bio_to_math             Converts parameters from the biological scale
                        to the math (unconstrained) scale
build_orthogonal_matrix
                        Build an orthogonal matrix from a
                        real-parameter vector
convert_equivalence_class
                        Converts a set of parameters to other
                        representatives of the same equivalence class
create_mask             Create a parameter mask aligned with
                        'make_mask_names()'
create_param_vector_masked
                        Create a complete parameter vector with
                        canonical names (no NAs allowed)
dist_between_params     Distance in parameter space between two sets of
                        parameters
env_data_array          Get an array of environmental data from
                        presence-absence points.
example_1               Consolidated example data for the xsdm package
example_2               Consolidated example data for the xsdm. This is
                        environmental data array and an occurrence
                        presence absence vector of Ophisaurus
                        ventralis. A named list containing all example
                        datasets used in the package's documentation
                        and examples.
example_3               Consolidated example data for the xsdm. This is
                        environmental data array and an occurrence
                        presence absence vector Blarina carolinensis A
                        named list containing all example datasets used
                        in the package's documentation and examples.
expit                   Functions to take the expit of numerical
                        vectors. expit exp(x)/(1 + exp(x))
extract_orthogonal_matrix_parameters
                        Extract a math-scale real-parameter vector
                        corresponding to a special orthogonal matrix
habitat_suitability     Tiled habitat-suitability map from
                        environmental raster stacks
interpret_parameters    Tool to help interpret xsdm model parameters
like_ltsg               Compute likelihood for LTSG model
like_neg_ltsgr          Long-term stochastic growth rate worker
                        function for the xsdm model
log1mexp                Numerically stable 'log(1 - exp(-a))'
log1pexp                Numerically stable 'log(1 + exp(x))'
log_prob_detect         Probability of detection of the species in each
                        location
log_prob_detect_cpp     Compute log detection probabilities from a flat
                        environmental data vector
loglik_bio              Log-likelihood function for the xsdm model,
                        parameters on the biological scale.
loglik_bio_cpp          Pure-C++ log-likelihood for the xsdm model
                        (biological-scale parameters)
loglik_math             Log-likelihood function for the xsdm model,
                        parameters on the math scale.
loglik_math_cpp         Pure-C++ log-likelihood for the xsdm model
                        (math-scale parameters)
make_mask_names         Function to facilitate the creation of the
                        argument 'mask' to the function 'loglik_math'
math_to_bio             Convert parameters from the math scale to the
                        biological scale
num_env_var             Get the number of environmental variables given
                        the number of parameters
num_par                 Get the number of parameters of the main xsdm
                        model given the number of environmental
                        variables to be considered
optimize_likelihood     Optimize the xsdm log-likelihood from multiple
                        starts (ucminfcpp)
profile_likelihood      Basic (non-adaptive) tool for profiling the
                        likelihood
start_parms             Starting parameters for the optimization
vsp                     Generate a virtual species probability map with
                        presence/absence sampling
xsdm-package            xsdm: Demographic Approach to Species
                        Distribution Model
