Passage to Spawner Submodel

Overview

The Passage to Spawner (P2S) is a Bayesian model that produces estimates of spawning adults for Battle Creek, Clear Creek, Deer Creek, and Mill Creek with uncertainty. The model can be used to get spawning adults for a tributary as part of any stock-recruit-based SRJPE model alternative.

Submodel Objective

The purpose of the P2S submodel is to take in observed upstream passage, or escapement, estimates from a tributary and model the relationship with spawner counts, either from redd surveys or holding surveys. The P2S produces estimated spawner counts with uncertainty for use in creating the stock portion of a stock-recruit model in the SRJPE.

The model also estimates a conversion rate, or proportion of adults that pass though the video counting systems that become spawning adults (i.e. prespawn mortality). The P2S can also be used for forecasting; it takes in a standardized environmental covariate and uses this variable to predict spawners from upstream passage counts. In this way, the P2S provides resiliency for years where data may be missing (i.e. years where upstream passage data were collected but spawner surveys were not conducted).

Conceptual model

This is a DRAFT conceptual model detailing where submodels fit into the overall SRJPE model ecosystem.

Submodel Architecture

The submodel takes observed data (in orange) and predicts spawner counts (in pink). Parameters estimated by the model are light pink; for more information, see documentation.

Model inputs

The model takes in two datasets:

Observed adult counts or estimates from all methods (upstream passage, holding surveys, redd surveys, and carcass surveys) aggregated by year and stream. This is in the SRJPEdata::observed_adult_input data object.
Observed environmental covariates aggregated by year within streams, and standardized (scaled to center on 0). This is in the SRJPEdata::adult_model_covariates_standard object.

Running the P2S submodel

The model is run for a given stream and environmental covariate.

Options for streams are battle creek, clear creek, deer creek, and mill creek.
Environmental covariates are water year type, growing degree days, and maximum flow.

# run the model for battle creek and water year type
battle_P2S_results <- run_passage_to_spawner_model(SRJPEdata::observed_adult_input,
                                                   SRJPEdata::adult_model_covariates_standard,
                                                   "battle creek",
                                                   "wy_type",
                                                   FALSE)
# run the model for clear creek and water year type
clear_P2S_results <- run_passage_to_spawner_model(SRJPEdata::observed_adult_input,
                                                  SRJPEdata::adult_model_covariates_standard,
                                                  "clear creek",
                                                  "wy_type",
                                                  FALSE)
# run the model for deer creek and water year type
deer_P2S_results <- run_passage_to_spawner_model(SRJPEdata::observed_adult_input,
                                                 SRJPEdata::adult_model_covariates_standard,
                                                 "deer creek",
                                                 "wy_type",
                                                 FALSE)
# run the model for mill creek and water year type
mill_P2S_results <- run_passage_to_spawner_model(SRJPEdata::observed_adult_input,
                                                 SRJPEdata::adult_model_covariates_standard,
                                                 "mill creek",
                                                 "wy_type",
                                                 FALSE)

Once the model has been fit to separate streams, you can combine them into one data frame:

# join model summaries
P2S_model_fits <- bind_rows(battle_P2S_results$formatted_pars,
                            clear_P2S_results$formatted_pars,
                            mill_P2S_results$formatted_pars,
                            deer_P2S_results$formatted_pars)

Model Output

The P2S model produces two objects when run:

a full_object, which contains all output of the STAN model (class stanfit)
formatted_pars, a data table with all parameter estimates and associated statistics.

The most recent results from fitting the model to all streams is stored as a data object SRJPEmodel::P2S_model_fits and contains the full parameter list, many of which are technical and not directly of interest to the SRJPEmodel ecosystem. SRJPEmodel has additional functions to extract parameter estimates of interest from this larger table and can quickly produce a table of predicted spawners by year and tributary.

Extract predicted spawners by year, with uncertainty

stream	year	median_predicted_spawners	lcl	ucl	data_type
battle creek	2001	30.72404	21.78930	41.77793	P2S_predicted_spawners
battle creek	2002	70.62890	56.14741	87.68848	P2S_predicted_spawners
battle creek	2003	152.91438	130.77486	178.05002	P2S_predicted_spawners
battle creek	2004	33.45492	24.34624	45.02828	P2S_predicted_spawners
battle creek	2005	44.07281	33.02084	57.61342	P2S_predicted_spawners

We can also see forecasted spawner count for a wet or dry year with uncertainty by looking at the abundance_forecast parameters, which use the average upstream passage as a predictor variable and water year type as the predictive covariate. Deer and Mill Creek model fits are limited in utility due to a lack of available data, so the confidence intervals for those tributaries are much greater than for Battle and Clear Creeks.

Resources

See data-raw/adult_model/passage_to_spawner_full_docmentation.Rmd for full documentation of development, testing, and results of the Passage to Spawner submodel. See adult data report for full documentation on adult Chinook salmon data collection.

Liz Stebbins, Ashley Vizek, Erin Cain, Josh Korman