Demographic Approach to Species Distribution Model

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Documentation for package ‘xsdm’ version 1.0.2

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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