Courtney D. Shelley
Aspiring Epidemiologist
equuSIR 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 equuSIR @ 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
equuSIR will allow you to see outbreaks in "real time" for both the current 2014 outbreak and past outbreak occurences. For the 2012 Outbreak,
data_2012[7:11, ] # display sample tidy data
## DURATION REPORT DATE STATE COUNTY FIPS.CODE ACTV CUMLTV QRNTN
## 7 238 4 2012-12-24 NM LINCOLN 27 0 1 1
## 8 238 4 2012-12-24 NM MORA 33 0 2 2
## 9 238 4 2012-12-24 NM RIO ARRIBA 39 0 5 5
## 10 238 4 2012-12-24 NM OTERO 35 0 1 1
## 11 238 4 2012-12-24 NM SANDOVAL 43 0 4 4
MAP_2012_238 <- choroplethr(df, lod="county", num_buckets=9, warn_na=FALSE, renderAsInsets=TRUE) +
scale_fill_brewer(palette="YlOrRd", na.value="white") +
ggtitle(expression(atop("2012 Outbreak",
atop(italic("Day 238")))))
## Scale for 'fill' is already present. Adding another scale for 'fill', which will replace the existing scale.
Maps are built on the choroplethr platform. Coloration is used to simulate a spreading wildfire of infection.
MAP_2012_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
