jSDM_gaussianfor fitting joint species distribution models from continuous Gaussian data, including an overdispersion parameter.
sp, which are depreciated, in the vignette Estimation of Madagascar’s plant biodiversity.
jSDM_binomial_probit_sp_constrainedwhich aims to improve the convergence of latent variable models fitting by selecting the species constrained to have positive values of factor loadings λ and new vignette Bernoulli probit regression with selected constrained species to illustrate its use.
jSDM_poisson_logfunctions to take into account interactions between species-specific traits and the environment in estimating species effects.
plot_associationsto plot species-species associations.
roxygen2for documentation and NAMESPACE
jSDM_binomial_probit_block_long_formatfor fitting joint species distribution models from presence-absence data in long format able to handle missing observations, multiple visits at sites and to integer species traits as explanatory variables.
jSDM_poisson_logfor fitting joint species distribution models from abundance data inspired by Hui and Francis K. C. 2016 Methods in Ecology and Evolution (doi:10.1111/2041-210X.12514).
jSDM_binomial_logitfor fitting joint species distribution models from presence-absence data at multiple-visited sites using a bayesian inference method inspired by Albert, James H. and Chib Siddhartha 1993 Journal of the American Statistical Association (doi:10.1080/01621459.1993.10476321).
get_enviro_corto extract covariances and correlations due to shared environmental responses.
pkgdownto build package website.