Package: PEcAnRTM 1.7.3.9000

Alexey Shiklomanov

PEcAnRTM: PEcAn Functions Used for Radiative Transfer Modeling

Functions for performing forward runs and inversions of radiative transfer models (RTMs). Inversions can be performed using maximum likelihood, or more complex hierarchical Bayesian methods. Underlying numerical analyses are optimized for speed using Fortran code.

Authors:Mike Dietze [aut], Shawn Serbin [aut], Alexey Shiklomanov [aut, cre], University of Illinois, NCSA [cph]

PEcAnRTM_1.7.3.9000.tar.gz

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PEcAnRTM.pdf |PEcAnRTM.html✨
PEcAnRTM/json (API)
NEWS

# Install 'PEcAnRTM' in R:
install.packages('PEcAnRTM', 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

    45 exports 202 stars 6.31 score 309 dependencies 132 scripts

    Last updated 5 hours agofrom:f22a7c4bbc. Checks:OK: 1 WARNING: 5. Indexed: yes.

    TargetResultDate
    Doc / VignettesOKSep 18 2024
    R-4.5-linux-x86_64WARNINGSep 18 2024
    R-4.4-mac-x86_64WARNINGSep 18 2024
    R-4.4-mac-aarch64WARNINGSep 18 2024
    R-4.3-mac-x86_64WARNINGSep 18 2024
    R-4.3-mac-aarch64WARNINGSep 18 2024

    Exports:burnin.thincheck.convergencedefault.settings.prospectdefparamdtnormEDREDR.preprocess.historyfortran_data_modulefoursailgeneralized_plate_modelgenerate.noiseget.EDR.outputinvert_btinvert.autoinvert.custominvert.lsqis_spectraload.from.namelognorm.mulognorm.sigmamatplotneffparams.prospect4params.prospect5params.prospect5bparams.prospectdparams2edrprint_results_summaryprior.defaultvals.prospectpriorfunc.prospectpro2spro4sailpro4saildprospectprospect_bt_priorresamplertnormsensor.listsensor.propersetup_edrspectraspectral.responsesummary_mvnormsummary_simplewavelengths

    Dependencies:abindadmiscalabamaamerifluxrapearrowaskpassassertthatbackportsbase64encBayesianToolsbigleafbitbit64bitopsblobbootbridgesamplingBrobdingnagbslibcacachemcallrCDMcellrangercheckmateclassclassIntclicliprclueclustercodacodetoolscolorspacecommonmarkconditionzcpp11crayoncrosstalkcrulcurldata.tableDBIdbplyrdeldirdendextendDEoptimRDHARMadiagramdigestdoParalleldownloaderdplRdplyrduckdbduckdbfse1071eggellipseemulatorevaluateexpmfansifarverfastmapfastmatchfauxpasfBasicsfontawesomeforeachforeignFormulafsfurrrfuturefuture.applygapgap.datasetsgclusgenericsgeonamesgetoptggplot2ggrepelglobalsgluegmmgridExtragssgtableHDIntervalheatmaplyhighrHmischmshoardrhtmlTablehtmltoolshtmlwidgetshttpcodehttpuvhttrIDPmiscigraphisobanditeratorsjquerylibjsonliteKernSmoothkknnknitrlabelinglaterlatticelavalazyevallifecyclelistenvlme4lmtestlqmmlubridatemagrittrMASSMatrixMatrixModelsmatrixStatsmcmcMCMCpackmemoisemgcvmimeminqamlegpmodeestmsmmunsellmvtnormnatservncdf4neonstoreneonUtilitiesnleqslvnlmenloptrnneonnetnumDerivopenssloptparseparallellypbapplypbvPEcAn.assim.batchPEcAn.benchmarkPEcAn.data.atmospherePEcAn.data.landPEcAn.DBPEcAn.emulatorPEcAn.loggerPEcAn.MAPEcAn.priorsPEcAn.remotePEcAn.settingsPEcAn.uncertaintyPEcAn.utilsPEcAn.visualizationPEcAn.workflowpermutephangornpillarpkgconfigplotlyplyrpngpolyclippolycorprettyunitsprocessxprodlimprogressprogressrpromisesproxypspurrrqapqgamqrngquadprogquantregR.methodsS3R.ooR.utilsR6randtoolboxrappdirsrasterratelimitrrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRCurlRdpackreadrreadxlREddyProcregistryrematchrentrezreshape2rexritisrjagsrjsonrlangrmarkdownrmutilrnclrngWELLrobustbaserotlrpartrredlistrstudioapirunjagsrvests2sandwichsassscalesselectrseriationsfshapeshinysignalSimilarityMeasuressirtsolartimesolriumsourcetoolsspspacefillrSparseGridSparseMspatialspatstat.dataspatstat.geomspatstat.univarspatstat.utilsSQUAREMstablestablediststatipstorrstringistringrsuntoolssurvivalswfscMiscsysTAMtaxizeterrathortibbletidyrtidyselecttimechangetimeDatetimeSeriestinytextmvtnormtraitstriebeardTruncatedNormaltruncnormTSPtzdbunitsurltoolsutf8uuidvctrsveganviridisviridisLitevroomwebshotwhiskerWikidataQueryServiceRWikidataRWikipediRwikitaxawithrwkworrmsxfunXMLxml2xtablextsyamlzipzoo

