| calc_linex_a | estimate optimal 'a' parameter for linex loss function |
| convert.HDS.to.mcmc | function to convert HierarchicalDS MCMC list vector (used in... |
| generate_inits | generate initial values for MCMC chain if not already... |
| generate_inits_misID | generate initial values for misID model if not already... |
| get_confusion_array | Fill confusion array - one confusion matrix for each... |
| get_confusion_mat | Fill a list with confusion matrices for each record |
| get_mod_matrix | function to produce a design matrix given a dataset and... |
| hierarchical_DS | Primary function for hierarchical, areal analysis of distance... |
| linear_adj | Produce an adjacency matrix for a vector |
| log_lambda_gradient | compute the first derivative of log_lambda likelihood... |
| log_lambda_log_likelihood | compute the likelihood for nu parameters |
| mcmc_ds | Function for MCMC analysis |
| plot_N_map | function to plot a map of abundance. this was developed for... |
| plot_obs_pred | plot 'observed' versus predicted values for abundance of each... |
| post_loss | function to calculate posterior predictive loss given the... |
| probit.fct | Mrds probit detection and related functions |
| rect_adj | Produce an RW1 adjacency matrix for a rectangular grid for... |
| rect_adj_RW2 | Produce an RW2 Adjacency matrix for a rectangular grid for... |
| rrw | SIMULATE AN ICAR PROCESS |
| simdata | MCMC output from running example in Hierarchical DS |
| sim_out | MCMC output from running example in Hierarchical DS |
| simulate_data | function to simulate double observer spatial distance... |
| square_adj | Produce an adjacency matrix for a square grid |
| stack_data | function to stack data (going from three dimensional array to... |
| stack_data_misID | function to stack data for midID updates (going from four... |
| summary_N | calculate parameter estimates and confidence intervals for... |
| switch_pdf | function to calculate the joint pdf for a sample of values... |
| switch_sample | function to sample from a specified probability density... |
| switch_sample_prior | function to sample from hyperpriors of a specified... |
| table.mcmc | function to export posterior summaries from an mcmc object to... |
