seascape models

Visualising uncertainty in time-series using animations

I was reading an example of visualising election outcome uncertainty using a wobbly needle and wondered, could animating uncertainty help communicate for the kind of work I do on population modelling?

One challenge when plotting uncertainty intervals for population trends is that confidence intervals don’t capture the wandering nature of population processes. The figure here shows the median of a poisson random walk, with 90% quantiles.

In fact, each trend line will wander around, like the next image. So, the median and intervals give a false impression that an individual trend will experience relative stability.

A graph of the median and quantiles doesn't represent the uncertainty in any single trend line very well.

I decided to try and animate the uncertainty, using R.

The first step was to try and install the R package animate. Unfortunately I was in a world of Unix coding pain trying to get animation to work. In particular to get R to talk to the ImageMagick program. After cutting and pasting numerous commands from StackOverflow to my terminal I gave up. It seems I need to update my OS before I can get any further (from Mavericks).

In the end I found I could use ImageMagick directly from the command line. So now what we need is a folder full of .png files that we wish to turn into the animation. That Unix code to do that is at the end of this blog.

First we should set up a random walk process. I decided to go for a Poisson random walk, because it will have integer numbers, like a real population. I wrote a little function to achieve this:

walkmod <- function(t, yinit, thetasd, rho){
  y <- numeric(t)
  y[1] <- yinit
  theta <- rnorm(t, sd = thetasd)
  for(i in 2:t){
    lambda <- (y[i-1]*rho + yinit*(1-rho))* exp(theta[i])
    y[i] <- rpois(1, lambda)

The core equation is in the for loop. It just says the mean abundance at a given time is dependent on abundance at the last time-step with correlation rho plus some extra variation theta. We then sample the observed abundance from a poisson distribution.

Now let’s use our function. We will load in the purrr package to help plotting replicate runs of the random walk and the leaflet package because it has some nice functions for making colour scales.

t <- 50
yinit <- 10
thetasd <- 0.01
rho <- 0.9
n <- 30
y <- matrix(NA, nrow = t, ncol = n)
tmat <- matrix(rep(1:t), nrow = t, ncol = n)
for (i in 1:n){
    y[,i] <- walkmod(t, yinit, thetasd, rho)
ymax <- max(y)
medy <- apply(y, 1 , median)

We just looped over the walkmod function n times so we could generate n random walks.

Now let’s build a colour scale. I would like to colour the lines by the abundance quantile they end on. So we apply colorQuantile to all abundances in the last time-step to get a red to blue (RdBu) colour palette for the lines:

quants <- c(0, 0.25, 0.5, 0.75, 1)
yquant <- quantile(y[t,], probs = quants)
mycols <- colorQuantile("RdBu", domain = y[t,], probs = quants)

The trick to making a .gif animation is just to make a bunch of figures and save them as .png files in the order you want them to animate (or if you can get animate package to work within R you can export the .gif directly without having to save the .pngs).

So we just loop over walkmod plotting our lines each time. Note I use walk from the purrr package to redraw the background lines in grey each time.

thispath <- "/insert/your/path/here/"
for (i in 1:n){
    fname <- paste(thispath, i, ".png", sep = "")
    png(filename =fname, width = 480, height = 480)
    plot(0, 0, xlim = c(0, t), ylim = c(0, ymax),
         bty = 'n', type = "n", las = 1,
         ylab = "Abundance", xlab = "Time")
    lines(1:t, medy, col = "grey90", lwd = 2)
    walk(1:i, ~lines(tmat[,.x], y[,.x], lwd = 0.7, col = grey(0.5, 0.2)))
  lines(1:t, y[,i], lwd = 2, col = mycols(y[t, i]))
    legend("topleft", legend = quants,
        lwd = 2, col = mycols(yquant),
    title = "Quantile t=100", cex = 0.8)

If you want to check this from R, without saving the files, then turn of the png() function that saves the files and insert Sys.sleep(0.1) at the end of the loop, so it will print each figure in turn but pause for 1/10 th of second each time.

We have one final figure to plot, that is the median line. We can do this outside the for loop:

fname <- paste(thispath, i+1, ".png",  sep = "")
png(filename =fname, width = 480, height = 480)
plot(0, 0, xlim = c(0, t), ylim = c(0, ymax),
     bty = 'n', type = "n", las = 1,
     ylab = "Abundance", xlab = "Time", main = "Median")
walk(1:i, ~lines(tmat[,.x], y[,.x], lwd = 0.5, col = grey(0.5, 0.2)))
lines(1:t, medy, lwd = 3, col = "purple")

Finally, here is the unix code to run imageMagick from your terminal to turn your saved .png files into a gif.

cd "your/path/here"
magick *.png images.gif
convert images.gif -set delay 30 \( +clone -set delay 100 \) +swap +delete images_pause.gif

The first line creates the gif and the second line adds a pause of 30 1/100ths of a second after each image and a pause of 1 second at the end of the loop.

Contact: Chris Brown

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Designed by Chris Brown. Source on Github