# LGCPs - Spatial covariates

#### David Borchers and Finn Lindgren

#### Generated on 2023-12-03

Source:`vignettes/articles/2d_lgcp_covars.Rmd`

`2d_lgcp_covars.Rmd`

Set things up

```
library(INLA)
library(inlabru)
library(fmesher)
library(RColorBrewer)
library(ggplot2)
bru_safe_sp(force = TRUE)
bru_options_set(control.compute = list(dic = TRUE)) # Activate DIC output
```

## Introduction

We are going to fit spatial models to the gorilla data, using factor
and continuous explanatory variables in this practical. We will fit one
using the factor variable `vegetation`

, the other using the
continuous covariate `elevation`

(Jump to the bottom of the practical if you want to start gently with a 1D example!)

## Get the data

`data(gorillas, package = "inlabru")`

This dataset is a list (see `help(gorillas)`

for details.
Extract the objects you need from the list, for convenience:

```
nests <- gorillas$nests
mesh <- gorillas$mesh
boundary <- gorillas$boundary
gcov <- gorillas$gcov
```

## Factor covariates

Look at the vegetation type, nests and boundary:

Or, with the mesh:

#### A model with vegetation type only

It seems that vegetation type might be a good predictor because
nearly all the nests fall in vegetation type `Primary`

. So we
construct a model with vegetation type as a fixed effect. To do this, we
need to tell ‘lgcp’ how to find the vegetation type at any point in
space, and we do this by creating model components with a fixed effect
that we call `vegetation`

(we could call it anything), as
follows:

`comp1 <- coordinates ~ vegetation(gcov$vegetation, model = "factor_full") - 1`

Notes: * We need to tell ‘lgcp’ that this is a factor fixed effect,
which we do with `model="factor_full"`

, giving one
coefficient for each factor level. * We need to be careful about
overparameterisation when using factors. Unlike regression models like
‘lm()’, ‘glm()’ or ‘gam()’, ‘lgcp()’, `inlabru`

does not
automatically remove the first level and absorb it into an intercept.
Instead, we can either use `model="factor_full"`

without an
intercept, or `model="factor_contrast"`

, which does remove
the first level.

`comp1alt <- coordinates ~ vegetation(gcov$vegetation, model = "factor_contrast") + Intercept(1)`

Fit the model as usual:

Predict the intensity, and plot the median intensity surface. (In older versions, predicting takes some time because we did not have vegetation values outside the mesh so ‘inlabru’ needed to predict these first. Since v2.0.0, the vegetation has been pre-extended.)

The `predidct`

function of `inlabru`

takes into
its `data`

argument a `SpatialPointsDataFrame`

, a
`SpatialPixelsDataFrame`

or a `data.frame`

. We can
use the `inlabru`

function `pixels`

to generate a
`SpatialPixelsDataFrame`

only within the boundary, using its
`mask`

argument, as shown below.

```
pred.df <- fm_pixels(mesh, mask = boundary, format = "sp")
int1 <- predict(fit1, pred.df, ~ exp(vegetation))
ggplot() +
gg(int1) +
gg(boundary, alpha = 0, lwd = 2) +
gg(nests, color = "DarkGreen")
```

Not surprisingly, given that most nests are in `Primary`

vegetation, the high density is in this vegetation. But there are
substantial patches of predicted high density that have no nests, and
some areas of predicted low density that have nests. What about the
estimated abundance (there are really 647 nests there):

#### A model with vegetation type and a SPDE type smoother

Lets try to `explain`

the pattern in nest distribution
that is not captured by the vegetation covariate, using an SPDE:

```
pcmatern <- inla.spde2.pcmatern(mesh,
prior.sigma = c(0.1, 0.01),
prior.range = c(0.1, 0.01)
)
comp2 <- coordinates ~
-1 +
vegetation(gcov$vegetation, model = "factor_full") +
mySmooth(coordinates, model = pcmatern)
```

And plot the median intensity surface

```
int2 <- predict(fit2, pred.df, ~ exp(mySmooth + vegetation), n.samples = 1000)
ggplot() +
gg(int2, aes(fill = q0.025)) +
gg(boundary, alpha = 0, lwd = 2) +
gg(nests)
```

