Package: PEcAn.DB 1.8.0.9000

David LeBauer

PEcAn.DB: 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:David LeBauer [aut, cre], Mike Dietze [aut], Rob Kooper [aut], Shawn Serbin [aut], Elizabeth Cowdery [aut], Ankur Desai [aut], Istem Fer [aut], Alexey Shiklomanov [aut], Tony Gardella [aut], Chris Black [aut], Liam Burke [aut], Ryan Kelly [aut], Dan Wang [aut], Carl Davidson [aut], Xiaohui Feng [aut], Shashank Singh [aut], University of Illinois, NCSA [cph]

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

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

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

On CRAN:

Conda:

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

11.88 score 216 stars 27 packages 127 scripts 63 exports 55 dependencies

Last updated 3 hours agofrom:97e61070b6. Checks:6 OK, 3 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 14 2025
R-4.5-winNOTEMar 14 2025
R-4.5-macNOTEMar 14 2025
R-4.5-linuxNOTEMar 14 2025
R-4.4-winOKMar 14 2025
R-4.4-macOKMar 14 2025
R-4.4-linuxOKMar 14 2025
R-4.3-winOKMar 14 2025
R-4.3-macOKMar 14 2025

Exports:%>%append.covariateassign.treatmentsbety2pecanbetyConnectconvert_inputdb_merge_intodb.closedb.existsdb.getShowQueriesdb.opendb.print.connectionsdb.querydb.showQueriesdbfile.checkdbfile.filedbfile.iddbfile.input.checkdbfile.input.insertdbfile.insertdbfile.movedbfile.posterior.checkdbfile.posterior.insertdbHostInfodefault_hostnamederive.traitderive.traitsdplyr.countfancy_scientificget_postgres_envvarsget_run_idsget_usersget_var_namesget_workflow_idsget.idget.trait.dataget.trait.data.pftinsert_tableinsert.format.varsload_data_single_runmatch_dbcolsmet_inputsncdays2datequery_pftsquery_priorsquery.file.pathquery.format.varsquery.pft_cultivarsquery.pft_speciesquery.priorsquery.sitequery.trait.dataquery.traitsrunssearch_referencesstamp_finishedstamp_startedsymmetric_setdifftake.samplestry2sqlitevar_names_allworkflowworkflows

Dependencies:abindaskpassblobclicodetoolscpp11curlDBIdbplyrdigestdplyrfansiforeachfsfurrrfuturegenericsglobalsgluehttriteratorsjsonlitelifecyclelistenvlubridatemagrittrmimencdf4opensslparallellyPEcAn.loggerPEcAn.remotePEcAn.utilspillarpkgconfigpurrrR.methodsS3R.ooR.utilsR6Rcpprlangstringistringrsystibbletidyrtidyselecttimechangetriebeardunitsurltoolsutf8vctrswithr

Create PostGIS polygon

David LeBauer

Rendered fromcreate_sites.geometry.Rmdusingknitr::rmarkdownon Mar 14 2025.

Last update: 2022-07-18
Started: 2017-10-06

BETYdb Access

David LeBauer

Rendered frombetydb_access.Rmdusingknitr::rmarkdownon Mar 14 2025.

Last update: 2022-07-25
Started: 2017-10-06

Readme and manuals

Help Manual

Help pageTopics
Append covariate data as a column within a tableappend.covariate
Apply Arrhenius scaling to 25 degC for temperature-dependent traitsarrhenius.scaling.traits
assign.treatmentsassign.treatments
Convert BETY variable names to MsTMIP and subsequently PEcAn standard namesbety2pecan
Connect to bety using current PEcAn configurationbetyConnect
Compares two listscheck.lists
Duplicate existing pft with associated priors, species, and cultivarsclone_pft
Convert between formats, reusing existing files where possibleconvert_input
Merge local data frame into SQL tabledb_merge_into
Generic function to close a database connectiondb.close
Test connection to databasedb.exists
db.getShowQueriesdb.getShowQueries
Open a database connectiondb.open
Debug leaked connectionsdb.print.connections
Generic function to query databasedb.query
db.showQueriesdb.showQueries
List files associated with a container and machine exist in `dbfiles` tabledbfile.check
Convert between file paths and idsdbfile.file dbfile.id
Check for a file in the input/dbfiles tablesdbfile.input.check
Insert file into tablesdbfile.input.insert
Insert file into tablesdbfile.insert
Move files to new locationdbfile.move
Check for a file in the input/dbfiles tablesdbfile.posterior.check
Insert file into tablesdbfile.posterior.insert
Database host informationdbHostInfo
default_hostnamedefault_hostname
Performs an arithmetic function, FUN, over a series of traits and returns the result as a derived trait.derive.trait
Performs an arithmetic function, FUN, over a series of traits and returns the result as a derived trait.derive.traits
Count rows of a data framedplyr.count
Convert number to scientific notation pretty expressionfancy_scientific
Fetch data and transform stats to SEfetch.stats2se
Function to filter out upper canopy leavesfilter.sunleaf.traits filter_sunleaf_traits
Look up Postgres connection parameters from environment variablesget_postgres_envvars
Get vector of run IDs for a given workflow IDget_run_ids
Get data frame of users and IDsget_users
Get vector of variable names for a particular workflow and run IDget_var_names
Get vector of workflow IDsget_workflow_ids
get.idget.id
Get trait data from the database.get.trait.data
Get trait data from the database for a single PFTget.trait.data.pft
Insert R data frame into SQL databaseinsert_table
Insert Format and Format-Variable Recordsinsert.format.vars
Load data for a single run of the modelload_data_single_run
Match names of local data frame to SQL tablematch_colnames
Match column names and classes between local and SQL tablematch_dbcols
Retrieve available met inputs for the given site, model, and hostnamemet_inputs
Convert netcdf number of days to a datetimencdays2date
Associate species with a PFT.pft.add.spp
Retrieve PFT ID, name, and type from BETYquery_pfts
Query priors using prepared statementsquery_priors
Queries covariates from database for a given vector of trait id'squery.covariates
Query data and transform stats to SE by calling 'fetch.stats2se';query.data
Get file path given id and machinequery.file.path
Look up names and units of input variables from a format id or input idquery.format.vars
Select cultivars associated with a PFTquery.pft_cultivars
Query species given pft namequery.pft_species
Query Priorsquery.priors
Given site_id, return site tablequery.site
Extract trait data from databasequery.trait.data
Query trait dataquery.traits
Query yield data and transform stats to SE by calling 'fetch.stats2se';query.yields
Get table of runs corresponding to a workflowruns
Perform crossref search for a single referencesearch_reference_single
Perform crossref search for a list of referencessearch_references
Stamp start and stop times of runsstamp_finished stamp_started
Symmetric set difference of two data framessymmetric_setdiff
Sample from normal distribution, given summary statstake.samples
Convert TRY text file to SQLite databasetry2sqlite
Get vector of variable names for a particular workflow and run IDvar_names_all
Get single workflow by workflow_idworkflow
list of workflows that existworkflows