API for ubms
Bayesian Models for Data from Unmarked Animals using 'Stan'
| Global functions | |
|---|---|
| $,ubmsFitList-method | Man page |
| Nmix_chisq | Source code |
| RSR | Man page Source code |
| Z_matrix | Source code |
| [,ubmsFit,character,missing,missing-method | Man page |
| [,ubmsFitList,numeric,missing,missing-method | Man page |
| [,ubmsSubmodelList,character,missing,missing-method | Man page |
| [[,ubmsFitList,numeric,missing-method | Man page |
| add_placeholder_priors | Source code |
| autoscale_prior | Source code |
| b_names | Source code |
| b_par | Source code |
| beta_names | Source code |
| beta_par | Source code |
| build_stan_inputs | Source code |
| calculate_par | Source code |
| cauchy | Man page Source code |
| check_formula | Source code |
| check_newdata | Source code |
| check_return_inputs | Source code |
| check_type | Source code |
| coef,ubmsFit-method | Man page |
| col_is_factor | Source code |
| combine_same_name | Source code |
| dist_code | Source code |
| distprob_exp_line | Source code |
| distprob_exp_point | Source code |
| distprob_haz_line | Source code |
| distprob_haz_point | Source code |
| distprob_normal_line | Source code |
| distprob_normal_point | Source code |
| drop_final_year | Source code |
| empty_loo | Source code |
| exp_counts_occu | Source code |
| exp_counts_occuRN | Source code |
| expand_model_matrix | Source code |
| expand_prior | Source code |
| expect_RMSE | Source code |
| expect_between | Source code |
| extract,ubmsFit-method | Man page |
| extract_log_lik | Man page |
| extract_log_lik,ubmsFit-method | Man page |
| extract_log_lik,ubmsFitDistsamp-method | Man page |
| extract_missing_sites | Source code |
| extract_posterior | Source code |
| fitList | Man page |
| fitList,list-method | Man page |
| fitList,ubmsFit-method | Man page |
| fit_class | Source code |
| fit_model | Source code |
| fitted,ubmsFit-method | Man page |
| gamma | Man page Source code |
| generate_inds | Source code |
| getY,ubmsFit-method | Man page |
| get_area | Source code |
| get_area_adjust | Source code |
| get_baseline_df | Source code |
| get_binned_residuals | Source code |
| get_breaks | Source code |
| get_cohorts | Source code |
| get_conv_const | Source code |
| get_detfun | Source code |
| get_elapsed_time,ubmsFit-method | Man page |
| get_group_vars | Source code |
| get_hist_data | Source code |
| get_link_name | Source code |
| get_loglik_colext | Source code |
| get_loglik_multinomPois | Source code |
| get_loglik_occu | Source code |
| get_loglik_occuRN | Source code |
| get_loglik_occuTTD | Source code |
| get_loglik_pcount | Source code |
| get_loo | Source code |
| get_margplot_data | Source code |
| get_max_obs | Source code |
| get_mean_line | Source code |
| get_n_pers | Source code |
| get_nrandom | Source code |
| get_obs_counts | Source code |
| get_p_for_multinom | Source code |
| get_pi_for_multinom | Source code |
| get_pifun_type | Source code |
| get_reTrms | Source code |
| get_row_reps | Source code |
| get_rsr_info | Source code |
| get_runtime | Source code |
| get_sample_lines | Source code |
| get_samples | Source code |
| get_sparse_Z | Source code |
| get_stancode,ubmsFit-method | Man page |
| get_xlev | Source code |
| gof | Man page |
| gof,ubmsFitAbun-method | Man page |
| gof,ubmsFitOccu-method | Man page |
| has_intercept | Source code |
| is_placeholder | Source code |
| kfold,ubmsFit-method | Man page |
| laplace | Man page Source code |
| ll_fold | Source code |
| logistic | Man page Source code |
| loglik_saved | Source code |
| loo,ubmsFit-method | Man page |
| marg_factor_plot | Source code |
| marg_numeric_plot | Source code |
| marginal_covariate_plot | Source code |
| modSel,ubmsFitList-method | Man page |
| name_to_modelcode | Source code |
| name_to_stanmodel | Source code |
| names,ubmsFit-method | Man page |
| names,ubmsFitList-method | Man page |
| normal | Man page Source code |
| nsamples,ubmsFit-method | Man page |
| null_prior | Source code |
| placeholderSubmodel | Source code |
| plot,ubmsFit,ANY-method | Man page |
| plot,ubmsGOF,ANY-method | Man page |
| plot_RSR | Source code |
| plot_binned_residuals | Source code |
| plot_effects | Man page |
| plot_effects,ubmsFit-method | Man page |
| plot_marginal | Man page |
| plot_marginal,ubmsFit-method | Man page |
| plot_pearson_residuals | Source code |
| plot_posteriors | Man page |
| plot_posteriors,ubmsFit-method | Man page |
| plot_residuals | Man page |
| plot_residuals,ubmsFit-method | Man page |
| plot_spatial | Man page Source code |
| plot_theme | Source code |
| posterior_linpred | Man page |
| posterior_linpred,ubmsFit-method | Man page |
| posterior_predict | Man page |
| posterior_predict,ubmsFit-method | Man page |
| predict | Man page |
| predict,ubmsFit-method | Man page |
| predict_raster | Source code |
| predict_terra | Source code |
| priors | Man page |
| process_coef_prior | Source code |
| process_covs | Source code |
| process_int_prior | Source code |
| process_sigma_prior | Source code |
| process_stanfit | Source code |
| process_z | Source code |
| projected | Man page |
| projected,ubmsFitColext-method | Man page |
| ranef | Man page |
| ranef,ubmsFit-method | Man page |
| rebuild_inputs | Source code |
| remove_RSR | Source code |
| remove_offset | Source code |
| remove_placeholders | Source code |
| removed_sites | Source code |
| residuals,ubmsFit-method | Man page |
| sig_par | Source code |
| sigma_names | Source code |
| sim_projected | Source code |
| sim_turnover | Source code |
| simz_multinom | Source code |
| simz_occuRN | Source code |
| simz_pcount | Source code |
| split_formula | Source code |
| split_p_by_T | Source code |
| split_psi_by_T | Source code |
| split_response_by_T | Source code |
| stan_colext | Man page Source code |
| stan_distsamp | Man page Source code |
| stan_multinomPois | Man page Source code |
| stan_occu | Man page Source code |
| stan_occuRN | Man page Source code |
| stan_occuTTD | Man page Source code |
| stan_pcount | Man page Source code |
| student_t | Man page Source code |
| submodel_set_missing | Source code |
| submodel_types | Source code |
| summary,ubmsFit-method | Man page |
| traceplot,ubmsFit-method | Man page |
| turnover | Man page |
| turnover,ubmsFitColext-method | Man page |
| ubms | Man page |
| ubms-package | Man page |
| ubmsFit | Source code |
| ubmsFitList-extractors | Man page |
| ubmsGOF | Source code |
| ubmsResponse | Source code |
| ubmsResponseDistsamp | Source code |
| ubmsResponseMultinomPois | Source code |
| ubmsResponseOccuTTD | Source code |
| ubmsSubmodel | Source code |
| ubmsSubmodelList | Source code |
| ubmsSubmodelScalar | Source code |
| ubmsSubmodelSpatial | Source code |
| ubmsSubmodelTransition | Source code |
| uniform | Man page Source code |
| waic,ubmsFit-method | Man page |
| was_parallel | Source code |
| which_per_sampled | Source code |
