generate_cell_draws_and_summarize: Generate cell draws and summary rasters from INLA model

In mbg: Model-Based Geostatistics

Generate cell draws and summary rasters from INLA model

Description

Use INLA posteriors to predict out across a grid

Usage

generate_cell_draws_and_summarize(
  inla_model,
  inla_mesh,
  n_samples,
  id_raster,
  covariates,
  inverse_link_function,
  nugget_in_predict = TRUE,
  admin_boundaries = NULL,
  ui_width = 0.95,
  verbose = TRUE
)

Arguments

inla_model	Output from fit_inla_model()
inla_mesh	An SPDE mesh used to define the spatial integration points of the INLA geostatistical model. Typically created using INLA::inla.mesh.2d() or a similar function.
n_samples	(numeric) Number of posterior predictive samples to draw.
id_raster	(terra::SpatRaster) raster showing all cell locations where predictions should be taken.
covariates	(list) Named list of all covariate effects included in the model, typically generated by load_covariates().
inverse_link_function	(character) If a link function was used in the INLA model, name of the R function to transform the predictive draws from link space to natural space. For example, in a logit-linked binomial model, pass 'plogis' (as a string is fine) to invert-logit the predictive draws.
nugget_in_predict	(logical(1), default TRUE) Should the nugget term be used as an IID noise term applied to each pixel-draw?
admin_boundaries	(sf object, default NULL) The same admin boundaries used to create the admin-level effect, if one was defined in the model. Only used if an admin-level effect was defined in the model.
ui_width	(numeric, default 0.95) Size of the uncertainty interval width when calculating the upper and lower summary rasters
verbose	(logical(1), default TRUE) Log progress for draw generation?

Details

Based on a fitted INLA model, the survey area defined in an ID raster, and a set of covariates, generate predictive grid cell draws and summary rasters across a study area.

Value

Named list containing at least the following items:

• "parameter_draws": posterior samples generated from INLA::inla.posterior.sample()

• "cell_draws": A matrix of grid cell draws. Each row represents a non-NA pixel in the id_raster, in the same order that would be pulled by terra::values(), and each column represents a different posterior draw.

• "cell_pred_mean": Mean predictive estimate by grid cell, formatted as a terra SpatRaster

• "cell_pred_lower": Lower bound of (X%) uncertainty interval, formatted as a terra SpatRaster

• "cell_pred_upper": Upper bound of (X%) uncertainty interval, formatted as a terra SpatRaster

mbg documentation built on April 4, 2025, 2:06 a.m.