Man pages for philpatton/cowbird
Recreate analysis in Patton et al (TBD)
| add_covariate | Add the covariate level (e.g., habitat:forest) to the table |
| add_model | Add the model type (observation, detection) to the table |
| add_parm | Add a latex style parameter name to the table |
| add_species | Add the species to the table |
| bundle_mcmc_samples | Function to bundles mcmc samples into a list |
| calc_elppd | Calculate elppd |
| calc_likelihood_cowbird | Function to calculate the likelihood of the cowbird model |
| calc_likelihood_host | Function to calculate the likelihood of the host model |
| calc_naive_state_cowbird | Naive occurrence state for the cowbird |
| calc_naive_state_host | Naive occurrence state for hosts |
| calc_pdwaic | Calculate pdwaic |
| calc_site_likelihood | Calculate the likelihood of the detections at a site |
| calc_waic | Calculate WAIC |
| check_all_models | Check all models |
| check_model | Check a model |
| cooccur_probs | Generate co-occurrence plot data.frame |
| cowbird_data | Detection data for the Shiny Cowbird and its Puerto Rican... |
| effective_sample_size | Calculate the effective sample size |
| evaluate_all_models | Function to estimate the WAIC for all three models model |
| evaluate_model | Function to estimate the WAIC for a model |
| extract_coda_samples | Extract MCMC samples from fit_model for use in coda. |
| fit_all_models | Fit every cowbird-host co-occurrence model |
| fit_model | Fit the cowbird-host co-occurrence models |
| gelman_rubin | Calculate the gelman rubin statistic |
| get_all_parameters | Generates vector of the primary parameters |
| get_checking_parameters | Generates vector of parameter needed to do posterior... |
| get_evaluation_parameters | Generates vector of parameter needed to evaluate models |
| get_habitat_names | Get the names of the habitats |
| get_host_full_name | Get the full names of the host species |
| get_host_names | Get the abbreviated names of the host species |
| get_hyper_parameters | Generates vector of of the hyper parameters |
| get_mcmc_ci | Extract the credible interval from the MCMC summary |
| get_mcmc_mean | Extract the mean from the MCMC summary |
| get_o | Create matrix containing the visit covariates affecting the... |
| get_predicition_parameters | Generates vector of parameter used in model predictions |
| get_table1_parameters | Generates vector of parameters in the Table 1 |
| get_table2_parameters | Generates vector of parameters in the Table 2 |
| get_table3_parameters | Generates vector of parameters in the Table 3 |
| get_v | Create matrix containing the site covariates affecting the... |
| get_w | Create matrix containing the site covariates affecting the... |
| get_x | Create matrix containing the host detections |
| get_y | Create matrix containing the cowbird detections |
| initialize_values | Initialize values for MCMC |
| is_detected | Determine if the species was detected |
| just_host | Make data.frame used in figure five |
| make_annotation_df | Generate data.frame used in 'plot_ppc' |
| make_data_list | Make a list of data for easy model fitting |
| make_figure_five | Generate Figure 5 |
| make_figure_four | Generate Figure 4 |
| make_figure_three | Generate Figure 3 |
| make_figure_two | Generate Figure 2 |
| make_table | Make a table |
| make_table_one | Make table 1 |
| make_table_three | Make table 3 |
| make_table_two | Make table 2 |
| multispecies_naive_state | Naive occurrence state for multiple species |
| plot_ppc_individual | Generate posterior predictive checking plots |
| ppc_table | Tabulate results of posterior predictive check |
| save_figure_five | Save Figure 5 |
| save_figure_four | Save Figure 4 |
| save_figure_three | Save Figure 3 |
| save_ppc | Save Figure 2 |
| sites_with_both | Make data.frame used in figure four |
| sites_with_both_observed | The observed number of sites with cowbird and each host |
| sites_with_both_predicted | The predicted number of sites with cowbird and each host |
| summarize_mcmc | Summarize the MCMC output |
