Package: PEcAn.uncertainty 1.8.0.9000

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

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PEcAn.uncertainty.pdf |PEcAn.uncertainty.html✨
PEcAn.uncertainty/json (API)
NEWS

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

Peer review:

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

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

    On CRAN:

    bayesiancyberinfrastructuredata-assimilationdata-scienceecosystem-modelecosystem-scienceforecastingmeta-analysisnational-science-foundationpecanplants

    8.88 score 203 stars 5 packages 15 scripts 31 exports 91 dependencies

    Last updated 1 days agofrom:cab30e89b4. Checks:OK: 1 WARNING: 6. Indexed: yes.

    TargetResultDate
    Doc / VignettesOKNov 20 2024
    R-4.5-winWARNINGNov 20 2024
    R-4.5-linuxWARNINGNov 20 2024
    R-4.4-winWARNINGNov 20 2024
    R-4.4-macWARNINGNov 20 2024
    R-4.3-winWARNINGNov 20 2024
    R-4.3-macWARNINGNov 20 2024

    Exports:ensemble.filenameensemble.tsflux.uncertaintyget.changeget.coef.varget.elasticityget.ensemble.samplesget.parameter.samplesget.resultsget.sensitivityinput.ens.genplot_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.splinefunsd.varsensitivity.analysissensitivity.filenamespline.truncatewrite.ensemble.configswrite.sa.configs

    Dependencies:abindaskpassblobclicodacodetoolscolorspacecpp11curlDBIdbplyrdigestdplyrfansifarverforeachfsfurrrfuturegenericsgetoptggplot2globalsgluegridExtragtablehttrisobanditeratorsjsonlitelabelinglatticelifecyclelistenvlubridatemagrittrMASSMatrixMatrixModelsmcmcMCMCpackmgcvmimemunsellmvtnormncdf4nlmeopenssloptparseparallellyPEcAn.DBPEcAn.emulatorPEcAn.loggerPEcAn.MAPEcAn.priorsPEcAn.remotePEcAn.settingsPEcAn.utilspillarpkgconfigplyrpurrrquantregR.methodsS3R.ooR.utilsR6randtoolboxRColorBrewerRcpprjagsrlangrngWELLscalesSparseMstringistringrsurvivalsystibbletidyrtidyselecttimechangetriebeardunitsurltoolsutf8vctrsviridisLitewithrXML

    Readme and manuals

    Help Manual

    Help pageTopics
    Generate ensemble filenamesensemble.filename
    Plots an ensemble time-series from PEcAn for the selected target variableensemble.ts
    Calculate parameters for heteroskedastic flux uncertaintyflux.uncertainty
    Get delta between sequential flux datapointsget.change
    Get coefficient of varianceget.coef.var
    Generic function for the elasticityget.elasticity
    Get Ensemble Samplesget.ensemble.samples
    Get g_i(phi_i)get.gi.phii
    Convert priors / MCMC samples to chains that can be sampled for model parametersget.parameter.samples
    Reads model output and runs sensitivity and ensemble analysesget.results
    Calculate the sensitivity of a function at the medianget.sensitivity
    Function for generating samples based on sampling method, parent or etcinput.ens.gen
    Calculates the excess kurtosis of a vectorkurtosis
    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
    Read ensemble outputread.ensemble.output
    Reads ensemble time-series from PEcAn for the selected target variableread.ensemble.ts
    Read Sensitivity Analysis outputread.sa.output
    run ensemble.analysisrun.ensemble.analysis
    run sensitivity.analysisrun.sensitivity.analysis
    Apply get.results to each of a list of settingsrunModule.get.results
    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
    Write sensitivity analysis config fileswrite.sa.configs