Package: PEcAnAssimSequential 1.10.0.9000

Mike Dietze

PEcAnAssimSequential: PEcAn Functions Used for 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:Mike Dietze

PEcAnAssimSequential_1.10.0.9000.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
PEcAnAssimSequential/json (API)
NEWS

# Install 'PEcAnAssimSequential' in R:
install.packages('PEcAnAssimSequential', 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 - binary JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS. JAGS was written with three aims in mind: * To have an engine for the BUGS language that runs on Unix * To be extensible, allowing users to write their own functions, distributions and samplers. * To be a plaftorm for experimentation with ideas in Bayesian modelling This package contains the 'jags' binary as well as the associated shared library modules loaded by the binary.
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

state-data-assimilationensemble-kalman-filterparticle-filterecological-forecastingforecast-verificationbayesiancyberinfrastructuredata-assimilationdata-scienceecosystem-modelecosystem-scienceforecastingmeta-analysisnational-science-foundationpecanplantsjagscpp

8.46 score 236 stars 49 scripts 66 exports 211 dependencies

Last updated from:3654c6a1cc. Checks:7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64NOTE262
source / vignettesOK340
linux-release-x86_64NOTE259
macos-release-arm64NOTE196
macos-oldrel-arm64NOTE136
windows-develNOTE234
windows-releaseNOTE162
windows-oldrelNOTE194
wasm-releaseOK224

Exports:adj.ensaggregatealltocsalrAnalysis.sdaassessParamsblock_matrixconj_wt_wishart_samplerConstruct_Hconstruct_nimble_HConstruct.H.multisiteConstruct.RContruct.PfCreate_Site_PFT_CSVdownscale_qsub_maindwtmnormEnKFEnKF.MultiSiteGEFGEF.MultiSiteGEF.MultiSite.Nimbleget_ensemble_weightsGrabFillMatrixhop_testinteractive.plotting.sdainv.alrload_data_paleon_sdaLocal.supportmatrix_networkmetSplitobs_timestep2timepointObs.data.prepare.MultiSiteoutlier.detector.boxplotpiecew.poly.localpost.analysis.ggplotpost.analysis.ggplot.violinpost.analysis.multisite.ggplotpostana.bias.plotting.sdapostana.bias.plotting.sda.corrpostana.timeser.plotting.sdaPrep_OBS_SDAqsub_sdaqsub_sda_batchRemote_Sync_launcherrescaling_stateVarsrwtmnormsample_metsampler_togglesda_assembleSDA_controlSDA_downscale_hrlySDA_OBS_AssemblerSDA_remote_launcherSDA_timeseries_plotsda_weights_sitesda.enkfsda.enkf_localsda.enkf.multisitesda.enkf.originalsda.qsub.job.submissionsimple.localstack_covariates_2_geotifftobit_model_censoredtobit.modeltobit2space.modely_star_create

Dependencies:abindamerifluxrarrowaskpassassertthatbase64encbigleafbitbit64bitopsblobbootbslibcacachemcallrcellrangerclassclassIntclicliprclueclustercodacodetoolscolorspacecommonmarkcpp11crayoncrosstalkcurldata.tableDBIdbplyrdendextendDEoptimRdigestdoParalleldplyrdtwdtwclustduckdbe1071eggevaluatefarverfastmapflexclustfontawesomeforeachfsfurrrfuturegclusgenericsgeonamesggplot2ggrepelglobalsgluegridExtragtableheatmaplyherehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2igraphisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevallifecyclelistenvlubridatemagrittrMASSMatrixMatrixModelsmcmcMCMCpackmemoisemgcvmimemlegpmodeltoolsMODISToolsmvtnormncdf4nimblenlmenumbersnumDerivopenssloptparseotelparallellyPEcAn.data.atmospherePEcAn.data.landPEcAn.data.remotePEcAn.DBPEcAn.emulatorPEcAn.loggerPEcAn.MAPEcAn.priorsPEcAn.remotePEcAn.settingsPEcAn.uncertaintyPEcAn.utilsPEcAn.workflowpermutepillarpkgconfigplotlyplyrpngpracmaprettyunitsprocessxprogresspromisesproxypspurrrqapquantregR.methodsS3R.ooR.utilsR6randtoolboxrappdirsrasterRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRcppThreadRcppTOMLRCurlreadrreadxlREddyProcregistryrematchreshape2reticulaterjagsrjsonrlangrmarkdownrngWELLrobustbaserprojrootRSpectras2S7sassscalessensitivityseriationsfshinyshinyjssolartimesourcetoolsspSparseMstringistringrsuntoolssurvivalsysterratibbletidyrtidyselecttimechangetinytextriebeardtruncnormTSPtzdbunitsurltoolsutf8vctrsveganviridisviridisLitevroomwebshotwithrwkxfunXMLxtablextsyamlzoo

