make_mesh: Construct an SPDE mesh for sdmTMB

In pbs-assess/sdmTMB: Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'

Construct an SPDE mesh for sdmTMB

Description

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,
  mesh = NULL,
  fmesher_func = fmesher::fm_rcdt_2d_inla,
  convex = NULL,
  concave = convex,
  ...
)

## S3 method for class '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 triangle edge length.
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".
mesh	An optional mesh created via fmesher instead of using the above convenience options.
fmesher_func	Which fmesher function to use. Options include fmesher::fm_rcdt_2d_inla() and fmesher::fm_mesh_2d_inla() along with version without the ⁠_inla⁠ on the end.
convex	If specified, passed to fmesher::fm_nonconvex_hull(). Distance to extend non-convex hull from data.
concave	If specified, passed to fmesher::fm_nonconvex_hull(). "Minimum allowed reentrant curvature". Defaults to convex.
...	Passed to graphics::plot().
x	Output from make_mesh().

Value

make_mesh(): A list of class sdmTMBmesh. The element mesh is the output from fmesher_func (default is fmesher::fm_mesh_2d_inla()). See mesh$mesh$n for the number of vertices.

plot.sdmTMBmesh(): A plot of the mesh and data points. To make your own ggplot2 version, pass your_mesh$mesh to inlabru::gg().

Examples

# Extremely simple cutoff:
mesh <- make_mesh(pcod, c("X", "Y"), cutoff = 5, type = "cutoff")
plot(mesh)

# Using a k-means algorithm to assign vertices:
mesh <- make_mesh(pcod, c("X", "Y"), n_knots = 50, type = "kmeans")
plot(mesh)


# But, it's better to develop more tailored meshes:

# Pass arguments via '...' to fmesher::fm_mesh_2d_inla():
mesh <- make_mesh(
  pcod, c("X", "Y"),
  fmesher_func = fmesher::fm_mesh_2d_inla,
  cutoff = 8, # minimum triangle edge length
  max.edge = c(20, 40), # inner and outer max triangle lengths
  offset = c(5, 40) # inner and outer border widths
)
plot(mesh)

# Or define a mesh directly with fmesher (formerly in INLA):
inla_mesh <- fmesher::fm_mesh_2d_inla(
  loc = cbind(pcod$X, pcod$Y), # coordinates
  max.edge = c(25, 50), # max triangle edge length; inner and outer meshes
  offset = c(5, 25),  # inner and outer border widths
  cutoff = 5 # minimum triangle edge length
)
mesh <- make_mesh(pcod, c("X", "Y"), mesh = inla_mesh)
plot(mesh)

pbs-assess/sdmTMB documentation built on Dec. 20, 2024, 1:51 p.m.