Package: PEcAn.uncertainty 1.9.0.9000

David LeBauer

PEcAn.uncertainty: PEcAn Functions Used for Propagating and Partitioning Uncertainties in Ecological Forecasts and Reanalysis

The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation.

Authors:David LeBauer, Mike Dietze, Xiaohui Feng, Dan Wang, Carl Davidson, Rob Kooper, Shawn Serbin

PEcAn.uncertainty_1.9.0.9000.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
PEcAn.uncertainty/json (API)

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

Bug tracker:https://github.com/pecanproject/pecan/issues

Uses libs:
  • jags– Just Another Gibbs Sampler for Bayesian MCMC
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

ecological-forecastingsensitivity-analysispecanuncertainty-propagationbayesiancyberinfrastructuredata-assimilationdata-scienceecosystem-modelecosystem-scienceforecastingmeta-analysisnational-science-foundationplantsjagscpp

9.50 score 247 stars 5 packages 34 scripts 38 exports 123 dependencies

Last updated from:fdb9b89d61. Checks:7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develWARNING172
source / vignettesOK262
linux-releaseWARNING200
macos-releaseWARNING118
macos-oldrelWARNING140
windows-develWARNING87
windows-releaseWARNING100
windows-oldrelWARNING76
wasm-releaseOK121

Exports:compute_sobol_indicesensemble.filenameensemble.tsflux.uncertaintygenerate_joint_ensemble_designgenerate_OAT_SA_designget_parameter_samplesget.changeget.coef.varget.elasticityget.ensemble.samplesget.parameter.samplesget.resultsget.sensitivityinput.ens.genload_pft_posteriorsplot_flux_uncertaintyplot_sensitivitiesplot_sensitivityplot_variance_decompositionread.ameriflux.L2read.ensemble.outputread.ensemble.tsread.sa.outputrun.ensemble.analysisrun.sensitivity.analysisrunModule.get.resultsrunModule.run.ensemble.analysisrunModule.run.sensitivity.analysissa_run_descriptionssa_run_id_tablesa_run_samplessa.splinefunsd.varsensitivity.analysissensitivity.filenamespline.truncatewrite.ensemble.configs

Dependencies:abindaskpassbase64encblobbootbslibcachemclasscliclueclustercodacodetoolscommonmarkcpp11curlDBIdbplyrdigestdplyrdtwdtwclustfarverfastmapflexclustfontawesomeforeachfsfurrrfuturegenericsggplot2ggrepelglobalsgluegridExtragtablehtmltoolshttpuvhttrisobanditeratorsjquerylibjsonlitelabelinglaterlatticelifecyclelistenvlubridatemagrittrMASSMatrixMatrixModelsmcmcMCMCpackmemoisemimemodeltoolsmvtnormncdf4numbersopenssloptparseotelparallellyPEcAn.DBPEcAn.emulatorPEcAn.loggerPEcAn.MAPEcAn.priorsPEcAn.remotePEcAn.settingsPEcAn.utilspillarpkgconfigplyrpromisesproxypurrrquantregR.methodsS3R.ooR.utilsR6randtoolboxrappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRcppThreadreshape2rjagsrlangrngWELLRSpectraS7sassscalessensitivityshinyshinyjssourcetoolsSparseMstringistringrsurvivalsystibbletidyrtidyselecttimechangetriebeardunitsurltoolsutf8vctrsviridisLitewithrXMLxtable

Readme and manuals

Help Manual

Help pageTopics
Compute Sobol indices from a finished PEcAn runcompute_sobol_indices
Generate ensemble filenamesensemble.filename
Plots an ensemble time-series from PEcAn for the selected target variableensemble.ts
Calculate parameters for heteroskedastic flux uncertaintyflux.uncertainty
Generate joint ensemble design for parameter samplinggenerate_joint_ensemble_design
Generate One-At-a-Time (OAT) input design for sensitivity analysisgenerate_OAT_SA_design
Generate parameter samples from priors and MCMC posteriors (pure function)get_parameter_samples
Get delta between sequential flux datapointsget.change
Get coefficient of varianceget.coef.var
Generic function for the elasticityget.elasticity
Get parameter values used in ensembleget.ensemble.samples
Get g_i(phi_i)get.gi.phii
Convert priors / MCMC samples to parameter sample chainsget.parameter.samples
Read model output and save parsed results for sensitivity and ensemble analysesget.results
Calculate the sensitivity of a function at the medianget.sensitivity
Generate an ensemble of samples from one inputinput.ens.gen
Calculates the excess kurtosis of a vectorkurtosis
Load PFT priors and posteriors from disk/databaseload_pft_posteriors
Plot fit for heteroskedastic flux uncertaintyplot_flux_uncertainty
Plot functions and quantiles used in sensitivity analysisplot_sensitivities
Sensitivity plotplot_sensitivity
Variance Decomposition Plotsplot_variance_decomposition
Read Ameriflux L2 Dataread.ameriflux.L2
Reads output from model ensembleread.ensemble.output
Reads ensemble time-series from PEcAn for the selected target variableread.ensemble.ts
Reads output of sensitivity analysis runsread.sa.output
Run ensemble analysis on finished model runsrun.ensemble.analysis
Run sensitivity analysis on finished model runsrun.sensitivity.analysis
Apply get.results to each of a list of settingsrunModule.get.results
Run ensemble analyses across all sites in settingsrunModule.run.ensemble.analysis
Run sensitivity analysis for every Settings in a MultiSettingsrunModule.run.sensitivity.analysis
Describe each run of a sensitivity analysis designsa_run_descriptions
Index a sensitivity analysis run's ids by PFT, quantile and traitsa_run_id_table
Expand SA quantile samples into one parameter set per runsa_run_samples
Spline estimate of univariate relationship between parameter value and model outputsa.splinefun
Calculates the standard deviation of the variance estimatesd.var
Performs univariate sensitivity analysis and variance decompositionsensitivity.analysis
Generate sensitivity analysis filenamessensitivity.filename
Spline Ensemblespline.ensemble
Truncate spline at zero if...spline.truncate
variance statisticsvariance.stats
Write ensemble config fileswrite.ensemble.configs