Courtney D. Shelley
Aspiring Epidemiologist
vs-app interactively builds maps to visualize outbreak patterns of current and historical Equine Vesicular stomatitis virus (VSV) outbreaks. The USDA Animal and Plant Health Inspection Services monitors and reports on VSV outbreaks. All data is publicly available at USDA APHIS.
Play with vs-app @ https://blackwidoww.shinyapps.io/vs-app/
See the apps codes and data @ https://github.com/BlackWidoww/vs-app
Watch this Slidify all over again @ http://rpubs.com/BlackWidoww/29751
vs-app will allow you to see outbreaks in "real time" for both the current 2014 outbreak and past outbreak occurences.
data(county.fips, package = "maps")
df = data.frame(region=county.fips$fips, value = NA) # Default all counties to NA cases
map <- read.csv(paste("data/vs_map_", input$year, ".csv", sep=""), header=TRUE)
#Dynamically calls year
MAP <- vsMap(map) #Internal function: cleans dates, FIPS codes for mapping
day = max(na.omit(MAP$DURATION[MAP$DURATION <= input$days])) #Set map output day
update.DF(MAP, day) #Internal function: update FIPS codes with
#case count and render map
Maps are built on the choroplethr platform. Coloration is used to simulate a spreading wildfire of infection.
For inputs of Year = 2012 and Day = 238:
Within the app you can further explore:
Current outbreak and additional historical outbreaks from 2004-2012
Additional narratives, background information, and epidemiological models
Individual infection levels for each outbreak to explore infection and recovery rates
Thanks for stopping by! @_BlackWidoww
