {10.1016/s0140-6736(14)60932-6}, + issn = {1474547X}, + pmid = {25209487} +} + +@article{Villar2015PostnatalProject, + title = {{Postnatal growth standards for preterm infants: The Preterm Postnatal Follow-up Study of the INTERGROWTH-21st Project}}, + year = {2015}, + journal = {The Lancet Global Health}, + author = {Villar, José and Giuliani, F. and Bhutta, Z. A. and Bertino, E. and Ohuma, E. O. and Ismail, Leila Cheikh and Barros, F. C. and Altman, D. G. and Victora, C. and Noble, J. A. and Gravett, M. G. and Purwar, M. and Pang, Ruyan and Lambert, A. and Papageorghiou, A. T. and Ochieng, R. and Jaffer, Y. A. and Kennedy, Stephen H. and Katz, M. and Bhan, M. K. and Garza, C. and Zaidi, S. and Langer, A. and Rothwell, P. M. and Weatherall, Sir D. and Kennedy, S. and Burton, F. and Carvalho, M. and Chumlea, W. C. and Lumbiganon, P. and Pang, R. 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Parker + orcid: 0000-0003-0872-7098 + affiliation: '1' + - name: Linda Vesel + orcid: 0000-0003-3753-4172 + affiliation: '2' + - name: Eric O. Ohuma + orcid: 0000-0002-3116-2593 + affiliation: '1' +affiliations: + - index: 1 + name: Maternal, Adolescent, Reproductive and Child Health Centre, London School of Hygiene & Tropical Medicine, London, UK + 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. + ror: 03vek6s52 + +date: 14 December 2024 +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. + +# Statement of need + +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 all of the growth +standards implemented within: + +- 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] +- WHO Child Growth Standards[@WHOMulticentreGrowthReferenceStudyGroup2006WHOAge; + @WHO2006WHODevelopment; @WHO2007WHODevelopment] + +This is more growth standards than made available in other R packages designed +to perform the same sorts of analyses. The following table displays +functionality of other R packages designed to implement the above growth +standards: + +| Software | Platform | WHO (0-5 years) | IG-21^st^ NBS | IG-21^st^ PNG | IG-21^st^ Fetal | Functionality | +|----|----|----|----|----|----|----| +| [gigs](https://www.github.com/ropensci/gigs/) | R | ✅ | ✅ | ✅ | ✅ | Values ↔ z-scores/centiles | +| [anthro](https://cran.r-project.org/web/packages/anthro/index.html) | R | ✅ | ❌ | ❌ | ❌ | Values → z-scores | +| [AGD](https://cran.r-project.org/web/packages/AGD/index.html) | R | ✅ | ❌ | ❌ | ❌ | Values ↔ z-scores | +| [childsds](https://cran.r-project.org/web/packages/childsds/index.html) | R | ✅ | ❌ | ❌ | ❌ | Values → z-scores/centiles | +| [ki-tools/growthstandards](https://www.github.com/ki-tools/growthstandards/) | R | ✅ | ✅ | ⚠️ | ⚠️ | Values ↔ z-scores/centiles | +| [nutriverse/intergrowth](https://github.com/nutriverse/intergrowth/) | R | ❌ | ❌ | ❌ | ⚠️ | Values → z-scores/centiles | +| [sitar](https://cran.r-project.org/web/packages/sitar/index.html) | R | ✅ | ❌ | ❌ | ❌ | Values ↔ z-scores/centiles | +| [zscorer](https://cran.r-project.org/web/packages/zscorer/index.html) | R | ✅ | ❌ | ❌ | ❌ | Values → z-scores/centiles | +| [gigs](https://www.github.com/ropensci/gigs-stata/) (Stata) | Stata | ✅ | ✅ | ✅ | ✅ | Values ↔ z-scores/centiles | +| [zanthro](https://journals.sagepub.com/doi/epdf/10.1177/1536867X1301300211) (Stata) | Stata | ✅ | ❌ | ❌ | ❌ | Values → z-scores/centiles | +| [gigs](https://github.com/SASPAC/gigs/) (SAS) | SAS | ✅ | ✅ | ✅ | ✅ | Values ↔ z-scores/centiles | + +The R [package website](https://docs.ropensci.org/gigs/) also includes +benchmarks of these packages relative to each other. For speed, ``gigs`` (for R) +outperforms almost all existing packages, or is at most a few milliseconds +slower. It does this whilst checking inputs to ensure they are formatted +correctly, to make life easier for ``gigs`` users. ``gigs`` is already in use by +researchers at LSHTM, Harvard, and an international collaboration studying +**... requires elaboration**. Thanks to its speed, input checking, and thorough +test suite, we believe it will come to be used widely by those looking to assess +newborn, infant, or child growth in R. + +# Acknowledgements + +The development of this package was supported by the Bill & Melinda Gates +Foundation under grant number 046290. We also want to thank our rOpenSci +reviewers and handling editor - Victor Ordu, Chitra Saraswati, and Rebecca +Killick - whose feedback and guidance through the rOpenSci software review +process has been extremely useful. + +# References \ No newline at end of file