Readme and manuals

Help Manual

Help pageTopics
adj.ensadj.ens
Aggregation Functionaggregate
alltocsalltocs
Additive Log Ratio transformalr
analysis_sda_blockanalysis_sda_block
Analysis.sdaAnalysis.sda
assess.paramsassess.params assessParams
block_matrixblock_matrix
block.2.vectorblock.2.vector
build_Xbuild_X
build.block.xybuild.block.xy
sda_assemblecheck.qsub.job.info
Weighted conjugate wishartconj_wt_wishart_sampler
Construc_HConstruct_H Construc_H
construct_nimble_Hconstruct_nimble_H
Construct.H.multisiteConstruct.H.multisite
Construct.RConstruct.R
Contruct.PfContruct.Pf
Title Identify pft for each site of a multi-site settings using NLCD and Eco-regionCreate_Site_PFT_CSV
debias.averagedebias.average
debias.extract.covdebias.extract.cov
debias.map.productsdebias.map.products
sda.bias.correctiondebias.ML
debias.res.lag.calcdebias.res.lag.calc
debias.residual.calcdebias.residual.calc
debias.train.accuracydebias.train.accuracy
downscale_maindownscale_main
downscale_qsub_maindownscale_qsub_main
weighted multivariate normal densitydwtmnorm
EnKFEnKF
EnKF.MultiSiteEnKF.MultiSite
GEFGEF GEF.MultiSite
multisite TWEnFGEF.MultiSite.Nimble
get_ensemble_weightsget_ensemble_weights
GrabFillMatrixGrabFillMatrix
hop_testhop_test
Internal functions for plotting SDA outputs. Interactive, post analysis time-series and bias plots in base plotting system and ggplotinteractive.plotting.sda post.analysis.ggplot post.analysis.ggplot.violin post.analysis.multisite.ggplot postana.bias.plotting.sda postana.bias.plotting.sda.corr postana.timeser.plotting.sda SDA_timeseries_plot
inverse of ALR transforminv.alr
load_data_paleon_sdaload_data_paleon_sda
load_nimbleload_nimble y_star_create
Local.supportLocal.support
matrix_networkmatrix_network
MCMC_block_functionMCMC_block_function
MCMC_functionMCMC_function
MCMC_InitMCMC_Init
metSplitmetSplit
convert from timestep to actual time points. supports year, month, week, and day as time unit.obs_timestep2timepoint
Obs.data.prepare.MultiSiteObs.data.prepare.MultiSite
outlier.detector.boxplotoutlier.detector.boxplot
parallel_predictionparallel_prediction
parallel_trainparallel_train
pecan_settings_2_ptspecan_settings_2_pts
piecew.poly.localpiecew.poly.local
SDA observation preparation function for LAI and AGBPrep_OBS_SDA
prepare_train_datprepare_train_dat
qsub_sdaqsub_sda
qsub_sda_batchqsub_sda_batch
Remote_Sync_launcherRemote_Sync_launcher
rescaling_stateVarsrescaling_stateVars
random weighted multivariate normalrwtmnorm
Sample meteorological ensemblessample_met
sample parameterssample.parameters
sampler togglingsampler_toggle
sda_assemblesda_assemble
SDA_controlSDA_control
SDA Downscale FunctionSDA_downscale
SDA　Downscale Function for Hourly DataSDA_downscale_hrly
Calculate Metrics for Downscaling ResultsSDA_downscale_metrics
Preprocess Data for DownscalingSDA_downscale_preprocess
sda_matchparamsda_matchparam
Assembler for preparing obs.mean and obs.cov for the SDA workflowSDA_OBS_Assembler
SDA_remote_launcherSDA_remote_launcher
Calculate ensemble weights for each site at time t.sda_weights_site
sda.bias.correctionsda.bias.correction
State Variable Data Assimilation: Ensemble Kalman Filter and Generalized ensemble filtersda.enkf
sda.enkf_localsda.enkf_local
State Variable Data Assimilation: Ensemble Kalman Filter and Generalized ensemble filtersda.enkf.multisite
State Variable Data Assimilation: Ensemble Kalman Filtersda.enkf.original
sda_assemblesda.qsub.job.submission
simple.localsimple.local
stack_covariates_2_dfstack_covariates_2_df
stack_covariates_2_geotiffstack_covariates_2_geotiff
tobit_model_censoredtobit_model_censored
TWEnFtobit.model
Fit tobit prior to ensemble memberstobit2space.model
update_qupdate_q