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University of Florida Thesis Or Dissertation Formatting THE USE OF BAYESIAN STATISTICS FOR FINE-SCALE MAPPING OF MALARIA RISK IN GHANA By PUNAM AMRATIA A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2018 © 2018 Punam Amratia To women in science ACKNOWLEDGMENTS I would like to thank and express my deepest gratitude to my supervisory committee, without whom this dissertation would not have been completed. I am especially grateful to the guidance of Dr. Denis Valle. I appreciate you giving me the chance to embark on the ambitious task of a PhD program at University of Florida. Without your patience in teaching me Bayesian Statistics this PhD would not exist, nor would it have given me a foundational platform to develop expertise in the field of infectious disease modelling. Your patience and challenges have made me into a stronger scientist and ready to face the world of malaria epidemiology. This work would also not have been possible were it not for Dr. Paul Psychas and his generosity to share the rich malaria dataset from his work in Ghana. Dr Psychas, I appreciate your valiant effort and patience with me as we worked through countless revisions of my writing. I am forever grateful for the insightful advice both academically and personally and look forward to continuing collaborations in the future. Thank you for welcoming this lost international student into your home during the many Thanksgivings and Christmas events in Gainesville. I will forever cherish our long chats about the politics, landscapes, people and cultures of our beloved Africa. Dr. Derek Cummings, I’m very grateful to have had the privilege of working with a world-class scientist like yourself. I appreciate immensely the insightful comments you have provided me about my work and welcoming me wholeheartedly into your lab. It has given me the opportunity to meet many bright rising stars in infectious disease epidemiology. To Dr. Greg Glass, I cannot thank you enough for always thinking of me when an opportunity for spatial modelling arose. It always made me feel like you believe in my skillset and I very much hope that we will get to work together in the future. I shall fondly miss your cheery hellos at EPI. 4 Dr Amr. Abd-Elrahman, it is my deepest regret that I never had the chance to physically meet you – yet I feel like I’ve known you for years. I came into this program with barely any knowledge about GIS and I am leaving this campus with an expertise in geospatial analysis and GIS because of you. Thank you for providing useful tips in remote sensing and being available for me when I needed advice. I would like to acknowledge my colleagues at the Emerging Pathogens Institute whom made my work environmental warm and friendly. I would also like to convey a big thank you to the School of Forest Resources Academic Coordinator – Amy Abernethy, for being the strong pillar keeping my PhD moving and supporting me during my time at UF. The Univerity of Florida Informatics Institute for funding me and providing me limitless opportunities in Gainesville. To my partner at R-ladies Gainesville, Dr. Geraldine Klarenberg, for encouraging me to be pro-active about creating a safe and supportive environment for women in data science. Most importantly, I would like to thank Dr. Benjamin Abuaku, Professor Kwado Koram, Dr. Collins Ahorlu, Sammuel Oppong and the Ghana National Malaria Control program for their valiant efforts and open collaboration for this work. We are also grateful to the experienced field staff who helped with data collection for the different cross-sectional surveys and lastly, we want to thank Supervisors from the National Malaria Control Programme, Noguchi Memorial Institute for Medical Research for ensuring quality data collection and allowing our participation in follow-on studies to their hard work. I also wish to thank my incredible Gainesville Family. This doctoral program has been fulfiling but also filled with stress and anxiety, but I have been blessed by having 5 incredibly supportive, motivating and inspirational friends. Dr Karoun Bagamian, you are my role model! I aspire to be as calm, patient, poised and efficient as you in my career. You have been there with me during the good times and the bad and I hope to work with you on many many more projects in the future. My other wonderful friends; Victoria McCloud, Daniel Barreto, Dr. Caroline Staub, Lindsey Laytner, William Kessler, Ana Carolina, Christine Swanson, Justin Millar, Jacey Hyde and Ben Toh Kok; thank you for being so supportive and filling my life with so much joy and happiness. I also would like to thank my Florida family – Sonal and Sunil Patel – for being my surrogate parents during this stressful time and providing me a home away from home when I needed it. Finally, to my parents (Parul and Dinesh Patel), brother (Dev Amratia) and sister-in-law (Saijal Naik) for being tremendously supportive of my life choices and always believing in me. My life has been filled with incredible opportunities because of you and this piece of work is as much yours as it is mine. 6 TABLE OF CONTENTS page ACKNOWLEDGMENTS .................................................................................................. 4 LIST OF TABLES .......................................................................................................... 10 LIST OF FIGURES ........................................................................................................ 11 LIST OF ABBREVIATIONS ........................................................................................... 12 ABSTRACT ................................................................................................................... 13 CHAPTER 1 INTRODUCTION .................................................................................................... 15 Global Malaria Distribution ...................................................................................... 15 Malaria in Ghana .................................................................................................... 16 Spatial Modelling and Disease Mapping ................................................................. 18 Aims ........................................................................................................................ 20 2 CHARACTERIZING LOCAL-SCALE HETEROGENEITY OF MALARIA RISK: A CASE STUDY IN BUNKPURUGU-YUNYOO DISTRICT IN NORTHERN GHANA ................................................................................................................... 23 Background ............................................................................................................. 23 Materials and Methods............................................................................................ 25 Study Area ........................................................................................................ 25 Malaria Survey Data ......................................................................................... 26 Variables Explored to Model Malaria Risk ........................................................ 27 Remote sensed variables .......................................................................... 27 GIS derived variables ................................................................................. 29 Adjusting the model for child age ............................................................... 30 Selecting a Suitable Set of Variable for Prediction ........................................... 30 Bayesian Geostatistical Model ......................................................................... 31 Model Validation ............................................................................................... 32 Extrapolation to Neighbouring Districts ............................................................ 32 Ethics Approval and Consent to Participate: .................................................... 33 Results .................................................................................................................... 33 Malaria Prevalence ........................................................................................... 33 Variable Selection ............................................................................................ 33 Geospatial Model Results................................................................................. 34 Model Validation ............................................................................................... 35 Extrapolation to Neighbouring District .............................................................. 35 Discussion .............................................................................................................. 36 7 3 IMPACT OF SAMPLE SIZE, SAMPLE DESIGN, AND GPS DISPLACEMENT ON LOCAL RISK MAPS OF MALARIA. .................................................................. 48 Background ............................................................................................................. 48 Methods .................................................................................................................. 50 Site Description ................................................................................................ 50 Malaria Survey Data ......................................................................................... 51 Spatial Covariates for Modelling ......................................................................
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