calc_linex_a            estimate optimal 'a' parameter for linex loss
                        function
convert.HDS.to.mcmc     function to convert HierarchicalDS MCMC list
                        vector (used in estimation) into an mcmc object
                        (cf. coda package)
generate_inits          generate initial values for MCMC chain if not
                        already specified by user
generate_inits_misID    generate initial values for misID model if not
                        already specified by user
get_confusion_array     Fill confusion array - one confusion matrix for
                        each individual (DEPRECATED)
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 user-specified formula object
hierarchical_DS         Primary function for hierarchical, areal
                        analysis of distance sampling data.  This
                        function pre-processes data and calls other
                        functions to perform the analysis, and is the
                        only function the user needs to call
                        themselves.
linear_adj              Produce an adjacency matrix for a vector
log_lambda_gradient     compute the first derivative of log_lambda
                        likelihood component for Langevin-Hastings
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 spatio-temporal models in mind
plot_obs_pred           plot 'observed' versus predicted values for
                        abundance of each species at each transect
post_loss               function to calculate posterior predictive loss
                        given the output object from hierarchicalDS
probit.fct              Mrds probit detection and related functions
rect_adj                Produce an RW1 adjacency matrix for a
                        rectangular grid for use with areal spatial
                        models (queens move)
rect_adj_RW2            Produce an RW2 Adjacency matrix for a
                        rectangular grid for use with areal spatial
                        models. This formulation uses cofficients
                        inspired by a thin plate spline, as described
                        in Rue & Held, section 3.4.2 Here I'm
                        outputting an adjacency matrix of 'neighbor
                        weights' which makes Q construction for regular
                        latices easy to do when not trying to make
                        inference about all cells (i.e., one can just
                        eliminate rows and columns associated with
                        cells one isn't interested in and set
                        Q=-Adj+Diag(sum(Adj))
rrw                     SIMULATE AN ICAR PROCESS
sim_out                 MCMC output from running example in
                        Hierarchical DS
simdata                 MCMC output from running example in
                        Hierarchical DS
simulate_data           function to simulate double observer spatial
                        distance sampling data subject to possible zero
                        inflation and species misidentification
square_adj              Produce an adjacency matrix for a square grid
stack_data              function to stack data (going from three
                        dimensional array to a two dimensional array
                        including only "existing" animals
stack_data_misID        function to stack data for midID updates (going
                        from four dimensional array to a two
                        dimensional array including observed groups
summary_N               calculate parameter estimates and confidence
                        intervals for various loss functions
switch_pdf              function to calculate the joint pdf for a
                        sample of values from one of a number of pdfs
switch_sample           function to sample from a specified probability
                        density function
switch_sample_prior     function to sample from hyperpriors of a
                        specified probability density function; note
                        that initial values for sigma of lognormal
                        random effects are fixed to a small value
                        (0.05) to prevent numerical errors
table.mcmc              function to export posterior summaries from an
                        mcmc object to a table