… and the expected integrated intensity (mean of abundance)

```
Lambda2 <- predict(
fit2,
fm_int(mesh, boundary),
~ sum(weight * exp(mySmooth + vegetation))
)
Lambda2
#> mean sd q0.025 q0.5 q0.975 median mean.mc_std_err
#> 1 683.0676 27.58948 630.5915 678.7792 732.9523 678.7792 2.758948
#> sd.mc_std_err
#> 1 1.82848
```

Look at the contributions to the linear predictor from the SPDE and from vegetation:

```
lp2 <- predict(fit2, pred.df, ~ list(
smooth_veg = mySmooth + vegetation,
smooth = mySmooth,
veg = vegetation
))
```

The function `scale_fill_gradientn`

sets the scale for the
plot legend. Here we set it to span the range of the three linear
predictor components being plotted (medians are plotted by default).

```
lprange <- range(lp2$smooth_veg$median, lp2$smooth$median, lp2$veg$median)
csc <- scale_fill_gradientn(colours = brewer.pal(9, "YlOrRd"), limits = lprange)
plot.lp2 <- ggplot() +
gg(lp2$smooth_veg) +
csc +
theme(legend.position = "bottom") +
gg(boundary, alpha = 0) +
ggtitle("mySmooth + vegetation")
plot.lp2.spde <- ggplot() +
gg(lp2$smooth) +
csc +
theme(legend.position = "bottom") +
gg(boundary, alpha = 0) +
ggtitle("mySmooth")
plot.lp2.veg <- ggplot() +
gg(lp2$veg) +
csc +
theme(legend.position = "bottom") +
gg(boundary, alpha = 0) +
ggtitle("vegetation")
multiplot(plot.lp2, plot.lp2.spde, plot.lp2.veg, cols = 3)
```

#### A model with SPDE only

Do we need vegetation at all? Fit a model with only an SPDE + Intercept, and choose between models on the basis of DIC, using ‘deltaIC()’.

```
comp3 <- coordinates ~ mySmooth(coordinates, model = pcmatern) + Intercept(1)
fit3 <- lgcp(comp3,
data = nests,
samplers = boundary,
domain = list(coordinates = mesh)
)
```

```
int3 <- predict(fit3, pred.df, ~ exp(mySmooth + Intercept))
ggplot() +
gg(int3) +
gg(boundary, alpha = 0) +
gg(nests)
```

```
Lambda3 <- predict(
fit3,
fm_int(mesh, boundary),
~ sum(weight * exp(mySmooth + Intercept))
)
Lambda3
#> mean sd q0.025 q0.5 q0.975 median mean.mc_std_err
#> 1 670.5688 28.82681 613.7787 670.9052 727.199 670.9052 2.882681
#> sd.mc_std_err
#> 1 1.945967
```

Model | DIC | Delta.DIC |
---|---|---|

fit1 | -562.5418 | 0.000 |

fit3 | 524.2575 | 1086.799 |

fit2 | 618.6010 | 1181.143 |

NOTE: the behaviour of DIC is currently a bit unclear, and is being investigated. WAIC is related to leave-one-out cross-validation, and is not appropriate to use with the current current LGCP likelihood implementation.

Classic mode:

Model | DIC | Delta.DIC |
---|---|---|

fit2 | 2224.131 | 0.00000 |

fit3 | 2274.306 | 50.17504 |

fit1 | 3124.784 | 900.65339 |

Experimental mode:

Model | DIC | Delta.DIC |
---|---|---|

fit1 | -563.3583 | 0.000 |

fit3 | 509.4010 | 1072.759 |

fit2 | 597.6459 | 1161.004 |

#### CV and SPDE parameters for Model 2

We are going with Model `fit2`

. Lets look at the spatial
distribution of the coefficient of variation

Plot the vegetation “fixed effect” posteriors. First get their names
- from `$marginals.random$vegetation`

of the fitted object,
which contains the fixed effect marginal distribution data

```
flist <- vector("list", NROW(fit2$summary.random$vegetation))
for (i in seq_along(flist)) flist[[i]] <- plot(fit2, "vegetation", index = i)
multiplot(plotlist = flist, cols = 3)
```

