Package index • salmonIPM

All functions

as.matrix(<salmonIPMfit>) as.array(<salmonIPMfit>) as.data.frame(<salmonIPMfit>): Extract posterior samples as a matrix, array or data frame

dist_gnormal(): Wrapper for gnorm::gnorm() distribution using distributional::dist_wrap()

dist_lkjcorr_marginal(): Wrapper for ggdist::lkjcorr_marginal() distribution using distributional::dist_wrap()

as_draws(<salmonIPMfit>) as_draws_matrix(<salmonIPMfit>) as_draws_array(<salmonIPMfit>) as_draws_df(<salmonIPMfit>) as_draws_list(<salmonIPMfit>) as_draws_rvars(<salmonIPMfit>): Create a draws object from a salmonIPMfit object

draws_df_lower_tri(): Remove redundant correlation matrix elements from a draws data frame

extract1(): Extract posterior samples for a single parameter

get_prior_info(): Extract prior info from Stan-formatted data and model code

include_pars(): Select parameters to include

launch_shinystan(<salmonIPMfit>): Launch the ShinyStan GUI with salmonIPM models

log_lik(<salmonIPMfit>) nsamples(<salmonIPMfit>): Pointwise log-likelihood matrix

loo(<salmonIPMfit>): Information criteria and cross-validation

par_defs(): Definitions of parameters and states in a salmonIPM model

par_model_matrix(): Helper function to construct covariate model matrices from a list of two-sided formulas.

plot_prior_posterior(): Plot prior and posterior distributions of model hyperparameters

print(<salmonIPMfit>): Print method for salmonIPMfit objects

normal() gnormal() lognormal() beta() dirichlet() uniform() lkj_corr(): Prior distributions

prior_summary(<salmonIPMfit>): Summarize the priors used in a salmonIPM model

run_recon(): Perform run reconstruction on brood table data

salmonIPM(): Fit an IPM or run-reconstruction regression model

salmonIPMfit(): Fitted model objects: the salmonIPMfit class

simIPM(): Simulate data from a salmonid IPM

SR(): Spawner-recruit functions

stan_data(): Prepare input data for IPMs or run-reconstruction models

stan_init(): Generate initial values for fitting IPMs or run-reconstruction spawner-recruit models.

stan_mean(): Extract posterior means from salmonIPMfit object

stan_pars(): Return the (hyper)parameters and states in a specified salmonIPM model

stan_prior(): Validate prior specification for an integrated spawner-recruit model.

summary(<salmonIPMfit>): Summary method for salmonIPMfit objects

test_unicode(): Test if unicode is rendering in test_unicode.Rd

validate_RRS(): Validate RRS specification