Disease Spread Simulator Cameron Stevens, Joey Merline, Anthony Castellone, Justin Hess CS 4624: Multimedia, Hypertext, and Information Access Professor Fox, Virginia Tech, Blacksburg VA 24061 Presented on 4/22/2021 Outline Background Overview Implementation Statistics/Backend UI Timeline Acknowledgements Questions Background Chronic Wasting Disease (CWD) Caused by infected proteins called prions Affects Cervidae family (Deer, Elk, Moose, Reindeer) Causes severe weight loss, neurological symptoms and death Spread Can pass between saliva, feces, urine and through water or soil. Affected deer can spread the prion for over a year before developing symptoms CWD has spread to over 25 states in the US deer with chronic wasting disease CWD by county across the US Background Chronic Wasting Disease in Virginia Disease first identified in US in the wild in 1981 (Colorado) CWD first seen in the eastern US in 2005 (West Virginia) The disease spread into Virginia by 2009 CWD now detected in 9 VA counties Impact of CWD Largest impact is Deer population health Infected Deer cannot be consumed Increased handling procedures to slow spread Studies have shown limited spread to other species Overview/Project Goals Predict & map CWD prevalence Predictions based on: Vegetation Age Population Density UI designed in R-Shiny Get user input Display output visuals Display prevalence values Statistical analysis done in R early wireframe of UI Data Samples from Virginia Department of Wildlife Resources roadkill hunters deer suspected of having CWD across several years and counties included sex, age, coordinates, CWD positivity Enhanced Vegetation Index data measure coverage of plants coefficients corresponding to coordinates medium to high vegetation index Statistics Observations follow a Bernoulli Distribution unobserved disease state sensitivity (P(detection | infected)) specificity (P(not detected | not infected)) unobserved disease state predicted by demographic variables general shape of Bernoulli distribution Data Processing Model set up in RStan R interface for Stan built in probability mass functions Organize data by county Separate by year model for each demographic variable lowest widely applicable information criterion (WAIC) based on mean/variance of likelihoods posterior distribution for best fit User Interface Toggle between views Tabs with various options to display data Sliders to edit values, alter outcomes User Interface - What if Scenarios Start from current data User adjusts sliders, change view at will Can handle significant changes User Interface - Continued Other forms of data visualization Current Data: Raw totals, ratio heatmap, graph coordinates Toggle view Charts: Graphs of infection rates Ratio of healthy to unhealthy deer Timeline April Wrapping things up R Shiny Polish off R Script May Future Bug fixes & Testing Refining features February Completed Groundwork Several meetings with client Basic R script, wireframes March More Progress R script near completion Statistical models Acknowledgements Professor Luis Escobar Assistant Professor, Department of Fish and Wildlife Conservation Mariana Castaneda-Guzman M.Sc. Student, Department of Fish and Wildlife Conservation Michael Tabak co-author of a similar study References B. Chesnutt, “Bernoulli Distribution: Definition, Equations & Examples,” Study.com. [Online]. Available: https://study.com/academy/lesson/bernoulli-distribution-definition-equations-examples.html. [Accessed: 03-May-2021]. “Photo Examples of CWD,” CWD-INFO. [Online]. Available: http://cwd-info.org/photo-examples-of-cwd/. [Accessed: 03-May-2021]. “Hunters asked to help battle chronic wasting disease,” Cache Valley Daily, 21-Sep-2019. [Online]. Available: https://www.cachevalleydaily.com/news/archive/2019/09/21/hunters-asked-to-help-battle-chronic-wasting-disease/#.YCSQMuhKiUk. [Accessed: 03-May-2021]. “Chronic Wasting Disease Occurrence,” Centers for Disease Control and Prevention, 24-Feb-2021. [Online]. Available: https://www.cdc.gov/prions/cwd/occurrence.html. [Accessed: 03-May-2021].