Package: PEcAn.data.land 1.8.0.9000

Mike Dietze

PEcAn.data.land: 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 [aut, cre], David LeBauer [aut], Xiaohui Feng [ctb], Dan Wang [ctb], Carl Davidson [ctb], Rob Kooper [ctb], Alexey Shiklomanov [ctb], University of Illinois, NCSA [cph]

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

# Install 'PEcAn.data.land' in R:
install.packages('PEcAn.data.land', 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:
  • BADM - Biomass and soil data from FluxNet sites
  • iscn_soc - Soil organic carbon (SOC) density based on eco-region level 2 code from the ISCN database.
  • soil_class - Default parameters for calculating soil properties from sand & clay content

On CRAN:

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

59 exports 202 stars 6.47 score 209 dependencies 8 dependents 19 scripts

Last updated 5 hours agofrom:f22a7c4bbc. Checks:OK: 1 ERROR: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 18 2024
R-4.5-winERRORSep 18 2024
R-4.5-linuxERRORSep 18 2024
R-4.4-winERRORSep 18 2024
R-4.4-macERRORSep 18 2024
R-4.3-winERRORSep 18 2024
R-4.3-macERRORSep 18 2024

Exports:BADM_IC_processbuildJAGSdata_InventoryRingsClean_Tucsoncohort2pooldataone_downloaddownload_package_rmdownload.SM_CDSens_veg_moduleEPA_ecoregion_finderextract_FIAextract_NEON_vegextract_SM_CDSextract_soil_gssurgoextract_soil_ncextract_vegextract.stringCodefia.to.psscssformat_identifierfrom.Tagfrom.TreeCodeget_resource_mapget_veg_moduleget.attributesget.soilgSSURGO.QueryIC_ISCN_SOCic_processid_resolveableInventoryGrowthFusionInventoryGrowthFusionDiagnosticsload_vegmatch_pftmatch_species_idmatchInventoryRingsmpot2smoistnetcdf.writer.BADMparse.MatrixNamespartition_rootsplot2AGBpool_ic_list2netcdfpool_ic_netcdf2listprepare_poolsput_veg_moduleRead_TucsonRead.IC.info.BADMsample_icsclassshp2kmlsoil_paramssoil_processsoil.unitssoil2netcdfsoilgrids_soilC_extractSoilgrids_SoilC_prepsubset_layerto.Tagto.TreeCodewrite_icwrite_veg

Dependencies:abindadmiscapeaskpassassertthatbackportsbase64encbitbit64blobbootbslibcachemCDMcheckmateclassclassIntclicliprclueclustercodacodetoolscolorspaceconditionzcpp11crayoncrulcurldata.tableDBIdbplyrdeldirdigestdownloaderdplRdplyrduckdbduckdbfse1071evaluatefansifarverfastmapfastmatchfBasicsfontawesomeforeachforeignFormulafsfurrrfuturegenericsgetoptggplot2ggrepelglobalsgluegridExtragssgtableHDIntervalhighrHmischmshoardrhtmlTablehtmltoolshtmlwidgetshttpcodehttrigraphisobanditeratorsjquerylibjsonliteKernSmoothkknnknitrlabelinglatticelazyevallifecyclelistenvlubridatemagrittrMASSMatrixmatrixStatsmemoisemgcvmimemodeestmunsellmvtnormnatservncdf4neonstoreneonUtilitiesnlmennetopenssloptparseparallellypbapplypbvPEcAn.benchmarkPEcAn.DBPEcAn.loggerPEcAn.remotePEcAn.settingsPEcAn.utilsPEcAn.visualizationphangornpillarpkgconfigplyrpngpolyclippolycorprettyunitsprogressproxypurrrquadprogR.methodsS3R.ooR.utilsR6rappdirsratelimitrRColorBrewerRcppRcppArmadilloreadrrentrezreshape2rexritisrjagsrlangrmarkdownrmutilrnclrotlrpartrredlistrstudioapirunjagsrvests2sassscalesselectrsfsignalSimilarityMeasuressirtsolriumspspatialspatstat.dataspatstat.geomspatstat.univarspatstat.utilsstablestablediststatipstorrstringistringrswfscMiscsysTAMtaxizeterrathortibbletidyrtidyselecttimechangetimeDatetimeSeriestinytextraitstriebeardtzdbunitsurltoolsutf8uuidvctrsviridisviridisLitevroomWikidataQueryServiceRWikidataRWikipediRwikitaxawithrwkworrmsxfunXMLxml2yamlzipzoo

