Package: PEcAn.data.atmosphere 1.8.0.9000

David LeBauer

PEcAn.data.atmosphere: PEcAn Functions Used for Managing Climate Driver Data

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 PECAn.data.atmosphere package converts climate driver data into a standard format for models integrated into PEcAn. As a standalone package, it provides an interface to access diverse climate data sets.

Authors:Mike Dietze [aut], David LeBauer [aut, cre], Carl Davidson [aut], Rob Kooper [aut], Deepak Jaiswal [aut], University of Illinois, NCSA [cph]

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

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

Peer review:

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

Datasets:

    On CRAN:

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

    11.56 score 203 stars 14 packages 64 scripts 108 exports 162 dependencies

    Last updated 3 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:.download.raw.met.module.extract.nc.module.met2model.moduleAirDensalign.metbuild_cf_variables_table_urlcfmet.downscale.dailycfmet.downscale.subdailycfmet.downscale.timecheck_met_input_fileclosest_xycos_solar_zenith_angledebias.metdebias.met.regressiondownload.Amerifluxdownload.AmerifluxLBLdownload.CRUNCEPdownload.ERA5.olddownload.FACEdownload.Fluxnet2015download.FluxnetLaThuiledownload.Geostreamsdownload.GFDLdownload.GLDASdownload.ICOSdownload.MACAdownload.MERRAdownload.MsTMIP_NARRdownload.NARRdownload.NARR_sitedownload.NEONmetdownload.NLDASdownload.NOAA_GEFSdownload.PalEONdownload.PalEON_ENSdownload.US_WCrdownload.US_Wlefdownscale_repeat_6hr_to_half_hrlydownscale_repeat_6hr_to_hrlydownscale_ShortWave_to_half_hrlydownscale_ShortWave_to_hrlydownscale_solar_geomdownscale_solar_geom_halfhourdownscale_spline_to_half_hrlydownscale_spline_to_hrlyequation_of_timeERA5_met_processexnerextract.local.CMIP5extract.local.NLDASextract.ncextract.nc.ERA5gen.subdaily.modelsget_cf_variables_tableget_NARR_threddsget.esget.lvget.ncvectorget.rhget.vpdlatlon2lcclightMElm_ensemble_simsload.cfmetmerge_met_variablemet_temporal_downscale.Gaussian_ensemblemet.processmet.process.stagemet2CF.ALMAmet2CF.Amerifluxmet2CF.AmerifluxLBLmet2CF.csvmet2CF.ERA5met2CF.FACEmet2CF.Geostreamsmet2CF.ICOSmet2CF.NARRmet2CF.PalEONmet2CF.PalEONregionalmetgapfillmetgapfill.NOAA_GEFSmodel.trainnc.mergenoaa_grid_downloadnoaa_stage2par2ppfdpecan_standard_met_tablepermute.ncpredict_subdaily_metprocess_gridded_noaa_downloadqair2rhread.registerrh2qairsave.betassave.modelsite_from_tagsite.lstsolarMJ2ppfdspin.metsplit_windsubdaily_predsw2parsw2ppfdtemporal_downscale_half_hourtemporal.downscale.functionsupscale_metwide2longwrite_noaa_gefs_netcdf

    Dependencies:abindamerifluxrarrowaskpassassertthatbase64encbigleafbitbit64bitopsblobbslibcacachemcallrcellrangerclassclassIntclicliprclustercodetoolscolorspacecpp11crayoncrosstalkcrulcurldata.tableDBIdbplyrdendextendDEoptimRdigestdplyre1071eggevaluatefansifarverfastmapfauxpasfontawesomeforeachfsfurrrfuturegclusgenericsgeonamesggplot2globalsgluegridExtragtableheatmaplyhighrhmshtmltoolshtmlwidgetshttpcodehttrisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevallifecyclelistenvlubridatemagrittrMASSMatrixmemoisemgcvmimemlegpmunsellncdf4nlmenneoopensslparallellyPEcAn.DBPEcAn.loggerPEcAn.remotePEcAn.utilspermutepillarpkgconfigplotlyplyrprettyunitsprocessxprogresspromisesproxypspurrrqapR.methodsS3R.ooR.utilsR6rappdirsrasterRColorBrewerRcppRCurlreadrreadxlREddyProcregistryrematchreshape2rjsonrlangrmarkdownrobustbases2sassscalesseriationsfsolartimespstringistringrsuntoolssysterratibbletidyrtidyselecttimechangetinytextriebeardtruncnormTSPtzdbunitsurltoolsutf8vctrsveganviridisviridisLitevroomwebshotwhiskerwithrwkxfunXMLxtsyamlzoo

    Comparing met data from various sources

    Rendered fromcompare_narr_cruncep_met.Rmdusingknitr::rmarkdownon Nov 20 2024.