Use `spde.posterior( )`

to obtain and then plot the SPDE
parameter posteriors and the Matern correlation and covariance functions
for this model.

```
spde.range <- spde.posterior(fit2, "mySmooth", what = "range")
spde.logvar <- spde.posterior(fit2, "mySmooth", what = "log.variance")
range.plot <- plot(spde.range)
var.plot <- plot(spde.logvar)
multiplot(range.plot, var.plot)
```

```
corplot <- plot(spde.posterior(fit2, "mySmooth", what = "matern.correlation"))
covplot <- plot(spde.posterior(fit2, "mySmooth", what = "matern.covariance"))
multiplot(covplot, corplot)
```

## Continuous covariates

Now lets try a model with elevation as a (continuous) explanatory variable. (First centre elevations for more stable fitting.)

```
elev <- gcov$elevation
elev$elevation <- elev$elevation - mean(elev$elevation, na.rm = TRUE)
ggplot() +
gg(elev) +
gg(boundary, alpha = 0)
```

The elevation variable here is of class ‘SpatialGridDataFrame’, that
can be handled in the same way as the vegetation covariate. However,
since in some cases data may be stored differently, other methods are
needed to access the stored values, or there’s some post-processing to
be done. In such cases, we can define a function that knows how to
evaluate the covariate at arbitrary points in the survey region, and
call that function in the component definition. In this case, we can use
a powerful method from the ‘sp’ package to do this. We use this to
create the needed function. The method `eval_spatial()`

is
the method that handles this automatically, and supports
`terra`

`SpatRaster`

and `sf`

geometry
points objects, and mismatching coordinate systems as well. In the
following evaluator example function, we only add infilling of missing
values as a post-processing step.

```
f.elev <- function(where) {
# Extract the values
v <- eval_spatial(elev, where, layer = "elevation")
# Fill in missing values
if (any(is.na(v))) {
v <- bru_fill_missing(elev, where, v)
}
return(v)
}
```

For brevity we are not going to consider models with elevation only, with elevation and a SPDE, and with SPDE only. We will just fit one with elevation and SPDE. We create our model to pass to lgcp thus:

```
matern <- inla.spde2.pcmatern(mesh,
prior.sigma = c(0.1, 0.01),
prior.range = c(0.1, 0.01)
)
ecomp <- coordinates ~ elev(f.elev(.data.), model = "linear") +
mySmooth(coordinates, model = matern) + Intercept(1)
```

Note how the elevation effect is defined. When we used the
`Spatial`

grid object directly (causing `inlabru`

to automatically call `eval_spatial()`

) we specified it
like

`vegetation(gcov$vegetation, model = "factor_full")`

whereas with the function method we specify the covariate like this:

`elev(f.elev(.data.), model = "linear")`

We also now include an intercept term.

The model is fitted in the usual way:

Summary and model selection

```
summary(efit)
#> inlabru version: 2.10.0.9000
#> INLA version: 23.11.26
#> Components:
#> elev: main = linear(f.elev(.data.)), group = exchangeable(1L), replicate = iid(1L)
#> mySmooth: main = spde(coordinates), group = exchangeable(1L), replicate = iid(1L)
#> Intercept: main = linear(1), group = exchangeable(1L), replicate = iid(1L)
#> Likelihoods:
#> Family: 'cp'
#> Data class: 'SpatialPointsDataFrame'
#> Predictor: coordinates ~ .
#> Time used:
#> Pre = 0.347, Running = 8.04, Post = 0.318, Total = 8.7
#> Fixed effects:
#> mean sd 0.025quant 0.5quant 0.975quant mode kld
#> elev 0.004 0.001 0.002 0.004 0.006 0.004 0
#> Intercept 1.132 0.477 0.160 1.143 2.042 1.143 0
#>
#> Random effects:
#> Name Model
#> mySmooth SPDE2 model
#>
#> Model hyperparameters:
#> mean sd 0.025quant 0.5quant 0.975quant mode
#> Range for mySmooth 1.76 0.206 1.393 1.75 2.20 1.720
#> Stdev for mySmooth 1.01 0.086 0.856 1.00 1.19 0.991
#>
#> Deviance Information Criterion (DIC) ...............: 518.63
#> Deviance Information Criterion (DIC, saturated) ....: NA
#> Effective number of parameters .....................: -827.49
#>
#> Watanabe-Akaike information criterion (WAIC) ...: 3097.09
#> Effective number of parameters .................: 899.76
#>
#> Marginal log-Likelihood: -1255.01
#> is computed
#> Posterior summaries for the linear predictor and the fitted values are computed
#> (Posterior marginals needs also 'control.compute=list(return.marginals.predictor=TRUE)')
deltaIC(fit1, fit2, fit3, efit)
#> Model DIC Delta.DIC
#> 1 fit1 -562.5418 0.000
#> 2 efit 518.6271 1081.169
#> 3 fit3 524.2575 1086.799
#> 4 fit2 618.6010 1181.143
```

