Fit Passage to Spawner (P2S) STAN Model

This functions take in a list of data required to run the Passage to Spawner STAN model. The function will return the full fitted stanfit object. See vignette("passage_to_spawner_submodel.Rmd", package = "SRJPEmodel") for more details.

fit_passage_to_spawner_model(data_inputs)

Arguments

data_inputs

A list object containing the following variables:

  • N number of years

  • observed_passage upstream passage for the associated years

  • observed_spawners observed spawner counts for the associated years. Redd counts for Battle and Clear Creeks.

  • percent_female Assumed sex ratio for the population and used to convert spawner counts to total population. 0.5 for redds, 1 for other spawner survey types.

  • environmental_covar the environmental covariate you want to run the model with.

  • ss_total total sum of squares.

  • average_upstream_passage average upstream passage across all years, used to forecast.

Value

a STANfit model object (see details)