All functions

PEcAn

R package to support PEcAn, the Predictive Ecosystem Analyzer

arrhenius.scaling()

Arrhenius scaling

as.sequence()

as.sequence

bibtexify()

bibtexify

bugs.rdist()

bugs.rdist

capitalize()

Capitalize a string

clear.scratch()

Clear EBI-CLUSTER worker node local scratch directories of old PEcAn output

convert.expr()

convert.expr

convert.input()

Convert between formats, reusing existing files where possible

create.base.plot()

Create Base Plot

days_in_year()

Number of days in a year

dhist()

Diagonally Cut Histogram

distn.stats()

Distribution Stats

distn.table.stats()

return mean and standard deviation of a distribution for each distribution in a table with colnames = c('distn', 'a', 'b'), e.g. in a table of priors

do_conversions()

do_conversions

download.file()

download.file

download.url()

Download file from the url.

ensemble.filename()

Generate ensemble filenames

full.path()

Creates an absolute path to a folder

get.ensemble.inputs()

get.ensemble.inputs

get.ensemble.samples()

Get Ensemble Samples

get.model.output()

Retrieve model output

get.parameter.stat()

Get Parameter Statistics

get.quantiles()

Get Quantiles

get.results()

Generate model output for PEcAn analyses

get.run.id()

Get Run ID

get.sa.sample.list()

get.sa.sample.list

get.sa.samples()

get sensitivity analysis samples

get.stats.mcmc()

Get stats for parameters in MCMC output

grid2netcdf()

grid2netcdf

iqr()

Interquartile range

left.pad.zeros()

Left Pad Zeros

listToArgString()

format a list of arguments as one comma-separated string

load.modelpkg()

Load model package

logger.debug()

Logger functions (imported temporarily from PEcAn.logger)

match_file()

Match a file

mcmc.list2init()

Convert mcmc.list to initial condition list

met2model.exists()

met2model.exists

misc.are.convertible()

misc.are.convertible

misc.convert()

misc.convert

mstmipvar()

MstMIP variable

n_leap_day()

n_leap_day

newxtable()

newxtable

paste.stats()

Paste Stats

pdf.stats()

Probability Distirbution Function Statistics

plot_data()

Add data to plot

r2bugs.distributions()

convert R parameterizations to BUGS paramaterizations

read.ensemble.output()

Read ensemble output

read.output()

Read model output

read.sa.output()

Read Sensitivity Analysis output

read_web_config()

read_web_config

regrid()

regrid

retry.func()

retry.func

rsync()

rsync

run.write.configs()

Run model specific write configuration functions

seconds_in_year()

Number of seconds in a given year

sendmail()

Clear EBI-CLUSTER worker node local scratch directories of old PEcAn output

sensitivity.filename()

Generate sensitivity analysis filenames

ssh()

SSH

standard_vars

Standardized variable names and units for PEcAn

status.check()

status.check

status.end()

status.end

status.skip()

status.skip

status.start()

status.start

summarize.result()

Summarize Results

tabnum()

Table numbers

temp.settings()

temp.settings

theme_border()

Theme border for plot

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 Stats

tryl()

tryl

units_are_equivalent()

Check if two unit strings are equivalent

vecpaste()

vecpaste

write.ensemble.configs()

Write ensemble configs

write.sa.configs()

Write sensitivity analysis config files

zero.bounded.density()

Zero Bounded Density

zero.truncate()

Zero Truncate