# Demographic Approach to Species Distribution Model

## Documentation for package ‘xsdm’ version 1.0.2

- DESCRIPTION file.
- Package NEWS.

## Help Pages

xsdm-package | xsdm: Demographic Approach to Species Distribution Model
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))'
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)
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
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 | xsdm: Demographic Approach to Species Distribution Model