bboutools/_pkgdown.yml at main · poissonconsulting/bboutools · GitHub

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url: https://poissonconsulting.github.io/bboutools/
template:
  package: poissontemplate

articles:
- title: Articles
  contents:
    - bboutools
    - articles/methods
    - articles/priors
    - articles/extensions

reference:
- title: "Fitting Models"
  desc: "Fit Bayesian and Maximum Likelihood survival and recruitment models."
  contents:
    - bb_fit_survival
    - bb_fit_survival_ml
    - bb_fit_recruitment
    - bb_fit_recruitment_ml

- title: "Priors"
  desc: "Specify Bayesian priors for model parameters."
  contents:
    - bb_priors_survival
    - bb_priors_survival_national
    - bb_priors_recruitment
    - bb_priors_recruitment_national

- title: "Predictions"
  desc: "Predict survival, recruitment, calf-cow ratio, growth, and population change."
  contents:
    - bb_predict_survival
    - bb_predict_survival_samples
    - bb_predict_recruitment
    - bb_predict_recruitment_samples
    - bb_predict_calf_cow_ratio
    - bb_predict_calf_cow_ratio_samples
    - bb_predict_growth
    - bb_predict_growth_samples
    - bb_predict_population_change
    - bb_predict_population_change_samples

- title: "Trend Predictions"
  desc: "Predict trend lines for models fit with year_trend = TRUE."
  contents:
    - bb_predict_survival_trend
    - bb_predict_survival_trend_samples
    - bb_predict_recruitment_trend
    - bb_predict_recruitment_trend_samples
    - bb_predict_calf_cow_ratio_trend
    - bb_predict_calf_cow_ratio_trend_samples

- title: "Plotting"
  desc: "Visualize model estimates and trends."
  contents:
    - bb_plot_year_survival
    - bb_plot_year_recruitment
    - bb_plot_year_calf_cow_ratio
    - bb_plot_year_growth
    - bb_plot_year_population_change
    - bb_plot_year_trend_survival
    - bb_plot_year_trend_recruitment
    - bb_plot_year_trend_calf_cow_ratio
    - bb_plot_month_survival
    - bb_plot_year
    - bb_plot_month

- title: "Model Summaries"
  desc: "Extract coefficients, estimates, and model summaries."
  contents:
    - coef
    - tidy
    - glance
    - estimates
    - augment
    - predict
    - logLik

- title: "Convergence Diagnostics"
  desc: "Assess MCMC convergence for Bayesian models."
  contents:
    - converged
    - rhat
    - esr

- title: "Model Properties"
  desc: "Query model dimensions and extract components."
  contents:
    - samples
    - model_code
    - pars
    - npars
    - nterms
    - nobs
    - nchains
    - niters

- title: "Model Code"
  desc: "Build NIMBLE model code."
  contents:
    - model_survival
    - model_recruitment

- title: "Deprecated"
  contents:
    - bb_predict_lambda

- title: "Utilities"
  contents:
    - licensing_md

- title: "S3 Methods"
  contents:
    - matches("\\.")