Reference

Model and Submodels Functions Functions used as to run submodels/models
BTSPAS-X Functions to run BTSPAS-X
prepare_pCap_inputs()	Prepare inputs for pCap STAN model
prepare_abundance_inputs()	Prepare inputs for abundance model
prepare_mainstem_pCap_data()	Prepare mainstem inputs for abundance model
build_spline_data()	Prepare spline parameters object for BT-SPAS-X model
fit_pCap_model()	Fit pCap model
generate_lt_pCap_Us()	Generate lt_pCap_U values from the pCap model object
fit_abundance_model_BUGS()	Fit abundance model in BUGS.
plot_juv_data()	BT SPAS X raw data plots
generate_diagnostic_plot_juv()	BT SPAS X diagnostic plots
extract_abundance_estimates()	Extract parameter estimates from abundance BUGS model object
extract_pCap_estimates()	Extract parameter estimates from the pCap BUGS model object
run_abundance_workflow()	Run abundance BUGS workflow.
run_bt_spas_x_JPE_sites()	Run all JPE sites.
P2S Functions to run P2S
prepare_P2S_inputs()	Prepare data for P2S
fit_passage_to_spawner_model()	Fit Passage to Spawner (P2S) STAN Model
extract_P2S_estimates()	Extract parameter estimates from P2S
generate_results_plot_p2s()	P2S results plots
Survival Functions to run Survival Model
prepare_survival_inputs()	Prepare inputs for survival model
fit_survival_model()	Fit Survival Model
extract_survival_estimates()	Extract parameter estimates from the survival STAN model object
generate_survival_rate_plot()	Plot smolt survival rate
Stock Recruit Functions to run Stock recruit Model
prepare_stock_recruit_inputs()	Prepare inputs for stock-recruit model
fit_stock_recruit_model()	Fit stock-recruit model in STAN
extract_stock_recruit_estimates()	Extract stock-recruit parameter estimates
generate_results_plot_sr()	Stock-recruit results plots
generate_diagnostic_plot_sr()	Stock-recruit diagnostic plots
generate_diagnostic_plot_sr_covar()	Stock-recruit diagnostic plots
Within season Functions to run within season model
prepare_inseason_inputs()	Prepare Inputs for In-Season Model
fit_inseason_model()	Fit In-Season STAN Model
extract_inseason_estimates()	Extract Parameter Estimates from In-Season Model
generate_results_plot_inseason()	Inseason forecast plot
Model Data Additional data beyons SRJPEdata needed to run model
bt_spas_x_bayes_params	BT-SPAS-X BUGS parameters
bt_spas_x_model_code	BT-SPAS-X STAN model code
survival_model_code	Survival model code
p2s_model_code	Passage to Spawner model code
Helper and Storage Functions Functions used as to generate model data / format model outputs / and interface with the database
compare_P2S_model_covariates()	Compare Environmental Covariates in Passage to Spawner (P2S) Model
get_model_object()	Get Model Object
get_model_results_parameters()	Get Model Parameter Results
get_most_recent_model_objects()	Get Most Recent Model Objects
get_most_recent_model_results()	Get Most Recent Model Results
store_model_fit()	Store Model Fits
search_model_run()	Search Model Run
generate_diagnostic_plot()	Diagnostic plots
pin_model_data()	Model Data Pin