BH_er_lambdacov_global_effectcov_global_responsecov_global: Effect response Beverton-Holt model with covariate effects on...

In ibartomeus/cxr: A Toolbox for Modelling Species Coexistence in R

Effect response Beverton-Holt model with covariate effects on lambda, effect, and response

Description

The function for calculating fecundity given effect and response values is taken from Godoy et al. (2014). Note that, as e and r are not pair-specific, all species parameters are fit in the same function.

Usage

BH_er_lambdacov_global_effectcov_global_responsecov_global(
  par,
  fitness,
  target,
  density,
  covariates,
  fixed_parameters
)

Arguments

par	1d vector with initial parameters in the order: lambda,lambda_cov,effect,effect_cov,response,response_cov,sigma
fitness	1d vector with fitness observations
target	matrix with species in rows, observations in columns. Value is 1 if a species is focal for a given observation, 0 otherwise.
density	matrix with species in rows, observations in columns. Value is density of each sp as neighbour for each observation.
covariates	numeric dataframe or matrix with observations in rows and covariates in columns. Each cell is the value of a covariate in a given observation
fixed_parameters	optional list specifying values of fixed parameters, with components "lambda","lambda_cov","effect","effect_cov", "response","response_cov".

Value

log-likelihood value

ibartomeus/cxr documentation built on Feb. 5, 2025, 1:01 p.m.