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

On CRAN:

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

11.54 score 205 stars 14 packages 64 scripts 108 exports 162 dependencies

Last updated 7 days agofrom:882766d7a0. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 17 2024
R-4.5-winWARNINGDec 17 2024
R-4.5-linuxWARNINGDec 17 2024
R-4.4-winWARNINGDec 17 2024
R-4.4-macWARNINGDec 17 2024
R-4.3-winWARNINGDec 17 2024
R-4.3-macWARNINGDec 17 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 Dec 17 2024.

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

Met Downscaling

Rendered fromcfmet_downscaling.Rmdusingknitr::rmarkdownon Dec 17 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 Dec 17 2024.

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

Temporally Downscale Meteorology

Rendered fromtdm_downscaling.Rmdusingknitr::rmarkdownon Dec 17 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