Novel Work Creating a Stata Command (Chapter 9)

I developed the idea to create a Stata command to facilitate the use of permuta-tion tests for SWTs. Katherine Fielding, James Hargreaves, Richard Hayes

Bibliography

and Calum Davey contributed ideas for functionality for the command. I then coded the command and conducted the majority of testing. The command was also tested by Calum Davey, James Hargreaves, and Katherine Fielding. I wrote the first draft of the manuscript and all co-authors provided comments on the text.

Bibliography

[1] Altman DG and Simera I. A history of the evolution of guidelines for reporting medical research: the long road to the EQUATOR Network.

Journal of the Royal Society of Medicine 2016. 109. (2):67–77.

[2] Kirkwood B and Sterne J. Essential Medical Statistics. Wiley, 2010.

[3] Falagas ME, Grigori T and Ioannidou E. A systematic review of trends in the methodological quality of randomized controlled trials in vari-ous research fields. Journal of Clinical Epidemiology 2009. 62. (3):227–

231.e229.

[4] Plint AC, Moher D, Morrison A, Schulz K, Altman DG, Hill C and Gaboury I. Does the CONSORT checklist improve the quality of reports of randomised controlled trials? A systematic review. Medical Journal of Australia 2006. 185. (5):263–267.

[5] Schultz TJ, Kitson AL, Soenen S, Long L, Shanks A, Wiechula R, Chap-man I and Lange K. Does a multidisciplinary nutritional intervention prevent nutritional decline in hospital patients? A stepped wedge ran-domised cluster trial. e-SPEN Journal 2014. 9. (2):e84–e90.

[6] Hayes RJ and Moulton LH. Cluster Randomised Trials. 1st ed. USA:

Chapman and Hall/CRC, 2009.

[7] Pagel C, Prost A, Lewycka S, Das S, Colbourn T, Mahapatra R, Azad K, Costello A and Osrin D. Intracluster correlation coefficients and coef-ficients of variation for perinatal outcomes from five cluster-randomised controlled trials in low and middle-income countries: results and meth-odological implications. Trials 2011. 12:151.

[8] Adams G, Gulliford MC, Ukoumunne OC, Eldridge S, Chinn S and Campbell MJ. Patterns of intra-cluster correlation from primary care research to inform study design and analysis. Journal of Clinical Epi-demiology 2004. 57. (8):785–794.

Bibliography

[9] Girling AJ and Hemming K. Statistical efficiency and optimal design for stepped cluster studies under linear mixed effects models. Statistics in Medicine 2016. 35. (13):2149–2166.

[10] Rhoda DA, Murray DM, Andridge RR, Pennell ML and Hade EM. Stud-ies with staggered starts: multiple baseline designs and group-randomized trials. American Journal of Public Health 2011. 101. (11):2164–2169.

[11] Zhan Z, Bock GH de and Heuvel ER van den. Statistical methods for uni-directional switch designs: Past, present, and future. Statistical Methods Medical Research 2017:962280216689280.

[12] Martin J, Taljaard M, Girling A and Hemming K. Systematic review finds major deficiencies in sample size methodology and reporting for stepped-wedge cluster randomised trials. BMJ Open 2016. 6. (2):e010166.

[13] Grayling MJ, Wason JM and Mander AP. Stepped wedge cluster ran-domized controlled trial designs: a review of reporting quality and design features. Trials 2017. 18. (1):33.

[14] Beard E, Lewis JJ, Copas A, Davey C, Osrin D, Baio G, Thompson JA, Fielding KL, Omar RZ, Ononge S, Hargreaves J and Prost A. Stepped wedge randomised controlled trials: systematic review of studies pub-lished between 2010 and 2014. Trials 2015. 16. (1):353.

[15] Brown CA and Lilford RJ. The stepped wedge trial design: a systematic review. BMC Medical Research Methodology 2006. 6. (1):54.

[16] Woertman W, Hoop E de, Moerbeek M, Zuidema SU, Gerritsen DL and Teerenstra S. Stepped wedge designs could reduce the required sample size in cluster randomized trials. Journal of Clinical Epidemiology 2013.

66. (7):752–758.

[17] Davey C, Hargreaves J, Thompson JA, Copas AJ, Beard E, Lewis JJ and Fielding KL. Analysis and reporting of stepped wedge randomised controlled trials: synthesis and critical appraisal of published studies, 2010 to 2014. Trials 2015. 16. (1):358.

[18] Copas AJ, Lewis JJ, Thompson JA, Davey C, Baio G and Hargreaves JR.

Designing a stepped wedge trial: three main designs, carry-over effects and randomisation approaches. Trials 2015. 16. (1):352.

[19] Hemming K, Haines T, Chilton P, Girling A and Lilford R. The stepped wedge cluster randomised trial: rationale, design, analysis, and reporting.

BMJ 2015. 350:h391.

Bibliography

[20] Hemming K and Girling A. A menu-driven facility for power and detectable-difference calculations in stepped-wedge cluster-randomized trials. Stata Journal 2014. 14. (2):363–380.

[21] Hooper R and Bourke L. Cluster randomised trials with repeated cross sections: alternatives to parallel group designs. BMJ 2015. 350:h2925.

[22] Twisk JW, Hoogendijk EO, Zwijsen SA and Boer MR de. Different meth-ods to analyze stepped wedge trial designs revealed different aspects of intervention effects. Journal of Clinical Epidemiology 2016. 72:75–83.

[23] Eldridge SM, Ashby D, Feder GS, Rudnicka AR and Ukoumunne OC.

