Prepare inputs for abundance model

prepare_abundance_inputs(
  site,
  run_year,
  effort_adjust = c(T, F),
  pcap_model_object,
  input_catch_data = NULL,
  input_efficiency_data = NULL
)

Arguments

site: site for which you want to fit the model
run_year: run year for which you want to fit the model
effort_adjust: whether or not you want to use catch adjusted by effort.
input_catch_data: Optional argument for weekly catch data. Defaults to SRJPEdata::weekly_juvenile_abundance_catch_data. If passed in, structure of data frame must match that of the default.
input_efficiency_data: Optional argument for weekly efficiency data. Defaults to SRJPEdata::SRJPEdata::weekly_juvenile_abundance_efficiency_data. If passed in, structure of data frame must match that of the default.

Value

a list:

abundance_inputs a list of data and inits for input into the abundance model.
model_name The version of the pCap logic to use for generating lt_pCap_U values. Either all_mark_recap, missing_mark_recap, no_mark_recap, or no_mark_recap_no_trib.
site The site run.
run_year The run year.
weeks_fit The weeks fit for the abundance model
weeks_date Associated dates for the weeks fit for the abundance model.
lt_pCap_Us A list containing output of generate_lt_pCap_Us: containing values of length Nstrata for lt_pCap_mu and lt_pCap_sd.

Details

This function prepares data for input into an abundance model.