Readme and manuals

Help Manual

Help pageTopics
Biomass and soil data from FluxNet sitesBADM
BADM_IC_processBADM_IC_process
Format ring & plot data for JAGAbuildJAGSdata_InventoryRings
Clean_TucsonClean_Tucson
cohort2poolcohort2pool
DataONE downloaddataone_download
Download NEON Soil Water Content and Soil Salinity data by date and site namedownload_NEON_soilmoist
download_packagesdownload_package_rm
Download CDS soil moisture data for the SDA workflow.download.SM_CDS
Sampling/ensemble moduleens_veg_module
EPA_ecoregion_finderEPA_ecoregion_finder
extract_FIAextract_FIA
extract_NEON_vegextract_NEON_veg
Extract CDS soil moisture data for the SDA workflow.extract_SM_CDS
Extract soil data from gssurgoextract_soil_gssurgo
Extract soil data from the gridpoint closest to a locationextract_soil_nc
extract_vegextract_veg
extract.stringCodeextract.stringCode
Create pss/css files based on data in the fia databasefia.to.psscss
format_identifierformat_identifier
from.Tagfrom.Tag
from.TreeCodefrom.TreeCode
get_resource_mapget_resource_map
Load/extract + match species moduleget_veg_module
Retrieve attribute information from a vector or raster layerget.attributes
get.soilget.soil
This function queries the gSSURGO database for a series of map unit keysgSSURGO.Query
Extract ISCN SOC initial conditions from existing ISCN database.IC_ISCN_SOC
ic_processic_process
id_resolveableid_resolveable
InventoryGrowthFusionInventoryGrowthFusion
InventoryGrowthFusionDiagnosticsInventoryGrowthFusionDiagnostics
Soil organic carbon (SOC) density based on eco-region level 2 code from the ISCN database.iscn_soc
load_vegload_veg
match_pftmatch_pft
Match BETY species ID.match_species_id
matchInventoryRingsmatchInventoryRings
Convert a matric potential to a soil moisturempot2smoist
netcdf.writer.BADAMnetcdf.writer.BADM
parse.MatrixNamesparse.MatrixNames
partition_rootspartition_roots
plot2AGBplot2AGB
pool_ic_list2netcdfpool_ic_list2netcdf
pool_ic_netcdf2listpool_ic_netcdf2list
prepare_poolsprepare_pools
Match species to PFTs + veg2model moduleput_veg_module
Read_TucsonRead_Tucson
Read.IC.info.BADMRead.IC.info.BADM
sample_icsample_ic
This function determines the soil class number based on the fraction of sand, clay, and siltsclass
Convert shapefile to KMLshp2kml
Default parameters for calculating soil properties from sand & clay contentsoil_class
Estimate soil parameters from texture class or sand/silt/claysoil_params
Module for managing soil texture extractionsoil_process
Get standard units for a soil variablesoil.units
Save soil texture & parameters in PEcAn standard netCDF CFsoil2netcdf
soilgrids_soilC_extractsoilgrids_soilC_extract
Prepare Soilgrids SoilC data for the SDA workflow.Soilgrids_SoilC_prep
Function to subset and clip a GIS vector or raster layer by a bounding box or clip/subset layer (e.g. shapefile/KML)subset_layer
to.Tagto.Tag
to.TreeCodeto.TreeCode
write_icwrite_ic
write_vegwrite_veg