Package index • PEcAn.utils

All functions

PEcAn.utils PEcAn.utils-package PEcAn PECAn pecan package-pecan: R package to support PEcAn, the Predictive Ecosystem Analyzer

arrhenius.scaling(): Arrhenius scaling

as.sequence(): Convert categorical variable into sequential integers

bibtexify(): bibtexify

bugs.rdist(): Sample from an R distribution using JAGS

capitalize(): Capitalize a string

cf2datetime(): Convert CF-style date-time to POSIXct date-time

clear.scratch(): Removes previous model run output from worker node local scratch directories on EBI-CLUSTER

convert.expr(): Convert expression to variable names

datetime2cf(): Convert POSIXct date-time to CF-style date-time

datetime2doy() cf2doy(): Extract Julian day from CF or POSIXct date-times

days_in_year(): Number of days in a year

distn.stats(): Distribution Stats

distn.table.stats(): Helper function for computing summary statistics of a parametric distribution

download.url(): Try and download a file.

download_file(): Simple function to use ncftpget for FTP downloads behind a firewall.

extract_nc_sda(): Extract netCDF file by site.id, time window, and variable name.

full.path(): Creates an absolute path to a folder.

get.ensemble.inputs(): get.ensemble.inputs

get.parameter.stat(): Get Parameter Statistics

get.quantiles(): Get Quantiles

get.run.id(): returns an id representing a model run

get.sa.sample.list(): get sensitivity samples as a list

get.sa.samples(): Get sensitivity analysis samples

get.stats.mcmc(): Further summarizes output from summary.mcmc

left.pad.zeros(): Left Pad Zeros

listToArgString(): format a list of arguments as one comma-separated string

load.modelpkg(): Load model package

load_local(): Load an RData file into a list

match_file(): Match a file

mcmc.list2init(): Convert mcmc.list to initial condition list

met2model.exists(): checks that met2model function exists

misc.are.convertible(): function to check whether units are convertible by misc.convert function

misc.convert(): conversion function for the unit conversions that udunits cannot handle but often needed in PEcAn calculations

mstmipvar(): return MstMIP variable as ncvar

n_leap_day(): n_leap_day

nc_merge_all_sites_by_year(): Combine many netCDFs into one file per year

nc_merge_single_site(): Merge model outputted netCDF files across ensembles for a single site.

nc_write_varfiles(): Summarize netcdf variables into text file

need_packages(): Check if required packages are installed, and throw an informative error if not.

newxtable(): New xtable

paste.stats(): Paste Stats

pdf.stats(): Probability Distribution Function Statistics

r2bugs.distributions(): convert R parameterizations to BUGS paramaterizations

read.output(): Read model output

read_web_config(): Read config.php file into an R list

retry.func(): Retry function X times before stopping in error

robustly(): Adverb to try calling a function n times before giving up

rsync(): R implementation of rsync

seconds_in_year(): Number of seconds in a given year

sendmail(): Sends email. This assumes the program sendmail is installed.

ssh(): R implementation of SSH

standard_vars: Standardized variable names and units for PEcAn

status.start() status.end() status.skip() status.check(): PEcAn workflow status tracking

summarize.result(): Summarize results of replicate observations in trait data query

tabnum(): Table numbers

temp.settings(): Create a temporary settings file

timezone_hour(): Timezone Hour

to_ncdim(): Make some values into an NCDF dimension variable

to_ncvar(): Define an NCDF variable

trait.lookup(): Dictionary of terms used to identify traits in ed, filenames, and figures

transformstats(): Transform misc. statistics to SE

tryl(): Test if function gives an error

ud_convert(): Convert units

unit_is_parseable(): Check whether a string can be interpreted as a unit

units_are_equivalent(): Check if two unit strings are equivalent

vecpaste(): Convert vector to comma delimited string

zero.bounded.density(): Zero bounded density using log density transform

zero.truncate(): Zero Truncate