get_stitched_index: Get stitched index across survey regions in synoptic trawl...
In pbs-assess/gfsynopsis: Data Synopsis Reports for PBS Groundfish

get_stitched_index

R Documentation

Get stitched index across survey regions in synoptic trawl and HBLL surveys

Description

Get stitched index across survey regions in synoptic trawl and HBLL surveys

Usage

get_stitched_index(
  survey_dat,
  species = "arrowtooth flounder",
  survey_type = "synoptic",
  model_type = "st-rw",
  form = NULL,
  family = sdmTMB::tweedie(),
  time = "year",
  spatial = "on",
  spatiotemporal = "rw",
  time_varying = NULL,
  time_varying_type = NULL,
  mesh = NULL,
  cutoff = 20,
  offset = "offset",
  priors = sdmTMB::sdmTMBpriors(),
  silent = TRUE,
  ctrl = sdmTMB::sdmTMBcontrol(nlminb_loops = 1L, newton_loops = 1L),
  gradient_thresh = 0.001,
  cache = NULL,
  check_cache = FALSE,
  cache_predictions = FALSE,
  cache_fits = FALSE,
  survey_grid = NULL,
  grid_dir
)

Arguments

`survey_dat`	A data frame from `prep_stitch_dat()`.
`species`	A string specifying the `species_common_name`.
`survey_type`	A string matching one of: "synoptic" (the default), "hbll_outside", "hbll_inside".
`model_type`	A string matching one of: "st-rw" (the default), "st-rw_tv-rw", or "custom".
`form`	Optional string specifying model formula. 'catch ~ 1' (the default, unless `family = poisson()` or `family = sdmTMB::censored_possion()` then "catch ~ 1 + (1\|obs_id)").
`family`	The family and link for `sdmTMB::sdmTMB()`.
`time`	An optional time column name (as character), used in `sdmTMB::sdmTMB()`. (default = 'year')
`spatial`	Estimate spatial random fields? See `sdmTMB::sdmTMB()`. (Default is 'rw').
`spatiotemporal`	Estimate the spatiotemporal random fields, see `sdmTMB::sdmTMB()`. (Default is 'rw').
`time_varying`	An optional one-sided formula describing covariates that should be modelled as a time-varying process. See `sdmTMB::sdmTMB()`. Default is `NULL` if `model_type = st-rw`, and `~1` if `model_type = 'st-rw_tv-rw'`.
`time_varying_type`	Type of time-varying process to apply to ‘time_varying’ formula. See `sdmTMB::sdmTMB()`. #' Default is `NULL` if `model_type = st-rw`, and `~1` if `model_type = 'st-rw_tv-rw'`.
`mesh`	Optional mesh object created using `sdmTMB::make_mesh()`.
`cutoff`	If `mesh = NULL`, mesh cutoff for `sdmTMB::make_mesh()`.
`offset`	A string naming the offset column in `dat` used in `sdmTMB::sdmTMB()`
`priors`	Optional penalties/priors used in `sdmTMB::sdmTMBpriors()`.
`silent`	A boolean. Silent or include optimization details.
`ctrl`	Optimization control options via `sdmTMB::sdmTMBcontrol()`.
`gradient_thresh`	Threshold used in `sdmTMB::sanity()` (default = 0.001).
`cache`	A string specifying file path to cache directory.
`check_cache`	Check whether index file already exists? Default = `FALSE`.
`cache_predictions`	Cache model predictions? Can be large.
`cache_fits`	Cache model fits? Can be large.
`survey_grid`	A data frame containing the spatial grid over which predictions are to be made. If `survey_grid` = NULL (the default). Grid should contain cell area.
`grid_dir`	Path where cleaned grids were stored from `prep_stitch_grids()`

Value

Either a string or dataframe:

⁠insufficient data to stitch regions⁠ if the number of positive sets is too low to stitch
⁠Failed sanity check⁠ if the model failed to converge
A dataframe containing the stitched index formatted to use with gfplot::plot_survey_index()