Package

Package description

jSDM-package

joint species distribution models

jSDM

Functions for joint species distribution models

jSDM_binomial_probit()

Binomial probit regression

jSDM_binomial_probit_sp_constrained

Binomial probit regression with the chosen constrained species

jSDM_binomial_probit_long_format()

Binomial probit regression on long format data

jSDM_binomial_logit()

Binomial logistic regression

jSDM_poisson_log()

Poisson regression with log link function

Data

Data-sets used in examples

frogs

frogs dataset

mosquitos

mosquitos dataset

eucalypts

eucalypts dataset

fungi

fungi dataset

birds

birds dataset

mites

mites dataset

aravo

Distribution of Alpine plants in Aravo (Valloire, France)

Miscellaneous

Miscellaneous functions

logit()

Generalized logit function

inv_logit()

Generalized inverse logit function

get_residual_cor()

Calculate the residual correlation matrix from a latent variable model (LVM)

get_enviro_cor()

Extract covariances and correlations due to shared environmental responses

plot_residual_cor()

Plot the residual correlation matrix from a latent variable model (LVM).

plot_associations()

plot_associations plot species-species associations

Predict

S3 method to predict from a jSDM model

predict(<jSDM>)

Predict method for models fitted with jSDM