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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 an occurence presence absence vector of Ophiurus 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 an occurence 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 xsdm-package
xsdm: Demographic Approach to Species Distribution Model