Package: PEcAn.utils 1.8.0.9000

Rob Kooper

PEcAn.utils: 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], Rob Kooper [aut, cre], David LeBauer [aut], Xiaohui Feng [aut], Dan Wang [aut], Carl Davidson [aut], Shawn Serbin [aut], Shashank Singh [aut], Chris Black [aut], Tanishq Jain [aut], University of Illinois, NCSA [cph]

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

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

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

Datasets:

On CRAN:

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

10.92 score 211 stars 35 packages 218 scripts 62 exports 27 dependencies

Last updated 2 days agofrom:38702163cb. Checks:1 OK, 7 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 17 2025
R-4.5-winWARNINGFeb 17 2025
R-4.5-macWARNINGFeb 17 2025
R-4.5-linuxWARNINGFeb 17 2025
R-4.4-winWARNINGFeb 17 2025
R-4.4-macWARNINGFeb 17 2025
R-4.3-winWARNINGFeb 17 2025
R-4.3-macWARNINGFeb 17 2025

Exports:arrhenius.scalingas.sequencebugs.rdistcf2datetimecf2doyclear.scratchconvert.exprconvert.inputdatetime2cfdatetime2doydays_in_yeardistn.statsdistn.table.statsdownload_filedownload.urlfull.pathget.ensemble.inputsget.parameter.statget.quantilesget.run.idget.sa.sample.listget.sa.samplesleft.pad.zeroslistToArgStringload_localload.modelpkgmatch_filemcmc.list2initmisc.are.convertiblemisc.convertmstmipvarn_leap_dayneed_packagespaste.statsr2bugs.distributionsread_web_configread.outputretry.funcrobustlyrsyncseconds_in_yearsendmailsshstatus.checkstatus.endstatus.skipstatus.startsummarize.resulttabnumtemp.settingstimezone_hourto_ncdimto_ncvartrait.lookuptransformstatstrylud_convertunit_is_parseableunits_are_equivalentvecpastezero.bounded.densityzero.truncate

Dependencies:abindclicpp11curldplyrfansigenericsgluelifecyclelubridatemagrittrncdf4PEcAn.loggerpillarpkgconfigpurrrR6Rcpprlangstringitibbletidyselecttimechangeunitsutf8vctrswithr

Readme and manuals

Help Manual

Help pageTopics
Arrhenius scalingarrhenius.scaling
Convert categorical variable into sequential integersas.sequence
bibtexifybibtexify
Sample from an R distribution using JAGSbugs.rdist
Capitalize a stringcapitalize
Convert CF-style date-time to POSIXct date-timecf2datetime
Removes previous model run output from worker node local scratch directories on EBI-CLUSTERclear.scratch
Convert expression to variable namesconvert.expr
Convert POSIXct date-time to CF-style date-timedatetime2cf
Extract Julian day from CF or POSIXct date-timescf2doy datetime2doy
Number of days in a yeardays_in_year
Distribution Statsdistn.stats
Helper function for computing summary statistics of a parametric distributiondistn.table.stats
Simple function to use ncftpget for FTP downloads behind a firewall.download_file
Try and download a file.download.url
Creates an absolute path to a folder.full.path
get.ensemble.inputsget.ensemble.inputs
Get Parameter Statisticsget.parameter.stat
Get Quantilesget.quantiles
returns an id representing a model runget.run.id
get sensitivity samples as a listget.sa.sample.list
Get sensitivity analysis samplesget.sa.samples
Further summarizes output from summary.mcmcget.stats.mcmc
Left Pad Zerosleft.pad.zeros
format a list of arguments as one comma-separated stringlistToArgString
Load an 'RData' file into a listload_local
Load model packageload.modelpkg
Match a filematch_file
Convert mcmc.list to initial condition listmcmc.list2init
checks that met2model function existsmet2model.exists
function to check whether units are convertible by misc.convert functionmisc.are.convertible
conversion function for the unit conversions that udunits cannot handle but often needed in PEcAn calculationsmisc.convert
return MstMIP variable as ncvarmstmipvar
n_leap_dayn_leap_day
Check if required packages are installed, and throw an informative error if not.need_packages
New xtablenewxtable
Paste Statspaste.stats
Probability Distribution Function Statisticspdf.stats
R package to support PEcAn, the Predictive Ecosystem AnalyzerPEcAn.utils-package package-pecan PECAn PEcAn pecan PEcAn.utils
convert R parameterizations to BUGS paramaterizationsr2bugs.distributions
Read 'config.php' file into an R listread_web_config
Read model outputread.output
Retry function X times before stopping in errorretry.func
Adverb to try calling a function 'n' times before giving uprobustly
R implementation of rsyncrsync
Number of seconds in a given yearseconds_in_year
Sends email. This assumes the program sendmail is installed.sendmail
R implementation of SSHssh
Standardized variable names and units for PEcAnstandard_vars
PEcAn workflow status trackingstatus status.check status.end status.skip status.start
Summarize results of replicate observations in trait data querysummarize.result
Table numberstabnum
Create a temporary settings filetemp.settings
Timezone Hourtimezone_hour
Make some values into an NCDF dimension variableto_ncdim
Define an NCDF variableto_ncvar
Dictionary of terms used to identify traits in ed, filenames, and figurestrait.lookup
Transform misc. statistics to SEtransformstats
Test if function gives an errortryl
Convert unitsud_convert
Check whether a string can be interpreted as a unitunit_is_parseable
Check if two unit strings are equivalentunits_are_equivalent
Convert vector to comma delimited stringvecpaste
Zero bounded density using log density transformzero.bounded.density
Zero Truncatezero.truncate