`NEWS.md`

- New function
`jSDM_gaussian`

for fitting joint species distribution models from continuous Gaussian data, including an overdispersion parameter. - Use of the R package
`terra`

instead of`raster`

and`sp`

, which are depreciated, in the vignette Estimation of Madagascar’s plant biodiversity.

- Add the possibility to consider only significant correlations in the
`get_residual_cor`

and`plot_residual_cor`

functions. - Documentation correction

- New function
`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*λ*and new vignette Bernoulli probit regression with selected constrained species to illustrate its use. - New vignette Estimation of Madagascar’s plant biodiversity available.

- Add the possibility of considering an additional hierarchical level in the Bayesian models of the
`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. - New vignette Bernoulli probit regression including species traits available.
- Separate the drawing of species effects beta and factor loading lambda in the functions
`jSDM_binomial_probit_block`

and`jSDM_binomial_probit_block_long_format`

renamed`jSDM_binomial_probit`

and`jSDM_binomial_probit_long_format`

. - New function
`plot_associations`

to plot species-species associations.

- Use of
`roxygen2`

for documentation and NAMESPACE - Rename
`jSDM_binomial_probit_block`

the function`jSDM_probit_block`

. - New function
`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. - New function
`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). - New function
`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). - Functions to fit models in which site effects are included as fixed effects, as random effects or not included and with or without latent variables.
- New function
`get_enviro_cor`

to extract covariances and correlations due to shared environmental responses. - Complete
`jSDM-package`

documentation - Add datasets (
`mosquitos`

,`fungi`

,`eucalypts`

,`birds`

,`mites`

,`aravo`

). - Seven new vignettes (Bayesian inference methods, Poisson log-linear regression, Bernoulli probit regression, Bernoulli probit regression with missing data and species traits, Binomial logistic regression, Running jSDM in parallel, Comparing SDMs and JSDMs and Comparison jSDM-Hmsc) are available.
- Complete and correct the vignette Comparison jSDM-boral.
- Add Code of conduct and Contributing section
- New package website available on GitHub: https://ecology.ghislainv.fr/jSDM/.

- First version of the jSDM R package
- Use of Rcpp and C++ code for Gibbs sampling
- Use of GSL (RcppGSL) for random draws
- Use of Armadillo (RcppArmadillo) for vector and matrix operations
- Functions to fit models from Warton et al. 2014
*Trends in Ecology and Evolution*(doi:10.1016/j.tree.2015.09.007). - We use
`pkgdown`

to build package website. - Package website available on GitHub: https://ecology.ghislainv.fr/jSDM/.

Developed by Jeanne Clément, Ghislain Vieilledent, .

Site built with pkgdown 2.0.7.