SPDE coordinate issue

[davidbolin]

The code below gives the following error, which seems to be caused by the name "s" for the coordinates.

Error in (function (data, model, stackmaker, n = 10, result = NULL, family, : INLA returned message: object 'pde2' not found In addition: Warning message: In INLA::f(field, model = pde2) : object 'pde2' not found

library(inlabru) seed <- 1 obs.loc <- 10 * cbind(runif(100), runif(100)) Y <- as.vector(rnorm(100)) df <- data.frame(Y=Y,x=obs.loc) x <- seq(from = 0, to = 10, length.out = 30) mesh <- inla.mesh.create(lattice = inla.mesh.lattice(x = x, y = x), extend = FALSE, refine = FALSE) spde2 <- inla.spde2.pcmatern(mesh, prior.range=c(1, 0.01), prior.sigma=c(10, 0.01))

comp <- Y ~ field(map = s, model = spde2) + Intercept

fit <- bru(comp, df, family = "gaussian")

[finnlindgren]

This has been fixed at some point in the past. The syntax has also changed slightly (map is now main, and doesn't need to be named). Modified code below now tends to crash INLA instead, due to the flat field leading to large range and tiny variance, and non-positive-definit precision.

library(inlabru)
seed <- 1
obs.loc <- 10 * cbind(runif(100), runif(100))
Y <- as.vector(rnorm(100))
df <- data.frame(Y = Y, x = obs.loc)
x <- seq(from = 0, to = 10, length.out = 20)
mesh <- INLA::inla.mesh.create(
  lattice = INLA::inla.mesh.lattice(x = x, y = x),
  extend = FALSE,
  refine = FALSE
)
spde2 <- INLA::inla.spde2.pcmatern(
  mesh,
  prior.range = c(1, 0.01),
  prior.sigma = c(10, 0.01)
)

comp <- Y ~ field(s, model = spde2) + Intercept(1)

fit <- bru(comp, data = df, family = "gaussian")