Animations of uncertainty in density maps

uncertainty-anim.R

# little animation to illustrate uncertainty in a density map

library(dsm)
library(mvtnorm)
library(ggplot2)
library(animation)
library(viridis)

# load the models and prediction data
# using data from the Duke spatial distance sampling course
# http://distancesampling.org/workshops/duke-spatial-2015/practicals.html

# models of sperm whales off the east coast of the US
load("sperm-data/count-models.RData")
load("sperm-data/predgrid.RData")


# ignoring detection function uncertainty for now...

# get the Lp matrix
Lp <- predict(dsm.nb.xy, newdata=predgrid, type="lpmatrix")

# how many realisations do we want?
frames <- 100

# generate the betas from the GAM "posterior"
betas <- rmvnorm(frames, coef(dsm.nb.xy), vcov(dsm.nb.xy))


# use a function to get animation to play nice...
anim_map <- function(){
  # loop to make plots
  for(frame in 1:frames){

    # make the prediction
    predgrid$preds <- predgrid$off.set * exp(Lp%*%betas[frame,])

    # plot it (using viridis)
    p <- ggplot(predgrid) +
          geom_tile(aes(x=x,y=y,fill=preds), width=sqrt(1e8), height=sqrt(1e8)) +
          scale_fill_viridis(limits=c(0,10))

    print(p)
  }
}

# make the animation!
ani.options(interval = 0.15)
saveGIF(anim_map(), outdir = "new")

Here is an example of an animation: