# A General Framework for Combining Ecosystem Models

## Documentation for package ‘EcoEnsemble’ version 1.2.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

EcoEnsemble-package | A general framework for combining ecosystem models
calc_ess | Generate samples from a fitted ensemble model to get MCMC effective sample size diagnostics
EcoEnsemble | A general framework for combining ecosystem models
EnsembleData | Constructor for the 'EnsembleData' class
EnsembleData-class | A class to hold the Ensemble data
EnsembleFit | The constructor for the 'EnsembleFit' object
EnsembleFit-class | A class to hold the samples or point estimates from the ensemble model.
EnsemblePrior | Constructor for the 'EnsemblePrior' class
EnsemblePrior-class | A class to hold the priors for the ensemble model.
EnsembleSample | A constructor for the 'EnsembleSample' object
EnsembleSample-class | A class to hold samples of the ensemble model
fit_ensemble_model | Fits the ensemble model
generate_sample | Generate samples from a fitted ensemble model.
generate_sample_array | Generate samples from a fitted ensemble model to get MCMC effective sample size diagnostics
gen_sample | Generate samples from a fitted ensemble model.
gen_sample_array | Generate samples from a fitted ensemble model to get MCMC effective sample size diagnostics
get_ESS_diag | Generate samples from a fitted ensemble model to get MCMC effective sample size diagnostics
get_mcmc_ensemble_model | Return the compiled ensemble model Stan object.
get_mle | Generate samples from a fitted ensemble model.
get_mle_array | Generate samples from a fitted ensemble model to get MCMC effective sample size diagnostics
get_parameters | Generate samples from a fitted ensemble model.
get_parameters_array | Generate samples from a fitted ensemble model to get MCMC effective sample size diagnostics
get_param_idx | Generate samples from a fitted ensemble model to get MCMC effective sample size diagnostics
get_transformed_data | Generate samples from a fitted ensemble model.
get_transformed_data_dri | Generate samples from a fitted ensemble model.
IndLTPrior | Constructor for the 'EnsemblePrior' class
IndLTPrior-class | A class to hold the priors for the ensemble model.
IndSTPrior | Constructor for the 'EnsemblePrior' class
IndSTPrior-class | A class to hold the priors for the ensemble model.
KalmanFilter_back | Backwards Kalman filter
plot.EnsembleSample | Plot the ensemble output
prior_ensemble_model | Generate samples of parameters from prior distribution
sample_prior | Generate samples of latent variables from prior predictive distribution
ShaSTPrior | Constructor for the 'EnsemblePrior' class
ShaSTPrior-class | A class to hold the priors for the ensemble model.
Sigma_ewe | Ecopath with EcoSim Sigma
Sigma_fs | FishSUMS Sigma
Sigma_lm | LeMans Sigma
Sigma_miz | mizer Sigma
Sigma_obs | Stock assessment Sigma
SSB_ewe | Ecopath with EcoSim SSB
SSB_fs | FishSUMS SSB
SSB_lm | LeMans SSB
SSB_miz | mizer SSB
SSB_obs | Stock assessment SSB
TruthPrior | Constructor for the 'EnsemblePrior' class
TruthPrior-class | A class to hold the priors for the truth model in the ensemble framework