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

PEcAn.uncertainty_1.8.0.9000.tar.gz
PEcAn.uncertainty_1.8.0.9000.zip(r-4.5)PEcAn.uncertainty_1.8.0.9000.zip(r-4.4)PEcAn.uncertainty_1.8.0.9000.zip(r-4.3)
PEcAn.uncertainty_1.8.0.9000.tgz(r-4.5-any)PEcAn.uncertainty_1.8.0.9000.tgz(r-4.4-any)PEcAn.uncertainty_1.8.0.9000.tgz(r-4.3-any)
PEcAn.uncertainty_1.8.0.9000.tar.gz(r-4.5-noble)PEcAn.uncertainty_1.8.0.9000.tar.gz(r-4.4-noble)
PEcAn.uncertainty_1.8.0.9000.tgz(r-4.4-emscripten)PEcAn.uncertainty_1.8.0.9000.tgz(r-4.3-emscripten)
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'))

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-Forge:

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

8.91 score 215 stars 5 packages 15 scripts 31 exports 91 dependencies

Last updated 10 hours agofrom:9a10f3bde6. Checks:1 OK, 8 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 06 2025
R-4.5-winWARNINGMar 06 2025
R-4.5-macWARNINGMar 06 2025
R-4.5-linuxWARNINGMar 06 2025
R-4.4-winWARNINGMar 06 2025
R-4.4-macWARNINGMar 06 2025
R-4.4-linuxWARNINGMar 06 2025
R-4.3-winWARNINGMar 06 2025
R-4.3-macWARNINGMar 06 2025

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