Package index • jsdmstan

Simulate data

Simulate data according to the jsdm model structures

jsdm_sim_data() gllvm_sim_data() mglmm_sim_data(): Generate simulated data within a variety of jSDM methodologies

rgampois() rlkj() rinvgamma() rstudentt(): Helper functions for simulating data

Model

Run jsdmstan models

stan_jsdm(): Fit jsdm models in Stan

stan_gllvm(): Alias for stan_jsdm with method = "gllvm"

stan_mglmm(): Alias for stan_jsdm with method = "mglmm"

update(<jsdmStanFit>): Update a jsdmStanFit model object with new data or Stan arguments

Set-up functions

Functions used to set up the prior structure (used in both data simulation and model fitting) and the Stan code used within model fitting

jsdm_stancode() print(<jsdmstan_model>): Make stancode for the jsdm model

jsdm_prior() print(<jsdmprior>): Create prior object for jsdmstan models and data simulation

Summaries

Extract useful quantities from the model objects. This includes overall summaries of model parameters and model diagnostics.

extract(): Extract samples from jsdmStanFit object

loo(<jsdmStanFit>): Efficient approximate leave-one-out cross-validation using the loo package

get_parnames() nuts_params(<jsdmStanFit>) log_posterior(<jsdmStanFit>) rhat(<jsdmStanFit>) neff_ratio(<jsdmStanFit>): Extract quantities useful for model summaries

print(<jsdmStanFit>): Print the default summary for the model

summary(<jsdmStanFit>): Summarise the model fit and data structure and give summaries for the parameters

print(<jsdmStanFamily>): Print jsdmStanFamily object

Graphical summaries

Plots of various model parameters, including jSDM specific summary plots as well as more general model summaries

corrplot(): Plot modelled correlations between species

envplot(): Plotting environmental effects on species

ordiplot(): Plotting an ordination plot for a GLLVM model

mcmc_plot(): MCMC plots implemented in bayesplot

plot(<jsdmStanFit>): Plot the traceplots and density plots for parameters within a jsdmStanFit object

Posterior prediction

Extract posterior distributions and predict from them, including graphical posterior checks

posterior_linpred(<jsdmStanFit>): Access the posterior distribution of the linear predictor

posterior_predict(<jsdmStanFit>): Draw from the posterior predictive distribution

posterior_shppred(): Access the posterior distribution of the linear predictor for the shape parameter

posterior_zipred(): Access the posterior distribution of the linear predictor for zero-inflation parameter

pp_check(<jsdmStanFit>): Posterior predictive checks for jsdmStanFit objects

multi_pp_check(): Multiple pp_check plots per species

jsdm_statsummary(): Extract site- or species-level summary statistics for predictions from a jsdmStanFit model

Other

Objects and classes used within jsdmstan

jsdmStanFit: jsdmStanFit class

jsdmStanFamily: jsdmStanFamily class

jsdmstan-package jsdmstan: The 'jsdmstan' package.

bunce71: Data from broadleaved woodlands across Great Britain, 1971

pinewood: Data from a survey of native pinewoods in Scotland, 1971