Package: PEcAn.ED2 1.8.0.9000

Mike Dietze

PEcAn.ED2: PEcAn Package for Integration of ED2 Model

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. This package provides functions to link the Ecosystem Demography Model, version 2, to PEcAn.

Authors:David LeBauer, Mike Dietze, Xiaohui Feng, Dan Wang, Carl Davidson, Rob Kooper, Shawn Serbin, Alexey Shiklomanov, Eric R. Scott

PEcAn.ED2_1.8.0.9000.tar.gz
PEcAn.ED2_1.8.0.9000.zip(r-4.5)PEcAn.ED2_1.8.0.9000.zip(r-4.4)PEcAn.ED2_1.8.0.9000.zip(r-4.3)
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PEcAn.ED2.pdf |PEcAn.ED2.html✨
PEcAn.ED2/json (API)
NEWS

# Install 'PEcAn.ED2' in R:
install.packages('PEcAn.ED2', 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:
  • pftmapping - Mapping of PEcAn PFT names to ED2 PFT numbers

On CRAN:

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

52 exports 202 stars 6.31 score 253 dependencies 145 scripts

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

TargetResultDate
Doc / VignettesOKSep 18 2024
R-4.5-winWARNINGSep 18 2024
R-4.5-linuxERRORSep 18 2024
R-4.4-winWARNINGSep 18 2024
R-4.4-macWARNINGSep 18 2024
R-4.3-winWARNINGSep 18 2024
R-4.3-macWARNINGSep 18 2024

Exports:check_csscheck_ed_metheadercheck_ed_metheader_formatcheck_ed2incheck_psscheck_sitecreate_csscreate_ed_vegcreate_psscreate_sitedownload_edied.varexample_cssexample_pssexample_siteget_ed2in_datesget_met_datesget_restartfile.ED2is.ed2inlist.files.nodirmet_flag_descriptionmet_variable_descriptionmet2model.ED2model2netcdf.ED2modify_ed2inparse.historyread_cssread_E_filesread_ed_metheaderread_ed_vegread_ed2inread_pssread_restart.ED2read_S_filesread_siteread_T_filesremove.config.ED2run_ed_singularitySAS.ED2SAS.ED2.param.Argstranslate_vars_edveg2model.ED2write_csswrite_ed_metheaderwrite_ed_vegwrite_ed2inwrite_psswrite_restart.ED2write_sitewrite.config.ED2write.config.jobsh.ED2write.config.xml.ED2

Dependencies:abindadmiscamerifluxrapearrowaskpassassertthatbackportsbase64encbigleafbitbit64bitopsblobbootbslibcacachemcallrCDMcellrangercheckmateclassclassIntclicliprclueclustercodacodetoolscolorspaceconditionzcpp11crayoncrosstalkcrulcurldata.tableDBIdbplyrdeldirdendextendDEoptimRdigestdownloaderdplRdplyrduckdbduckdbfse1071eggevaluatefansifarverfastmapfastmatchfauxpasfBasicsfontawesomeforeachforeignFormulafsfurrrfuturegclusgenericsgeonamesgetoptggplot2ggrepelglobalsgluegridExtragssgtablehdf5rHDIntervalheatmaplyhighrHmischmshoardrhtmlTablehtmltoolshtmlwidgetshttpcodehttrigraphisobanditeratorsjquerylibjsonliteKernSmoothkknnknitrlabelinglaterlatticelazyevallifecyclelistenvlubridatemagrittrMASSMatrixmatrixStatsmemoisemgcvmimemlegpmodeestmunsellmvtnormnatservncdf4neonstoreneonUtilitiesnlmenneonnetopenssloptparseparallellypbapplypbvPEcAn.benchmarkPEcAn.data.atmospherePEcAn.data.landPEcAn.DBPEcAn.loggerPEcAn.remotePEcAn.settingsPEcAn.utilsPEcAn.visualizationpermutephangornpillarpkgconfigplotlyplyrpngpolyclippolycorprettyunitsprocessxprogresspromisesproxypspurrrqapquadprogR.methodsS3R.ooR.utilsR6rappdirsrasterratelimitrRColorBrewerRcppRcppArmadilloRCurlreadrreadxlREddyProcregistryrematchrentrezreshape2rexritisrjagsrjsonrlangrmarkdownrmutilrnclrobustbaserotlrpartrredlistrstudioapirunjagsrvests2sassscalesselectrseriationsfsignalSimilarityMeasuressirtsolartimesolriumspspatialspatstat.dataspatstat.geomspatstat.univarspatstat.utilsstablestablediststatipstorrstringistringrsuntoolsswfscMiscsysTAMtaxizeterrathortibbletidyrtidyselecttimechangetimeDatetimeSeriestinytextraitstriebeardtruncnormTSPtzdbunitsurltoolsutf8uuidvctrsveganviridisviridisLitevroomwebshotwhiskerWikidataQueryServiceRWikidataRWikipediRwikitaxawithrwkworrmsxfunXMLxml2xtsyamlzipzoo