Lessons for cluster randomized trials in the twenty-first century: a sys-tematic review of trials in primary care. Clinical Trials 2004. 1. (1):80–

90.

[24] Simpson JM, Klar N and Donnor A. Accounting for cluster randomiza-tion: a review of primary prevention trials, 1990 through 1993. American Journal of Public Health 1995. 85. (10):1378–1383.

[25] Donner A, Brown KS and Brasher P. A methodological review of non-therapeutic intervention trials employing cluster randomization, 1979-1989. International Journal of Epidemiology 1990. 19. (4):795–800.

[26] Ivers NM, Taljaard M, Dixon S, Bennett C, McRae A, Taleban J, Skea Z, Brehaut JC, Boruch RF, Eccles MP, Grimshaw JM, Weijer C, Zwar-enstein M and Donner A. Impact of CONSORT extension for cluster randomised trials on quality of reporting and study methodology: re-view of random sample of 300 trials, 2000-8. BMJ 2011. 343:d5886.

[27] Campbell MK, Piaggio G, Elbourne DR, Altman DG and Group C.

Consort 2010 statement: extension to cluster randomised trials. BMJ 2012. 345:e5661.

[28] Bland JM. Cluster randomised trials in the medical literature: two bib-liometric surveys. BMC Medical Research Methodology 2004. 4. (1):21.

[29] Arnup SJ, Forbes AB, Kahan BC, Morgan KE and McKenzie JE. Appro-priate statistical methods were infrequently used in cluster-randomized crossover trials. Journal of Clinical Epidemiology 2016. 74:40–50.

[30] Johnson S, Whitelaw A, Glazebrook C, Israel C, Turner R, White IR, Croudace T, Davenport F and Marlow N. Randomized trial of a parent-ing intervention for very preterm infants: outcome at 2 years. Journal of Pediatrics 2009. 155. (4):488–494.

Bibliography

[31] Prost A, Binik A, Abubakar I, Roy A, De Allegri M, Mouchoux C, Dre-ischulte T, Ayles H, Lewis JJ and Osrin D. Logistic, ethical, and political dimensions of stepped wedge trials: critical review and case studies. Tri-als 2015. 16. (1):351.

[32] Kotz D, Spigt M, Arts IC, Crutzen R and Viechtbauer W. Use of the stepped wedge design cannot be recommended: a critical appraisal and comparison with the classic cluster randomized controlled trial design.

Journal of Clinical Epidemiology 2012. 65. (12):1249–1252.

[33] Doussau A and Grady C. Deciphering assumptions about stepped wedge designs: the case of Ebola vaccine research. Journal of Medical Ethics 2016.

[34] Zhan Z, Heuvel ER van den, Doornbos PM, Burger H, Verberne CJ, Wiggers T and Bock GH de. Strengths and weaknesses of a stepped wedge cluster randomized design: its application in a colorectal cancer follow-up study. Journal of Clinical Epidemiology 2014. 67. (4):454–461.

[35] Mdege ND, Man MS, Taylor Nee Brown CA and Torgerson DJ. System-atic review of stepped wedge cluster randomized trials shows that design is particularly used to evaluate interventions during routine implement-ation. Journal of Clinical Epidemiology 2011. 64. (9):936–948.

[36] Hargreaves JR, Prost A, Fielding KL and Copas AJ. How important is randomisation in a stepped wedge trial? Trials 2015. 16. (1):359.

[37] Hemming K and Girling A. The efficiency of stepped wedge vs. cluster randomized trials: stepped wedge studies do not always require a smaller sample size. Journal of Clinical Epidemiology 2013. 66. (12):1427–1428.

[38] Hemming K, Girling A, Martin J and Bond SJ. Stepped wedge cluster randomized trials are efficient and provide a method of evaluation without which some interventions would not be evaluated. Journal of Clinical Epidemiology 2013. 66. (9):1058–1059.

[39] Hussey MA and Hughes JP. Design and analysis of stepped wedge cluster randomized trials. Contemporary Clinical Trials 2007. 28. (2):182–191.

[40] Ji X, Fink G, Robyn PJ and Small SS. Randomization inference for stepped-wedge cluster-randomised trials: An application to community-based health insurance. Annals of Applied Statistics 2017. 11. (1):1–20.

Bibliography

[41] Scott JM, deCamp A, Juraska M, Fay MP and Gilbert PB. Finite-sample corrected generalized estimating equation of population average treatment effects in stepped wedge cluster randomized trials. Statistical Methods in Medical Research 2017. 26. (2):583–597.

[42] Moulton LH, Golub JE, Durovni B, Cavalcante SC, Pacheco AG, Sara-ceni V, King B and Chaisson RE. Statistical design of THRio: a phased implementation clinic-randomized study of a tuberculosis preventive ther-apy intervention. Clinical Trials 2007. 4. (2):190–199.

[43] Matthews JNS and Forbes AB. Stepped wedge designs: insights from a design of experiments perspective. Statistics in Medicine 2017:1–18.

[44] Barker D, McElduff P, D’Este C and Campbell MJ. Stepped wedge cluster randomised trials: a review of the statistical methodology used and available. BMC Medical Research Methodology 2016. 16. (1):69.

[45] Davey C, Aiken AM, Hayes RJ and Hargreaves JR. Re-analysis of health and educational impacts of a school-based deworming programme in western Kenya: a statistical replication of a cluster quasi-randomized stepped-wedge trial. International Journal of Epidemiology 2015. 44.

(5):1581–1592.

2 Stepped-Wedge Trial Case