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.