    Last update: 2024-07-31
    Started: 2014-05-28

    Met Downscaling

    Rendered fromcfmet_downscaling.Rmdusingknitr::rmarkdownon Nov 20 2024.

    Last update: 2024-07-31
    Started: 2014-07-30

    PEcAn: Importing Met data from Bondville, IL Ameriflux station

    David LeBauer

    Rendered fromameriflux_demo.Rmdusingknitr::rmarkdownon Nov 20 2024.

    Last update: 2024-09-09
    Started: 2015-04-30

    Temporally Downscale Meteorology

    Rendered fromtdm_downscaling.Rmdusingknitr::rmarkdownon Nov 20 2024.

    Last update: 2024-07-31
    Started: 2017-07-13

    Readme and manuals

    Help Manual

    Help pageTopics
    Air DensityAirDens
    align.metalign.met
    Construct a URL to a specific version of the CF variables table XMLbuild_cf_variables_table_url
    Simple, Fast Daily to Hourly Climate Downscalingcfmet.downscale.daily
    Subdaily to hourly (or less) downscalingcfmet.downscale.subdaily
    Temporal downscaling of daily or subdaily CF met datacfmet.downscale.time
    Check a meteorology data file for compliance with the PEcAn standardcheck_met_input_file
    Check that the unit of a variable in a NetCDF file is equivalent to the expected unit.check_unit
    Given latitude and longitude coordinates, find NARR x and y indicesclosest_xy
    Create `ncvar` object from variable namecol2ncvar
    Cosine of Solar Zenith Anglecos_solar_zenith_angle
    debias_metdebias.met debias_met
    debias.met.regressiondebias.met.regression
    download_NOAA_GEFS_EFIdownload_NOAA_GEFS_EFI
    download.Amerifluxdownload.Ameriflux
    Download Ameriflux LBL CSV filesdownload.AmerifluxLBL
    Download CRUNCEP datadownload.CRUNCEP
    Download ERA 5 datadownload.ERA5.old
    Download Raw FACE data from the internetdownload.FACE
    download.Fluxnet2015download.Fluxnet2015
    download.FluxnetLaThuiledownload.FluxnetLaThuile
    Download Geostreams data from Clowder APIdownload.Geostreams
    Download GFDL CMIP5 outputs for a single grid point using OPeNDAP and convert to CFdownload.GFDL
    Download GLDAS datadownload.GLDAS
    Download ICOS Ecosystem data productsdownload.ICOS
    download.MACAdownload.MACA
    Download MERRA datadownload.MERRA
    download.MsTMIP_NARRdownload.MsTMIP_NARR
    Download NARR filesdownload.NARR
    Download NARR time series for a single sitedownload.NARR_site
    Download NEON Site Met CSV filesdownload.NEONmet
    Download NLDAS met datadownload.NLDAS
    Download NOAA GEFS Weather Datadownload.NOAA_GEFS
    download.PalEONdownload.PalEON
    Download PalEON met ensemble filesdownload.PalEON_ENS
    download.raw.met.module.download.raw.met.module download.raw.met.module
    download.US-WCrdownload.US_WCr
    download.US_Wlefdownload.US_Wlef
    Internal helper to downscale a single row from a daily filedownscale_one_cfmet_day
    Downscale repeat to half hourlydownscale_repeat_6hr_to_half_hrly
    Downscale repeat to hourlydownscale_repeat_6hr_to_hrly
    Downscale shortwave to half hourlydownscale_ShortWave_to_half_hrly
    Downscale shortwave to hourlydownscale_ShortWave_to_hrly
    Calculate potential shortwave radiationdownscale_solar_geom
    Calculate potential shortwave radiationdownscale_solar_geom_halfhour
    Downscale spline to half hourlydownscale_spline_to_half_hrly
    Downscale spline to hourlydownscale_spline_to_hrly
    Equation of time: Eccentricity and obliquityequation_of_time
    Met Processes for ERA5 dataERA5_met_process
    Exner functionexner
    Extract NLDAS from local download Extract NLDAS meteorology for a point from a local download of the full gridextract.local.CMIP5
