Construct an SPDE mesh for sdmTMB — make

Construct an SPDE mesh for use with sdmTMB.

Usage

make_mesh(
  data,
  xy_cols,
  type = c("kmeans", "cutoff", "cutoff_search"),
  cutoff,
  n_knots,
  seed = 42,
  refine = list(min.angle = 21, max.edge = Inf, max.n.strict = -1, max.n = 1000),
  mesh = NULL
)

# S3 method for sdmTMBmesh
plot(x, ...)

Arguments

data: A data frame.
xy_cols: A character vector of x and y column names contained in data. These should likely be in an equal distance projection. For a helper function to convert to UTMs, see add_utm_columns().
type: Method to create the mesh. Also see mesh argument to supply your own mesh.
cutoff: An optional cutoff if type is "cutoff". "The minimum allowed distance between points in the mesh". See INLA::inla.mesh.create(). Smaller values create meshes with more knots. Points further apart than this value will receive a separate vertex in the mesh before any mesh refinement.
n_knots: The number of desired knots if type is not "cutoff".
seed: Random seed. Affects stats::kmeans() determination of knot locations if type = "kmeans".
refine: Logical or list to pass to INLA::inla.mesh.create().
mesh: An optional mesh created via INLA instead of using the above convenience options.
x: Output from make_mesh().
...: Passed to graphics::plot().

Value

make_mesh(): A list of class sdmTMBmesh. The element mesh is the output from INLA::inla.mesh.create() and the element spde is the output from INLA::inla.spde2.matern().

plot.sdmTMBmesh(): A plot of the mesh and data points. If inlabru and ggplot2 are installed, a ggplot2 object is returned, otherwise a base graphics R plot is returned. To make your own, pass your_mesh$mesh to inlabru::gg().

Examples

mesh <- make_mesh(pcod, c("X", "Y"), cutoff = 30, type = "cutoff")
plot(mesh)


# \donttest{
mesh <- make_mesh(pcod, c("X", "Y"), cutoff = 5, type = "cutoff")
plot(mesh)


mesh <- make_mesh(pcod, c("X", "Y"), n_knots = 50, type = "cutoff_search")
#> cutoff = 1.00 | knots = 2641 | ↓ 
#> cutoff = 100.00 | knots = 26 | ↑ 
#> cutoff = 10.00 | knots = 205 | ↓ 
#> cutoff = 31.62 | knots = 49 | ↑ 
#> cutoff = 17.78 | knots = 89 | ↓ 
#> cutoff = 23.71 | knots = 61 | ↓ 
#> cutoff = 27.38 | knots = 53 | ↓ 
#> cutoff = 29.43 | knots = 50 | ✔ 
plot(mesh)


mesh <- make_mesh(pcod, c("X", "Y"), n_knots = 50, type = "kmeans")
plot(mesh)


# Defining a mesh directly with INLA:
bnd <- INLA::inla.nonconvex.hull(cbind(pcod$X, pcod$Y), convex = -0.05)
inla_mesh <- INLA::inla.mesh.2d(
  boundary = bnd,
  max.edge = c(20, 50),
  offset = -0.05,
  cutoff = c(2, 5),
  min.angle = 10
)
mesh <- make_mesh(pcod, c("X", "Y"), mesh = inla_mesh)
plot(mesh)

# }