Build a tobs model object

Inferred model type from arguments:

• Single-season: no col_formula, no species

• Dynamic: col_formula and/or ext_formula provided

• Integrated: integrated = TRUE, y a list of matrices

Usage

.tobs_build_model(
  occ_formula,
  det_formula = NULL,
  data,
  y,
  col_formula = NULL,
  ext_formula = NULL,
  species = NULL,
  integrated = FALSE,
  abundance = FALSE,
  count = FALSE,
  count_response = "poisson",
  count_trials = NULL,
  det_visit_formula = NULL,
  det_visit_data = NULL,
  site.map = NULL
)

Details

Community families (ms_occu / ms_dyn_occu / ms_int_occu / ms_occu_cover / ms_count / jsdm) have their own in-tree binders + Laplace-EM fitter and do not pass through here.

A structured term enters the process whose formula it is written in. For an integrated model this makes detection = ~ x + spde(lon, lat, ...) a detection-arm field: the occupancy state stays whatever the occupancy formula says, and the continuous Matern field sits on the detection logit. The detection arm there is one arm observed through S sources, so the field is one structure fit once per source block – source s fits its own realization at its own sites, and two sources covering the same location each carry their own value there, the same way each source carries its own detection coefficients. fit$spatial_field_det is the per-source named list of mesh fields (source names as given on y); project a source's field to its sites with fit$spatial$tulpa_spec$A.

The arm accepts a continuous spde() field under method = "laplace". The areal kinds and the temporal / re / svc / latent classes are grid-integrated as latent blocks on the state arm, so they are written on the occupancy formula; on a detection formula they error with a pointer rather than being fit against the wrong arm.

Each source of an integrated response surveys its own subset of the sites in data, in its own order, so a source's rows are joined to the site-level frame on a site key rather than read in row order. The key is site.map when given – a list of one entry per source, each naming or indexing one site of data per source row – otherwise rownames(y[[s]]) matched against rownames(data). A source carrying neither key is keyed by row position, which requires one row per site; a shorter one errors with a pointer to site.map. simulate_int_occu() names its response rows, so its output joins on that key.