Files in philpatton/cowbird

Recreate analysis in Patton et al (TBD)

R/bundle_mcmc_samples.R R/calc_naive_state.R R/calc_site_likelihood.R R/calc_waic.R R/check_all_models.R R/check_model.R R/cowbird_data.R R/effective_sample_size.R R/evaluate_all_models.R R/evaluate_model.R R/extract_coda_samples.R R/fit_all_models.R R/fit_model.R R/gelman_rubin.R R/get_names.R R/get_parameters.R R/initialize_values.R R/make_data_list.R R/make_figure_five.R R/make_figure_four.R R/make_figure_three.R R/make_figure_two.R R/make_plots.R R/make_tables.R R/ppc_table.R R/summarize_mcmc_samples.R README.md man/add_covariate.Rd man/add_model.Rd man/add_parm.Rd man/add_species.Rd man/bundle_mcmc_samples.Rd man/calc_elppd.Rd man/calc_likelihood_cowbird.Rd man/calc_likelihood_host.Rd man/calc_naive_state_cowbird.Rd man/calc_naive_state_host.Rd man/calc_pdwaic.Rd man/calc_site_likelihood.Rd man/calc_waic.Rd man/check_all_models.Rd man/check_model.Rd man/cooccur_probs.Rd man/cowbird_data.Rd man/effective_sample_size.Rd man/evaluate_all_models.Rd man/evaluate_model.Rd man/extract_coda_samples.Rd man/fit_all_models.Rd man/fit_model.Rd man/gelman_rubin.Rd man/get_all_parameters.Rd man/get_checking_parameters.Rd man/get_evaluation_parameters.Rd man/get_habitat_names.Rd man/get_host_full_name.Rd man/get_host_names.Rd man/get_hyper_parameters.Rd man/get_mcmc_ci.Rd man/get_mcmc_mean.Rd man/get_o.Rd man/get_predicition_parameters.Rd man/get_table1_parameters.Rd man/get_table2_parameters.Rd man/get_table3_parameters.Rd man/get_v.Rd man/get_w.Rd man/get_x.Rd man/get_y.Rd man/initialize_values.Rd man/is_detected.Rd man/just_host.Rd man/make_annotation_df.Rd man/make_data_list.Rd man/make_figure_five.Rd man/make_figure_four.Rd man/make_figure_three.Rd man/make_figure_two.Rd man/make_table.Rd man/make_table_one.Rd man/make_table_three.Rd man/make_table_two.Rd man/multispecies_naive_state.Rd man/plot_ppc_individual.Rd man/ppc_table.Rd man/save_figure_five.Rd man/save_figure_four.Rd man/save_figure_three.Rd man/save_ppc.Rd man/sites_with_both.Rd man/sites_with_both_observed.Rd man/sites_with_both_predicted.Rd man/summarize_mcmc.Rd tests/testthat.R tests/testthat/test_all_models.R tests/testthat/test_inits.R tests/testthat/test_model1.R tests/testthat/test_model2.R tests/testthat/test_model3.R vignettes/cowbird.Rmd