## Introduction

We’re going to estimate distribution and abundance from a line transect survey of dolphins in the Gulf of Mexico. These data are also available in the R package dsm (where they go under the name mexdolphins). In inlabru the data are called mexdolphin.

## Setting things up

library(inlabru)
library(INLA)
library(ggplot2)

## Get the data

We’ll start by loading the data and extracting the mesh (for convenience).

data(mexdolphin, package = "inlabru")
mesh <- mexdolphin$mesh Plot the data (the initial code below is just to get rid of tick marks) noyticks <- theme( axis.text.y = element_blank(), axis.ticks = element_blank() ) noxticks <- theme( axis.text.x = element_blank(), axis.ticks = element_blank() ) ggplot() + gg(mexdolphin$ppoly) +
gg(mexdolphin$samplers, color = "grey") + gg(mexdolphin$points, size = 0.2, alpha = 1) +
noyticks +
noxticks +
theme(legend.key.width = unit(x = 0.2, "cm"), legend.key.height = unit(x = 0.3, "cm")) +
theme(legend.text = element_text(size = 6)) +
guides(fill = FALSE) +
coord_equal()

## Spatial model with a half-normal detection function

The samplers in this dataset are lines, not polygons, so we need to tell inlabru about the strip half-width, W, which in the case of these data is 8. We start by plotting the distances and histogram of frequencies in distance intervals:

W <- 8
ggplot(data.frame(mexdolphin$points)) + geom_histogram(aes(x = distance), breaks = seq(0, W, length = 9), boundary = 0, fill = NA, color = "black" ) + geom_point(aes(x = distance), y = 0, pch = "|", cex = 4) We need to define a half-normal detection probability function. This must take distance as its first arguent and the linear predictor of the sigma parameter (which we will call lsig) as its second:  hn <- function(distance, lsig) { exp(-0.5 * (distance / exp(lsig))^2) } Specify and fit an SPDE model to these data using a half-normal detection function form. We need to define a (Matern) covariance function for the SPDE matern <- inla.spde2.pcmatern(mexdolphin$mesh,
prior.sigma = c(2, 0.01),
prior.range = c(50, 0.01)
)

We need to now separately define the components of the model (the SPDE, the Intercept and the detection function parameter lsig)

cmp <- ~ mySPDE(main = coordinates, model = matern) +
lsig(1) + Intercept(1)

… and the formula, which describes how these components are combined to form the linear predictor (remembering that we need an offset due to the unknown direction of the detections!):

form <- coordinates + distance ~ mySPDE +
log(hn(distance, lsig)) +
Intercept + log(2)

Then fit the model, passing both the components and the formula (previously the formula was constructed invisibly by inlabru), and specify integration domains for the spatial and distance dimensions:

fit <- lgcp(
components = cmp,
mexdolphin$points, samplers = mexdolphin$samplers,
domain = list(
coordinates = mesh,
distance = INLA::inla.mesh.1d(seq(0, 8, length.out = 30))
),
formula = form
)

Look at the SPDE parameter posteriors

spde.range <- spde.posterior(fit, "mySPDE", what = "range")
plot(spde.range)

spde.logvar <- spde.posterior(fit, "mySPDE", what = "log.variance")
plot(spde.logvar)

Predict spatial intensity, and plot it:

pxl <- pixels(mesh, nx = 100, ny = 50, mask = mexdolphin$ppoly) pr.int <- predict(fit, pxl, ~ exp(mySPDE + Intercept)) ggplot() + gg(pr.int) + gg(mexdolphin$ppoly) +
gg(mexdolphin$samplers, color = "grey") + gg(mexdolphin$points, size = 0.2, alpha = 1) +
noyticks +
noxticks +
theme(legend.key.width = unit(x = 0.2, "cm"), legend.key.height = unit(x = 0.3, "cm")) +
theme(legend.text = element_text(size = 6)) +
guides(fill = FALSE) +
coord_equal()

Predict the detection function and plot it, to generate a plot like the one below. Here, we should make sure that it doesn’t try to evaluate the effects of components that can’t be evaluated using the given input data. Here, we’re only providing distances and no spatial coordinates, so we cannot evaluate the spatial random field in this predict() call. We can specify this by providing a vector of component names to include in the prediction calculations, here only “lsig”, with include = "lsig". See ?predict.bru for more information.

distdf <- data.frame(distance = seq(0, 8, length = 100))
dfun <- predict(fit, distdf, ~ hn(distance, lsig), include = "lsig")
plot(dfun)

The average detection probability within the maximum detection distance is estimated to be 0.7134929.

