Package: EcoEnsemble 1.1.0

Michael A. Spence

EcoEnsemble: A General Framework for Combining Ecosystem Models

Fit and sample from the ensemble model described in Spence et al (2018): "A general framework for combining ecosystem models"<doi:10.1111/faf.12310>.

Authors:Michael A. Spence [aut, cre], James A. Martindale [aut], Michael J. Thomson [aut]

EcoEnsemble_1.1.0.tar.gz
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EcoEnsemble.pdf |EcoEnsemble.html✨
EcoEnsemble/json (API)
NEWS

# Install 'EcoEnsemble' in R:
install.packages('EcoEnsemble', repos = c('https://cefasrepres.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/cefasrepres/ecoensemble/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

5.85 score 1 stars 19 scripts 241 downloads 19 exports 61 dependencies

Last updated 5 months agofrom:a7f436d914. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-win-x86_64NOTEOct 31 2024
R-4.5-linux-x86_64NOTEOct 31 2024
R-4.4-win-x86_64NOTEOct 31 2024
R-4.4-mac-x86_64NOTEOct 31 2024
R-4.4-mac-aarch64NOTEOct 31 2024
R-4.3-win-x86_64NOTEOct 31 2024
R-4.3-mac-x86_64NOTEOct 31 2024
R-4.3-mac-aarch64NOTEOct 31 2024

Exports:EnsembleDataEnsembleFitEnsemblePriorEnsembleSamplefit_ensemble_modelgen_samplegenerate_sampleget_mcmc_ensemble_modelget_mleget_parametersget_transformed_dataget_transformed_data_driIndLTPriorIndSTPriorKalmanFilter_backprior_ensemble_modelsample_priorShaSTPriorTruthPrior

Dependencies:abindbackportsBHcallrcheckmateclicolorspacecowplotdescdistributionaldplyrfansifarvergenericsggplot2gluegridExtragtableinlineisobandlabelinglatticelifecycleloomagrittrMASSMatrixmatrixcalcmatrixStatsmgcvmunsellnlmenumDerivpillarpkgbuildpkgconfigplyrposteriorprocessxpsQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelreshape2rlangrstanrstantoolsscalesStanHeadersstringistringrtensorAtibbletidyselectutf8vctrsviridisLitewithr

Beta Conjugate Prior

Thomas I. J. Bartos, Michael A. Spence, Michael J. Thomson

Rendered fromBetaConjugatePrior.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-06-26
Started: 2024-06-26

EcoEnsemble

James A. Martindale and Michael A. Spence

Rendered fromEcoEnsemble.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-05-16
Started: 2022-01-28

Exploring priors

Michael A. Spence, James A. Martindale and Michael J. Thomson

Rendered fromExploringPriors.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2023-05-19
Started: 2022-09-26

Including drivers

Thomas I. J. Bartos and Michael A. Spence

Rendered fromIncludingDrivers.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-06-26
Started: 2024-06-26

Case Study: Synthetic Data

James A. Martindale, Michael J. Thomson and Michael A. Spence

Rendered fromSyntheticData.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2023-05-19
Started: 2022-09-26

Readme and manuals

Help Manual

Help pageTopics
A general framework for combining ecosystem modelsEcoEnsemble-package EcoEnsemble
Constructor for the 'EnsembleData' classEnsembleData
A class to hold the Ensemble dataEnsembleData-class
The constructor for the 'EnsembleFit' objectEnsembleFit
A class to hold the samples or point estimates from the ensemble model.EnsembleFit-class
A class to hold the priors for the ensemble model.EnsemblePrior-class
A constructor for the 'EnsembleSample' objectEnsembleSample
A class to hold samples of the ensemble modelEnsembleSample-class
Fits the ensemble modelfit_ensemble_model
Generate samples from a fitted ensemble model.generate_sample gen_sample get_mle get_parameters get_transformed_data get_transformed_data_dri
Return the compiled ensemble model Stan object.get_mcmc_ensemble_model
Constructor for the 'EnsemblePrior' classEnsemblePrior IndLTPrior IndSTPrior ShaSTPrior TruthPrior
A class to hold the priors for the ensemble model.IndLTPrior-class
A class to hold the priors for the ensemble model.IndSTPrior-class
Backwards Kalman filterKalmanFilter_back
Plot the ensemble outputplot.EnsembleSample
Generate samples of parameters from prior distributionprior_ensemble_model
Generate samples of latent variables from prior predictive distributionsample_prior
A class to hold the priors for the ensemble model.ShaSTPrior-class
Ecopath with EcoSim SigmaSigma_ewe
FishSUMS SigmaSigma_fs
LeMans SigmaSigma_lm
mizer SigmaSigma_miz
Stock assessment SigmaSigma_obs
Ecopath with EcoSim SSBSSB_ewe
FishSUMS SSBSSB_fs
LeMans SSBSSB_lm
mizer SSBSSB_miz
Stock assessment SSBSSB_obs
A class to hold the priors for the truth model in the ensemble frameworkTruthPrior-class