    The PEcAn RTM package

    Alexey Shiklomanov

    Rendered frompecanrtm.vignette.Rmdusingknitr::rmarkdownon Sep 18 2024.

    Last update: 2024-09-06
    Started: 2015-07-06

    Readme and manuals

    Help Manual

    Help pageTopics
    Select spectra[.spectra
    Select spectra by wavelength[[.spectra
    Assign values to spectra by wavelength[[<-.spectra
    Burn-in and thinning of MCMC samplesburnin.thin
    Combine spectra by wavelengthcbind.spectra
    Check convergence of multiple MCMC chainscheck.convergence
    Defult inversion settings for PROSPECT 5 modelsdefault.settings.prospect
    Get default parametersdefparam
    Truncated normal distribution densitydtnorm
    ED radiative transfer module (EDR) wrapper functionEDR
    Preprocess history file for EDREDR.preprocess.history
    List to FORTRAN data modulefortran_data_module
    SAIL modelfoursail
    Generalized plate modelgeneralized_plate_model
    Generate autocorrelated spectral noisegenerate.noise
    Read EDR outputget.EDR.output
    Perform Bayesian inversion using BayesianTools packageinvert_bt
    Inversion with automatic convergence checkinginvert.auto
    Bayesian inversion of a modelinvert.custom
    Least squares model inversioninvert.lsq
    Load object from an RData fileload.from.name
    Functions for default priors Lognormal mean parameterslognorm.mu
    Lognormal sigma parameterlognorm.sigma
    Matplot generic methodmatplot
    Matplot default methodmatplot.default
    Plot multiple spectra on same graphmatplot.spectra
    Effective sample sizeneff
    PROSPECT 4 parametersparams.prospect4
    PROSPECT 5 parametersparams.prospect5
    PROSPECT 5B parametersparams.prospect5b
    PROSPECT D parametersparams.prospectd
    Convert named parameter vector to EDR-compatible inputsparams2edr
    Plot spectra vs. wavelengthplot.spectra
    Neatly print inversion results summaryprint_results_summary
    Print method for spectra S3 classprint.spectra
    Default prior parameters for PROSPECT modelsprior.defaultvals.prospect
    Default PROSPECT 5 prior functionpriorfunc.prospect
    Coupled PROSPECT-Two-stream modelpro2s
    PRO4SAIL modelpro4sail
    PRO4SAILD modelpro4saild
    PROSPECT (4, 5, or 5B) modelprospect
    Quick BayesianTools prior creator for PROSPECT modelprospect_bt_prior
    Read and process RSR data from directoryread.rsr.folder
    Resample vector, matrix, or spectraresample resample.default resample.matrix resample.spectra
    Generate relative spectral response (RSR) matrix based on FWHM datarsr.from.fwhm
    Generic log-likelihood generator for RTMsrtm_loglike
    Random sampling from one-sided truncated normal distributionrtnorm
    Sensor spectral response functionssensor.list
    Sensor list with proper namessensor.proper
    Setup EDR runsetup_edr
    Spectra S3 classis_spectra spectra
    Convolution of spectra to sensor RSRspectral.response
    Structure of 'spectra' objectstr.spectra
    Multivariate normal fitsummary_mvnorm
    Simple summary statistics on MCMC samplessummary_simple
    Trim RSR matrix to wavelength limitstrim.rsr
    Retrieve wavelengths from spectra objectwavelengths