We can look at the posterior for expected number of dolphins as usual:

predpts <- ipoints(mexdolphin$ppoly, mexdolphin$mesh)
Lambda <- predict(fit, predpts, ~ sum(weight * exp(mySPDE + Intercept)))
Lambda
#>       mean       sd   q0.025     q0.5   q0.975   median mean.mc_std_err
#> 1 261.3017 66.11277 174.9504 249.0343 435.6058 249.0343        6.611277
#>   sd.mc_std_err
#> 1      6.241738

and including the randomness about the expected number. In this case, it turns out that you need lots of posterior samples, e.g. 2,000 to smooth out the Monte Carlo error in the posterior, and this takes a little while to compute:

Ns <- seq(50, 450, by = 1)
Nest <- predict(fit, predpts,
~ data.frame(
N = Ns,
density = dpois(Ns,
lambda = sum(weight * exp(mySPDE + Intercept))
)
),
n.samples = 2000
)

Nest$plugin_estimate <- dpois(Nest$N, lambda = Lambda$mean) ggplot(data = Nest) + geom_line(aes(x = N, y = mean, colour = "Posterior")) + geom_line(aes(x = N, y = plugin_estimate, colour = "Plugin")) ## Hazard-rate Detection Function Try doing this all again, but use this hazard-rate detection function model: hr <- function(distance, lsig) { 1 - exp(-(distance / exp(lsig))^-1) } Solution: formula1 <- coordinates + distance ~ mySPDE + log(hr(distance, lsig)) + Intercept + log(2) fit1 <- lgcp( components = cmp, mexdolphin$points,
samplers = mexdolphin$samplers, domain = list( coordinates = mesh, distance = INLA::inla.mesh.1d(seq(0, 8, length.out = 30)) ), formula = formula1 ) Plots:  spde.range <- spde.posterior(fit1, "mySPDE", what = "range") plot(spde.range) spde.logvar <- spde.posterior(fit1, "mySPDE", what = "log.variance") plot(spde.logvar)  pxl <- pixels(mesh, nx = 100, ny = 50, mask = mexdolphin$ppoly)
pr.int1 <- predict(fit1, pxl, ~ exp(mySPDE + Intercept))

ggplot() +
gg(pr.int1) +
gg(mexdolphin$ppoly) + gg(mexdolphin$samplers, color = "grey") +
gg(mexdolphin$points, size = 0.2, alpha = 1) + noyticks + noxticks + theme(legend.key.width = unit(x = 0.2, "cm"), legend.key.height = unit(x = 0.3, "cm")) + theme(legend.text = element_text(size = 6)) + guides(fill = FALSE) + coord_equal()  distdf <- data.frame(distance = seq(0, 8, length = 100)) dfun1 <- predict(fit1, distdf, ~ hr(distance, lsig)) plot(dfun1)  predpts <- ipoints(mexdolphin$ppoly, mexdolphin$mesh) Lambda1 <- predict(fit1, predpts, ~ sum(weight * exp(mySPDE + Intercept))) Lambda1 #> mean sd q0.025 q0.5 q0.975 median mean.mc_std_err #> 1 328.7458 93.74092 177.9023 309.3045 570.0777 309.3045 9.374092 #> sd.mc_std_err #> 1 7.700364 Ns <- seq(50, 650, by = 1) Nest1 <- predict( fit1, predpts, ~ data.frame( N = Ns, density = dpois(Ns, lambda = sum(weight * exp(mySPDE + Intercept)) ) ), n.samples = 2000 ) Nest1$plugin_estimate <- dpois(Nest1$N, lambda = Lambda1$mean)
ggplot(data = Nest1) +
geom_line(aes(x = N, y = mean, colour = "Posterior")) +
geom_line(aes(x = N, y = plugin_estimate, colour = "Plugin"))