Predict and plot the density

```
e.int <- predict(efit, pred.df, ~ exp(mySmooth + elev + Intercept))
e.int.log <- predict(efit, pred.df, ~ (mySmooth + elev + Intercept))
ggplot() +
gg(e.int, aes(fill = log(sd))) +
gg(boundary, alpha = 0) +
gg(nests, shape = "+")
```

```
ggplot() +
gg(e.int.log, aes(fill = exp(mean + sd^2 / 2))) +
gg(boundary, alpha = 0) +
gg(nests, shape = "+")
```

Now look at the elevation and SPDE effects in space. Leave out the Intercept because it swamps the spatial effects of elevation and the SPDE in the plots and we are interested in comparing the effects of elevation and the SPDE.

First we need to predict on the linear predictor scale.

```
e.lp <- predict(
efit,
pred.df,
~ list(
smooth_elev = mySmooth + elev,
elev = elev,
smooth = mySmooth
)
)
```

The code below, which is very similar to that used for the vegetation factor variable, produces the plots we want.

```
lprange <- range(e.lp$smooth_elev$mean, e.lp$elev$mean, e.lp$smooth$mean)
library(RColorBrewer)
csc <- scale_fill_gradientn(colours = brewer.pal(9, "YlOrRd"), limits = lprange)
plot.e.lp <- ggplot() +
gg(e.lp$smooth_elev, mask = boundary) +
csc +
theme(legend.position = "bottom") +
gg(boundary, alpha = 0) +
ggtitle("SPDE + elevation")
plot.e.lp.spde <- ggplot() +
gg(e.lp$smooth, mask = boundary) +
csc +
theme(legend.position = "bottom") +
gg(boundary, alpha = 0) +
ggtitle("SPDE")
plot.e.lp.elev <- ggplot() +
gg(e.lp$elev, mask = boundary) +
csc +
theme(legend.position = "bottom") +
gg(boundary, alpha = 0) +
ggtitle("elevation")
multiplot(plot.e.lp,
plot.e.lp.spde,
plot.e.lp.elev,
cols = 3
)
```

You might also want to look at the posteriors of the fixed effects and of the SPDE. Adapt the code used for the vegetation factor to do this.

```
LambdaE <- predict(
efit,
fm_int(mesh, boundary),
~ sum(weight * exp(Intercept + elev + mySmooth))
)
LambdaE
#> mean sd q0.025 q0.5 q0.975 median mean.mc_std_err
#> 1 669.4047 25.16072 628.5246 667.963 713.6262 667.963 2.516072
#> sd.mc_std_err
#> 1 1.836454
```

```
flist <- vector("list", NROW(efit$summary.fixed))
for (i in seq_along(flist)) {
flist[[i]] <- plot(efit, rownames(efit$summary.fixed)[i])
}
multiplot(plotlist = flist, cols = 2)
```

Plot the SPDE parameter posteriors and the Matern correlation and covariance functions for this model.

```
spde.range <- spde.posterior(efit, "mySmooth", what = "range")
spde.logvar <- spde.posterior(efit, "mySmooth", what = "log.variance")
range.plot <- plot(spde.range)
var.plot <- plot(spde.logvar)
multiplot(range.plot, var.plot)
```

```
corplot <- plot(spde.posterior(efit, "mySmooth", what = "matern.correlation"))
covplot <- plot(spde.posterior(efit, "mySmooth", what = "matern.covariance"))
multiplot(covplot, corplot)
```