Readme and manuals

Help Manual

Help pageTopics
Check if value is between (inclusive) a rangebetween
Check individual ED input filescheck_css check_pss check_site
Check individual ED metfilecheck_ed_metfile
Check ED met header objectcheck_ed_metheader check_ed_metheader_format
Check ED2INcheck_ed2in
Convert parameters from PEcAn database default units to ED defaultsconvert.samples.ED
Create css, pss, and site files from examplescreate_css create_pss create_site
Create full ED vegetation input objectcreate_ed_veg
Get all the dates in a monthdates_in_month
Download ED inputsdownload_edi
Lookup function for translating commonly used ED variables returns out list, readvar variables to read from file, expr if any derivation is neededed.var
Convert ED2IN 'ITIMEA/Z' string to hour and minuteed2in2time
Example css, pss, and site objectsexample_css example_pss example_site
Extract pft numbers from settings$pftsextract_pfts
Get ED2 config.xml fileget_configxml.ED2
Extract sequence of dates from ED2IN fileget_ed2in_dates
Parse latitude or longitudeget_latlon
Get meteorology datesget_met_dates
Get ED history restart file pathget_restartfile.ED2
Check if object is 'ed2in'is.ed2in
List only files in a directorylist.files.nodir
Description of meteorology flagsmet_flag_description
Description of meteorology variablesmet_variable_description
met2model wrapper for ED2met2model.ED2
Code to convert ED2's -T- HDF5 output into netCDF formatmodel2netcdf.ED2
Modify a reference 'data.frame'modify_df
Modify an ED2IN objectmodify_ed2in
Create a CSV from history.xml outputed by EDparse.history
Generate ED2 cohort to patch mapping vectorpatch_cohort_index
Mapping of PEcAn PFT names to ED2 PFT numberspftmapping
Format file name for ED vegetation inputsprepare_ed_veg_filename
Print method for 'ed2in'print.ed2in
Put -E- values to nc_var listput_E_values
Function for put -T- values to nc_var listput_T_values
Read individual css, pss, and site filesread_css read_pss read_site
Function for reading -E- filesread_E_files
Read ED meteorology header fileread_ed_metheader
Read ED2 vegetation inputsread_ed_veg
Read ED2IN file to named listread_ed2in
State data assimilation read-restart for ED2read_restart.ED2
Read "S" files output by ED2read_S_files
Function for reading -T- filesread_T_files
Clear out old config and ED model run files.remove.config.ED2
Run ED singularity containerrun_ed_singularity
Use semi-analytic solution to accelerate model spinupSAS.ED2
sets parameters and defaults for the ED2 semi-analytical spin-upSAS.ED2.param.Args
Format ED2IN tag-value listtags2char
Function translating pecan vars to ED varstranslate_vars_ed
Writes ED specific IC filesveg2model.ED2
Write individual ED inputswrite_css write_pss write_site
Write ED meteorlogy headerwrite_ed_metheader
Write ED inputs to directorywrite_ed_veg
Write ED2IN list to filewrite_ed2in write_ed2in.default write_ed2in.ed2in
Write ED2 restart file from SDA resultswrite_restart.ED2
Write ED configuration fileswrite.config.ED2
Write ED2 job.sh filewrite.config.jobsh.ED2
Write ED2 config.xml filewrite.config.xml.ED2
Imports from other packageszz.imports