Foot and Mouth disease animation • sparr

Below is example output of spatio-temporal smoothing the foot and mouth disease outbreak in Cumbria, UK from days 10 through 231.

Code

The following code generates the above animation.

library(sparr)
library(animation)

data(fmd)
fmd_case <- fmd$cases
fmd_cont <- fmd$controls

hlam <- LIK.spattemp(fmd_case)

f.breve <- spattemp.density(fmd_case, h=hlam[1], lambda=hlam[2], tlim=c(10,230))
g.tilde <- bivariate.density(fmd_cont, h0=hlam[1])
rho.breve <- spattemp.risk(f=f.breve,g=g.tilde, tolerate=TRUE)

colpal <- spatstat.options("image.colfun")
fmdcolours <- colourmap(colpal(128),breaks=c(-80,seq(-7,4,length=128)))
mytimes <- 10:230
animation::saveVideo(
  for(i in 1:length(mytimes)){
    plot(rho.breve,tselect=mytimes[i],type="conditional",col=fmdcolours,
         tol.args=list(levels=c(0.05,0.0001),lty=2:1,drawlabels=FALSE),
         sleep=0,override.par=FALSE)
    title(xlab="Easting",ylab="Northing")
  },
  video.name="fmd.mp4", other.opts = '-b:v 1M -pix_fmt yuv420p', ani.width=640, ani.height=640, interval=1/12)