Compare survey indices across different mesh cutoff values

Refits an sdmTMB model using a range of mesh cutoff values and compares the resulting survey indices and predictions to the original (reference) model. Useful for assessing the sensitivity of an index to mesh resolution.

Usage

compare_meshes(
  object,
  mesh_cutoffs,
  newdata,
  object_crs = NULL,
  bias_correct = FALSE,
  level = 0.95,
  area = 1,
  save_models = FALSE,
  silent = TRUE,
  n_workers = 1,
  nsplit = 3,
  future_seed = TRUE,
  reference_name = "Reference"
)

Arguments

object

A fitted model from sdmTMB::sdmTMB().

mesh_cutoffs

Numeric vector of mesh cutoff values (in the units of the model coordinates, typically km) to compare.

newdata

A data frame for predictions, with the same predictor columns as the fitted data and a time column matching the fitted data. Must contain X and Y columns.

object_crs

Coordinate reference system for the model data. If NULL (default), extracted from the model's mesh.

bias_correct

Logical. Apply bias correction via TMB::sdreport()? Default FALSE.

level

Numeric. Confidence level for index intervals. Default 0.95.

area

Grid cell area for area-weighted index calculation. Passed to sdmTMB::get_index_split().

save_models

Logical. Retain fitted model objects in the output? Default FALSE.

silent

Logical. Suppress model output? Default TRUE.

n_workers

Integer. Number of parallel workers. Default 1.

nsplit

Integer. Number of splits for sdmTMB::get_index_split(). Default 3.

future_seed

Logical or integer. Future-compatible random seed for parallel processing.

reference_name

Character. Label for the reference (original) model. Default "Reference".

Value

An object of class sdmTMB_mesh_comparison, a list with index, pred_diff (and optionally models). Carries crs and reference_name attributes.

See also

sdmTMB::sdmTMB(), sdmTMB::get_index_split(), plot.sdmTMB_mesh_comparison()

Author

Mikko Vihtakari

Examples

# \donttest{
mesh <- sdmTMB::make_mesh(sdmTMB::pcod, c("X", "Y"), cutoff = 20)
m <- sdmTMB::sdmTMB(
  data = sdmTMB::pcod, formula = density ~ 0 + as.factor(year),
  time = "year", mesh = mesh, family = sdmTMB::tweedie(link = "log")
)
nd <- sdmTMB::replicate_df(sdmTMB::qcs_grid, "year", unique(sdmTMB::pcod$year))
mesh_indices <- compare_meshes(
  object = m, mesh_cutoffs = c(10, 30), newdata = nd, object_crs = 32609,
  reference_name = "20 km"
)
plot(mesh_indices)

# }