Package index • bboutools

Fitting Models Fit Bayesian and Maximum Likelihood survival and recruitment models.
`bb_fit_survival()`	Fit Survival Model
`bb_fit_survival_ml()`	Fit Survival Model with Maximum Likelihood
`bb_fit_recruitment()`	Fit Recruitment Model
`bb_fit_recruitment_ml()`	Fit Recruitment Model with Maximum Likelihood
Priors Specify Bayesian priors for model parameters.
`bb_priors_survival()`	Survival model default priors
`bb_priors_survival_national()`	Disturbance-informed national survival priors
`bb_priors_recruitment()`	Recruitment model default priors
`bb_priors_recruitment_national()`	Disturbance-informed national recruitment priors
Predictions Predict survival, recruitment, calf-cow ratio, growth, and population change.
`bb_predict_survival()`	Predict Survival
`bb_predict_survival_samples()`	Predict Survival Samples
`bb_predict_recruitment()`	Predict Recruitment
`bb_predict_recruitment_samples()`	Predict Recruitment Samples
`bb_predict_calf_cow_ratio()`	Predict Calf-Cow Ratio
`bb_predict_calf_cow_ratio_samples()`	Predict Calf-Cow Ratio Samples
`bb_predict_growth()` `bb_predict_lambda()`	Predict Population Growth Lambda
`bb_predict_growth_samples()`	Predict Population Growth Lambda Samples
`bb_predict_population_change()`	Predict Population Change
`bb_predict_population_change_samples()`	Predict Population Change Samples
Trend Predictions Predict trend lines for models fit with year_trend = TRUE.
`bb_predict_survival_trend()`	Predict Survival Trend
`bb_predict_survival_trend_samples()`	Predict Survival Trend Samples
`bb_predict_recruitment_trend()`	Predict Recruitment Trend
`bb_predict_recruitment_trend_samples()`	Predict Recruitment Trend Samples
`bb_predict_calf_cow_ratio_trend()`	Predict Calf-Cow Ratio Trend
`bb_predict_calf_cow_ratio_trend_samples()`	Predict Calf-Cow Ratio Trend Samples
Plotting Visualize model estimates and trends.
`bb_plot_year_survival()`	Plot Year Survival
`bb_plot_year_recruitment()`	Plot Year Recruitment
`bb_plot_year_calf_cow_ratio()`	Plot Year Calf-Cow Ratio
`bb_plot_year_growth()`	Plot Year Population Growth
`bb_plot_year_population_change()`	Plot Year Population Change
`bb_plot_year_trend_survival()`	Plot Annual Survival Trend
`bb_plot_year_trend_recruitment()`	Plot Annual Recruitment Trend
`bb_plot_year_trend_calf_cow_ratio()`	Plot Annual Calf-Cow Ratio Trend
`bb_plot_month_survival()`	Plot Monthly Survival
`bb_plot_year()`	Plot Year
`bb_plot_month()`	Plot Month
Model Summaries Extract coefficients, estimates, and model summaries.
`reexports` `augment` `coef` `glance` `logLik` `nobs` `predict` `tidy` `estimates` `nchains` `npars` `nterms` `niters` `rhat` `esr` `converged` `pars`	Objects exported from other packages
Convergence Diagnostics Assess MCMC convergence for Bayesian models.
`reexports` `augment` `coef` `glance` `logLik` `nobs` `predict` `tidy` `estimates` `nchains` `npars` `nterms` `niters` `rhat` `esr` `converged` `pars`	Objects exported from other packages
Model Properties Query model dimensions and extract components.
`samples()`	Get MCMC samples
`model_code()`	Get Model Code
`reexports` `augment` `coef` `glance` `logLik` `nobs` `predict` `tidy` `estimates` `nchains` `npars` `nterms` `niters` `rhat` `esr` `converged` `pars`	Objects exported from other packages
Model Code Build NIMBLE model code.
`model_survival()`	Build Nimble survival model.
`model_recruitment()`	Build Nimble recruitment model.
Deprecated
`bb_predict_growth()` `bb_predict_lambda()`	Predict Population Growth Lambda
Utilities
`licensing_md()`	Licensing Markdown
S3 Methods
`augment(<bboufit>)`	Get Augmented Data from bboufit Object
`augment(<bboufit_ml>)`	Get Augmented Data from bboufit_ml Object
`bb_plot_month()`	Plot Month
`bb_plot_month_survival()`	Plot Monthly Survival
`bb_plot_year()`	Plot Year
`bb_plot_year_calf_cow_ratio()`	Plot Year Calf-Cow Ratio
`bb_plot_year_recruitment()`	Plot Year Recruitment
`bb_plot_year_survival()`	Plot Year Survival
`bb_plot_year_trend_calf_cow_ratio()`	Plot Annual Calf-Cow Ratio Trend
`bb_plot_year_trend_recruitment()`	Plot Annual Recruitment Trend
`bb_plot_year_trend_survival()`	Plot Annual Survival Trend
`coef(<bboufit>)`	Get Tidy Tibble from bboufit Object.
`coef(<bboufit_ml>)`	Get Tidy Tibble from bboufit_ml Object.
`converged(<bboufit>)`	Get Convergence of bboufit Object
`converged(<bboufit_ml>)`	Get Convergence of bboufit_ml Object
`esr(<bboufit>)`	Get Effective Sample Rate of bboufit Object
`estimates(<bboufit>)`	Estimates for bboufit Object
`estimates(<bboufit_ml>)`	Estimates for bboufit_ml Object
`glance(<bboufit>)`	Get a Glance Summary of bboufit Object
`glance(<bboufit_ml>)`	Get a Glance Summary of bboufit_ml Object
`model_code()`	Get Model Code
`nchains(<bboufit>)`	Get Number of Chains from bboufit Object
`niters(<bboufit>)`	Get Number of Iterations from bboufit Object
`npars(<bboufit>)`	Get Number of Parameters from bboufit Object
`npars(<bboufit_ml>)`	Get Number of Parameters from bboufit_ml Object
`nterms(<bboufit>)`	Get Number of Terms from bboufit Object
`nterms(<bboufit_ml>)`	Get Number of Terms from bboufit_ml Object
`pars(<bboufit>)`	Get Parameters from bboufit Object
`pars(<bboufit_ml>)`	Get Parameters from bboufit_ml Object
`predict(<bboufit_recruitment>)`	Predict Recruitment
`predict(<bboufit_survival>)`	Predict Survival
`rhat(<bboufit>)`	Get Rhat of bboufit Object
`samples()`	Get MCMC samples
`tidy(<bboufit>)`	Get Tidy Tibble from bboufit Object.
`tidy(<bboufit_ml>)`	Get Tidy Tibble from bboufit_ml Object.

Reference

Fitting Models

Priors

Predictions

Trend Predictions

Plotting

Model Summaries

Convergence Diagnostics

Model Properties

Model Code

Deprecated

Utilities

S3 Methods