    Extract NLDAS from local download Extract NLDAS meteorology for a point from a local download of the full gridextract.local.NLDAS
    extract.ncextract.nc
    ERA5_extractextract.nc.ERA5
    Generate Subdaily Modelsgen.subdaily.models
    Generate NARR url from a vector of datesgenerate_narr_url
    Retrieve the current CF variables table from 'cfconventions.org' and convert it into a 'data.frame'get_cf_variables_table
    Authentication lookup helperget_clowderauth
    Retrieve NARR data using threddsget_NARR_thredds
    Retrieve NARR data from a given URLget_narr_url
    get esget.es
    Latent heat of vaporizationget.lv
    Get time series vector from netCDF fileget.ncvector
    get RHget.rh
    VPDget.vpd
    half_hour_downscalehalf_hour_downscale temporal_downscale_half_hour
    Convert latitude and longitude to x-y coordinates (in km) in Lambert conformal conic projection (used by NARR)latlon2lcc
    Convert latitude and longitude coordinates to NARR indiceslatlon2narr
    Simulates the light macro environmentlightME
    lm_ensemble_simslm_ensemble_sims
    Load met data from PEcAn formatted met driverload.cfmet
    Merge a new met variable from an external file (e.g. CO2) into existing met filesmerge_met_variable
    met_temporal_downscale.Gaussian_ensemblemet_temporal_downscale.Gaussian_ensemble
    met.processmet.process
    met.process.stagemet.process.stage
    met2CF.ALMAmet2CF.ALMA
    met2CF.Amerifluxmet2CF.Ameriflux
    met2CF.AmerifluxLBLmet2CF.AmerifluxLBL
    Convert met data from CSV to CFmet2CF.csv
    met2cf.ERA5met2CF.ERA5
    convert FACE files to CF filesmet2CF.FACE
    Convert geostreams JSON to CF met filemet2CF.Geostreams
    Convert variables ICOS variables to CF format.met2CF.ICOS
    Convert NARR files to CF filesmet2CF.NARR
    met2CF.PalEONmet2CF.PalEON
    met2CF.PalEONregionalmet2CF.PalEONregional
    Take an Ameriflux NetCDF file Fill missing met values using MDS approach using MPI-BGC REddyProc library Currently Future version: Choose which variables to gap fill Future version will first downscale and fill with NARR, then REddyProcmetgapfill
    Gapfill NOAA_GEFS weather datametgapfill.NOAA_GEFS
    model.trainmodel.train
    NARR flux and sfc variablesnarr_all_vars narr_flx_vars narr_sfc_vars
    nc.mergenc.merge
    Download gridded forecast in the box bounded by the latitude and longitude listnoaa_grid_download
    noaa_stage2noaa_stage2
    par2ppfdpar2ppfd
    Conversion table for PEcAn standard meteorologypecan_standard_met_table
    permute.ncpermute.nc
    Post process raw NARR downloaded data framepost_process
    predict_subdaily_metpredict_subdaily_met
    Write NetCDF file for a single year of dataprepare_narr_year
    Extract and temporally downscale points from downloaded grid filesprocess_gridded_noaa_download
    qair2rhqair2rh
    Read a specific variable from a NARR NetCDF fileread_narr_var
    read.registerread.register
    RH to SHrh2qair rh2rv
    save.betassave.betas
    save.modelsave.model
    Function to find the site code for a specific tagsite_from_tag
    Find time zone for a sitesite.lst
    MJ to PPFDsolarMJ2ppfd
    Spin-up meteorologyspin.met
    Split wind_speed into eastward_wind and northward_windsplit_wind
    take mean at fixed intervals along a vectorstep_means
    subdaily_predsubdaily_pred
    SW to PARsw2par
    SW to PPFDsw2ppfd
    Downscale NOAA GEFS from 6hr to 1hrtemporal_downscale
    temporal_downscale_functionstemporal.downscale.functions
    upscale_metupscale_met
    Wide to Longwide2long
    Write NOAA GEFS netCDFwrite_noaa_gefs_netcdf