jSDM_gaussian
for fitting joint species distribution models from continuous Gaussian
data, including an overdispersion parameter.terra
instead of
raster
and sp
, which are depreciated, in the
vignette Estimation
of Madagascar’s plant biodiversity.get_residual_cor
and plot_residual_cor
functions.jSDM_binomial_probit_sp_constrained
which aims to improve the convergence of latent variable models fitting
by selecting the species constrained to have positive values of factor
loadings jSDM_binomial_probit
,
jSDM_binomial_logit
and jSDM_poisson_log
functions to take into account interactions between species-specific
traits and the environment in estimating species effects.jSDM_binomial_probit_block
and
jSDM_binomial_probit_block_long_format
renamed jSDM_binomial_probit
and jSDM_binomial_probit_long_format
.plot_associations
to plot species-species associations.roxygen2
for documentation and NAMESPACEjSDM_binomial_probit_block
the function
jSDM_probit_block
.jSDM_binomial_probit_block_long_format
for
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_log
for 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_logit
for 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_cor
to extract covariances and correlations due to shared environmental
responses.jSDM-package
documentationmosquitos
,
fungi
,
eucalypts
,
birds
,
mites
,
aravo
).pkgdown
to build package website.mirror server hosted at Truenetwork, Russian Federation.