Also estimate abundance. The `data.frame`

in the second
call leads to inclusion of `N`

in the prediction object, for
easier plotting.

```
Lambda <- predict(
efit, fm_int(mesh, boundary),
~ sum(weight * exp(mySmooth + elev + Intercept))
)
Lambda
#> mean sd q0.025 q0.5 q0.975 median mean.mc_std_err
#> 1 669.5452 30.31325 613.6689 666.8134 728.8881 666.8134 3.031325
#> sd.mc_std_err
#> 1 2.124781
Nest.e <- predict(
efit,
fm_int(mesh, boundary),
~ data.frame(
N = 200:1000,
density = dpois(200:1000,
lambda = sum(weight * exp(mySmooth + elev + Intercept))
)
),
n.samples = 2000
)
```

Plot in the same way as in previous practicals

```
Nest.e$plugin_estimate <- dpois(Nest.e$N, lambda = Lambda$median)
ggplot(data = Nest.e) +
geom_line(aes(x = N, y = mean, colour = "Posterior")) +
geom_line(aes(x = N, y = plugin_estimate, colour = "Plugin"))
```

### Non-spatial evaluation of the covariate effect

The previous examples of posterior prediction focused on spatial
prediction. From `inlabru`

version 2.2.8, a feature is
available for overriding the component input value specification from
the component definition. Each model component can be evaluated
directly, for arbitrary values by functions named by adding the suffix
`_eval`

to the end of the component name in the predictor
expression, and disabling normal component evaluation for all components
with `include = character(0)`

(since we’re both bypassing the
normal input to the `elev`

component, and not supplying data
for the other components). From version `2.8.0`

,
`inlabru`

attempts to automatically detect which model
components are used in the expression, and the `include`

argument can usually be left out entirely.

Since the elevation effect in this model is linear, the resulting plot isn’t very interesting, but the same method can be applied to non-linear effects as well, and combined into general R expressions.

```
elev.pred <- predict(
efit,
data.frame(elevation = seq(0, 100, length.out = 1000)),
formula = ~ elev_eval(elevation),
include = character(0) # Not needed from version 2.8.0
)
ggplot(elev.pred) +
geom_line(aes(elevation, mean)) +
geom_ribbon(
aes(elevation,
ymin = q0.025,
ymax = q0.975
),
alpha = 0.2
) +
geom_ribbon(
aes(elevation,
ymin = mean - 1 * sd,
ymax = mean + 1 * sd
),
alpha = 0.2
)
```

## A 1D Example

Try fitting a 1-dimensional model to the point data in the
`inlabru`

dataset `Poisson2_1D`

. This comes with a
covariate function called `cov2_1D`

. Try to reproduce the
plot below (used in lectures) showing the effects of the
`Intercept + z`

and the `SPDE`

. (You may find it
helpful to build on the model you fitted in the previous practical,
adding the covariate to the model specification.)

```
data(Poisson2_1D)
ss <- seq(0, 55, length = 200)
z <- cov2_1D(ss)
x <- seq(1, 55, length = 100)
mesh <- fm_mesh_1d(x, degree = 1)
comp <- x ~
beta_z(cov2_1D(x), model = "linear") +
spde1D(x, model = inla.spde2.matern(mesh)) +
Intercept(1)
fitcov1D <- lgcp(comp, pts2, domain = list(x = mesh))
pr.df <- data.frame(x = x)
prcov1D <- predict(
fitcov1D,
pr.df,
~ list(
total = exp(beta_z + spde1D + Intercept),
fx = exp(beta_z + Intercept),
spde = exp(spde1D)
)
)
ggplot() +
gg(prcov1D$total, color = "red") +
geom_line(aes(x = prcov1D$spde$x, y = prcov1D$spde$median), col = "blue", lwd = 1.25) +
geom_line(aes(x = prcov1D$fx$x, y = prcov1D$fx$median), col = "green", lwd = 1.25) +
geom_point(data = pts2, aes(x = x), y = 0.2, shape = "|", cex = 4) +
xlab(expression(bold(s))) +
ylab(expression(hat(lambda)(bold(s)) ~ ~"and its components")) +
annotate(geom = "text", x = 40, y = 6, label = "Intensity", color = "red") +
annotate(geom = "text", x = 40, y = 5.5, label = "z-effect", color = "green") +
annotate(geom = "text", x = 40, y = 5, label = "SPDE", color = "blue")
```