SIMULATING DIFFUSION OF CHOLERA IN GHANA JULIANA USEYA February, 2011 SUPERVISORS: Mrs. Ir. Ellen-Wien P. W. M. Augustijn-Beckers Dr. Raul R. Zurita-Milla SIMULATING DIFFUSION OF CHOLERA IN GHANA JULIANA USEYA Enschede, The Netherlands, February, 2011 Thesis submitted to the Faculty of Geo-information Science and Earth Observation of the University of Twente in partial fulfilment of the requirements for the degree of Master of Science in Geo-information Science and Earth Observation. Specialization: Geoinformatics SUPERVISORS: Mrs. Ir. Ellen-Wien P. W. M. Augustijn-Beckers Dr. Raul R. Zurita-Milla THESIS ASSESSMENT BOARD: Dr. Ir. R. A. de By(chair) Dr. Ir. P. R. van Oel (External Examiner) Disclaimer This document describes work undertaken as part of a programme of study at the Faculty of Geo-information Science and Earth Observation of the University of Twente. All views and opinions expressed therein remain the sole responsibility of the author, and do not necessarily represent those of the Faculty. ABSTRACT Despite all the widely available cholera awareness information, people are still suffering and dying of cholera. People do not know how much contribution is made by the different mechanisms of cholera transmission during its propagation. The main objective of this research is to develop an Agent-Based Modelling (ABM) prototype that simulates the diffusion of cholera and evaluates the contributions from the different mechanisms during a cholera outbreak in Kumasi, Ghana. Four cholera transmission mechanisms, a hydrological model, a cholera disease model, daily activity model, housefly model and a synthetic population were integrated in an ABM simulation proto- type to simulate the propagation of cholera and was implemented in NetLogo. People with blood type ‘O’ have a higher risk of contracting cholera than others, and low hygiene standards, unsafe water supply and low income levels are factors which perpetuate the spread of cholera. Human- to-environment-human transmission mechanism plays a major role in the diffusion of cholera and human-to-human transmission has the least contribution. Keywords Cholera, Transmission mechanism, Agent-Based Modelling i TABLE OF CONTENTS Abstract i Acknowledgements vii 1 Introduction 1 1.1 Motivation and problem statement . 1 1.2 Research Identification . 2 1.2.1 General objective . 2 1.2.2 Specific objective . 2 1.2.3 Research questions . 2 1.2.4 Methodology . 3 1.2.5 Thesis structure . 4 2 Literature review 5 2.1 Cholera . 5 2.1.1 Cholera transmission . 6 2.1.2 Factors influencing the spread . 8 2.1.3 Cholera mortality . 10 2.1.4 Susceptibility . 10 2.1.5 Cholera in Ghana . 10 2.2 Kumasi Metropolitan, Ghana . 10 2.2.1 Study area . 10 2.2.2 Characteristics of Kumasi area . 11 2.2.3 Characteristics of communities . 13 2.2.4 Behavior of people in Kumasi . 13 2.2.5 Limitations of data acquisition on Kumasi . 13 2.3 Agent-based modelling . 14 2.3.1 Elements of an Agent-based simulation model . 14 2.3.2 Environment . 15 2.4 Conceptual design modelling for ABM . 20 2.4.1 How to build a flexible and extensible prototype simulation model . 23 2.5 Useful related work . 24 3 Conceptual Design Modelling 27 3.1 Overview . 27 3.1.1 Purpose . 27 3.1.2 State variables and scales . 27 3.2 Process overview and scheduling . 29 3.2.1 Activity diagram . 35 3.2.2 Sequence Diagram . 36 ii 4 Data preparation 39 4.1 Data Collection . 39 4.2 Data preparation . 41 4.3 Spatial Environment . 41 4.3.1 Preparation of shapefiles for spatial objects . 41 4.3.2 Preparation of elevation data . 42 4.3.3 Preparation of raster layer for hydrological model . 45 4.3.4 Preparation of Density Distribution Map for Houseflies . 46 4.4 Synthetic Population . 48 4.4.1 Generating a synthetic population for Aboabo community . 49 4.4.2 Creating a list of individuals with different age groups . 49 4.5 Spatial distribution of households . 52 4.6 Preparation of rainfall data . 53 5 Implementation of Cholera Simulation Prototype 55 5.1 NetLogo . 55 5.2 Design Concepts . 55 5.3 Loading of the spatial environment . 56 5.4 Loading objects . 58 5.5 Loading the synthetic population and creating individuals turtles’ breed . 58 5.6 Enabling turtles (population) with behaviour . 59 5.6.1 Fetching water . 60 5.6.2 Dumping waste . 61 5.6.3 Cooking . 61 5.6.4 Eating and drinking . 61 5.7 Disease Model . 61 5.8 Sub-models . 62 6 Verification, Results and Discussion 69 6.1 Verification . 69 6.1.1 Expectations of the prototype . 69 6.1.2 Determine the effect of varying the parameters and testing whether the sliders work . 74 6.2 Results and Discussion . 75 6.2.1 Determining number of simulation runs . 75 6.2.2 Determination of parameters . 78 6.2.3 Spatial distribution of infection cases . 85 6.2.4 Analysing cholera infections by hygiene level, blood type and income level 86 6.2.5 Reproductive rate (Ro) ........................... 88 7 Conclusion, limitations and recommendations 89 7.1 Conclusion . 89 7.2 Limitations . 90 7.3 Recommendations . 90 A APPENDIX 93 iii LIST OF TABLES 4.1 Census statistics . 50 4.2 Synthetic Population . 51 4.3 Households’ characteristics . 52 5.1 Daily ticks and activities . 61 6.1 Agents fetching water . 70 6.2 Agents dumping waste . 71 6.3 Children playing at dumpsites . 71 6.4 Effect of changing parameters . 74 6.5 Individual runs . 76 6.6 Average values for different number of runs . 77 6.7 Sensitivity of HEH . 79 6.8 Sensitivity of VT . 80 6.9 Sensitivity of HH . 82 6.10 Matrix . 82 iv LIST OF FIGURES 2.1 Cholera risk factors . 9 2.2 Kumasi, Ghana . 11 2.3 Seven elements of the ODD protocol grouped into 3 blocks . 22 3.1 Conceptual Framework . 28 3.2 Class Diagram . 29 3.3 Disease Model . 30 3.4 Environment to Human Transmission . 31 3.5 Human to Environment to Human Transmission . 32 3.6 Vector Transmission . 33 3.7 Human to Human Transmission . 34 3.8 Daily Activity Diagram . 35 3.9 Seqeunce diagram . 37 4.1 Google Image . 40 4.2 Flow chart for data preparation . 41 4.3 Aboabo suburb in Kumasi . 42 4.4 Attribute Table . 43 4.5 Elevation Raster . ..