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Use inlabru as engine

Source: R/engine_inlabru.R
engine_inlabru.Rd

Model components are specified with general inputs and mapping methods to the latent variables, and the predictors are specified via general R expressions, with separate expressions for each observation likelihood model in multi-likelihood models. The inlabru engine - similar as the engine_inla function acts a wrapper for INLA, albeit "inlabru" has a number of convenience functions implemented that make in particular predictions with new data much more straight forward (e.g. via posterior simulation instead of fitting). Since more recent versions "inlabru" also supports the addition of multiple likelihoods, therefore allowing full integrated inference.

Usage

engine_inlabru(
  x,
  optional_mesh = NULL,
  max.edge = NULL,
  offset = NULL,
  cutoff = NULL,
  proj_stepsize = NULL,
  strategy = "auto",
  int.strategy = "eb",
  area = "gpc2",
  timeout = NULL,
  type = "response",
  ...
)

Source

https://inlabru-org.github.io/inlabru/articles/

Arguments

x

distribution() (i.e. BiodiversityDistribution) object.

optional_mesh

A directly supplied "INLA" mesh (Default: NULL)

max.edge

The largest allowed triangle edge length, must be in the same scale units as the coordinates. Default is an educated guess (Default: NULL).

offset

interpreted as a numeric factor relative to the approximate data diameter. Default is an educated guess (Default: NULL).

cutoff

The minimum allowed distance between points on the mesh. Default is an educated guess (Default: NULL).

proj_stepsize

The stepsize in coordinate units between cells of the projection grid (Default: NULL)

strategy

Which approximation to use for the joint posterior. Options are "auto" ("default"), "adaptative", "gaussian", "simplified.laplace" & "laplace".

int.strategy

Integration strategy. Options are "auto", "grid", "eb" ("default") & "ccd".

area

Accepts a character denoting the type of area calculation to be done on the mesh (Default: 'gpc2').

timeout

Specify a timeout for INLA models in sec. Afterwards it passed.

type

The mode used for creating posterior predictions. Either summarizing the linear "predictor" or "response" (Default:"response").

...

Other variables

Value

An Engine.

Details

All INLA engines require the specification of a mesh that needs to be provided to the "optional_mesh" parameter. Otherwise the mesh will be created based on best guesses of the data spread. A good mesh needs to have triangles as regular as possible in size and shape: equilateral.

* "max.edge": The largest allowed triangle edge length, must be in the same scale units as the coordinates Lower bounds affect the density of triangles * "offset": The automatic extension distance of the mesh If positive: same scale units. If negative, interpreted as a factor relative to the approximate data diameter i.e., a value of -0.10 will add a 10% of the data diameter as outer extension. * "cutoff": The minimum allowed distance between points, it means that points at a closer distance than the supplied value are replaced by a single vertex. it is critical when there are some points very close to each other, either for point locations or in the domain boundary. * "proj_stepsize": The stepsize for spatial predictions, which affects the spatial grain of any outputs created.

Priors can be set via INLAPrior.

Note

How INLA Meshes are generated, substantially influences prediction outcomes. See Dambly et al. (2023).

References

  • Bachl, F. E., Lindgren, F., Borchers, D. L., & Illian, J. B. (2019). inlabru: an R package for Bayesian spatial modelling from ecological survey data. Methods in Ecology and Evolution, 10(6), 760-766.

  • Simpson, Daniel, Janine B. Illian, S. H. Sørbye, and Håvard Rue. 2016. “Going Off Grid: Computationally Efficient Inference for Log-Gaussian Cox Processes.” Biometrika 1 (103): 49–70.

  • Dambly, L. I., Isaac, N. J., Jones, K. E., Boughey, K. L., & O'Hara, R. B. (2023). Integrated species distribution models fitted in INLA are sensitive to mesh parameterisation. Ecography, e06391.

See also

Other engine: engine_bart(), engine_breg(), engine_gdb(), engine_glm(), engine_glmnet(), engine_inla(), engine_scampr(), engine_stan(), engine_xgboost()

Examples

if (FALSE) { # \dontrun{
# Add inlabru as an engine
x <- distribution(background) |> engine_inlabru()
} # }