Package index • kelpbio

Fitting Models

Fit Bayesian Stan models.

kb_fit_weight_nereo(): Fit a Nereocystis Weight Model
kb_fit_progress(): Completed Fraction of a Running Fit

Priors

Specify priors for model parameters.

kb_priors_weight_nereo(): Default Priors for the Nereocystis Weight Model
kb_prior_normal(): Normal Prior
kb_prior_exponential(): Exponential Prior

Data

Validate and explore input data.

kb_check_data_weight_nereo(): Validate Nereocystis Weight Model Data
data_weight_sim_nereo: Simulated Nereocystis Weight Dataset
fit_weight_sim_nereo: Example Weight Model Fit

Predictions and Plotting

Predict and visualise model output.

kb_predict_weight(): Predict Weight for New Data
kb_predict_weight_by(): Predict Weight Over a Diameter Sequence by Grouping Factor
kb_plot_predictions(): Plot Model Predictions

Model Summaries and Diagnostics

Summarise fits, extract coefficients and draws, and assess convergence.

samples(): Posterior Draws
kb_stancode(): Stan Source for a Model Fit
tidy(<kb_fit_weight>): Tidy a Weight Model Fit
coef(<kb_fit>): Coefficients of a Model Fit
glance(<kb_fit>): Model Fit Diagnostic Summary
summary(<kb_fit>): Summarise a Model Fit
augment(<kb_fit>): Augment Model Data
converged(<kb_fit>): Convergence of a Model Fit
prior_summary(<kb_fit>): Prior Summary
log_lik(<kb_fit>): Pointwise Log-Likelihood
fitted(<kb_fit_weight>): Fitted Weights
residuals(<kb_fit_weight>): Deviance Residuals
predict(<kb_fit_weight>): Predict Method for a Weight Model Fit
posterior_epred(<kb_fit_weight>): Expected Weight Posterior Draws
posterior_linpred(<kb_fit_weight>): Linear-Predictor Posterior Draws
posterior_predict(<kb_fit_weight>): Posterior-Predictive Weight Draws
autoplot(<kb_predictions>): Autoplot Method for Predictions