## Comparing the models

deltaIC(fit1, fit)
#>   Model       DIC Delta.DIC
#> 1   fit -802.2352  0.000000
#> 2  fit1 -800.1403  2.094873

# Look at the goodness-of-fit of the two models in the distance dimension
bc <- bincount(
result = fit,
observations = mexdolphin$points$distance,
breaks = seq(0, max(mexdolphin$points$distance), length = 9),
predictor = distance ~ hn(distance, lsig)
)
attributes(bc)$ggp  bc1 <- bincount( result = fit1, observations = mexdolphin$points$distance, breaks = seq(0, max(mexdolphin$points$distance), length = 9), predictor = distance ~ hn(distance, lsig) ) attributes(bc1)$ggp

## Fit Models only to the distance sampling data

Half-normal first

formula <- distance ~ log(hn(distance, lsig)) + Intercept
cmp <- ~ lsig(1) + Intercept(1)
dfit <- lgcp(
components = cmp,
mexdolphin$points, domain = list(distance = INLA::inla.mesh.1d(seq(0, 8, length.out = 30))), formula = formula, options = list(bru_initial = list(lsig = 1, Intercept = 3)) ) detfun <- predict(dfit, distdf, ~ hn(distance, lsig)) Half-normal next formula1 <- distance ~ log(hr(distance, lsig)) + Intercept cmp <- ~ lsig(1) + Intercept(1) dfit1 <- lgcp( components = cmp, mexdolphin$points,
domain = list(distance = INLA::inla.mesh.1d(seq(0, 8, length.out = 30))),
formula = formula1
)
detfun1 <- predict(dfit1, distdf, ~ hr(distance, lsig))

Compare detection function models by DIC:

deltaIC(dfit1, dfit)
#>   Model       DIC Delta.DIC
#> 1  dfit -8.626852  0.000000
#> 2 dfit1 -6.512819  2.114033

Plot both lines on histogram of observations First scale lines to have same area as that of histogram Half-normal:

hnline <- data.frame(distance = detfun$distance, p = detfun$mean, lower = detfun$q0.025, upper = detfun$q0.975)
wts <- diff(hnline$distance) wts[1] <- wts[1] / 2 wts <- c(wts, wts[1]) hnarea <- sum(wts * hnline$p)
n <- length(mexdolphin$points$distance)
scale <- n / hnarea
hnline$En <- hnline$p * scale
hnline$En.lower <- hnline$lower * scale
hnline$En.upper <- hnline$upper * scale

Hazard-rate:

hrline <- data.frame(distance = detfun1$distance, p = detfun1$mean, lower = detfun1$q0.025, upper = detfun1$q0.975)
wts <- diff(hrline$distance) wts[1] <- wts[1] / 2 wts <- c(wts, wts[1]) hrarea <- sum(wts * hrline$p)
n <- length(mexdolphin$points$distance)
scale <- n / hrarea
hrline$En <- hrline$p * scale
hrline$En.lower <- hrline$lower * scale
hrline$En.upper <- hrline$upper * scale

Combine lines in a single object for plotting

dlines <- rbind(
cbind(hnline, model = "Half-normal"),
cbind(hrline, model = "Hazard-rate")
)

Plot without the 95% credible intervals

ggplot(data.frame(mexdolphin$points)) + geom_histogram(aes(x = distance), breaks = seq(0, 8, length = 9), alpha = 0.3) + geom_point(aes(x = distance), y = 0.2, shape = "|", size = 3) + geom_line(data = dlines, aes(x = distance, y = En, group = model, col = model)) Plot with the 95% credible intervals (without taking the count rescaling into account) ggplot(data.frame(mexdolphin$points)) +
geom_histogram(aes(x = distance), breaks = seq(0, 8, length = 9), alpha = 0.3) +
geom_point(aes(x = distance), y = 0.2, shape = "|", size = 3) +
geom_line(data = dlines, aes(x = distance, y = En, group = model, col = model)) +
geom_ribbon(
data = dlines, aes(x = distance, ymin = En.lower, ymax = En.upper, group = model, col = model, fill = model),
alpha = 0.2, lty = 2
)