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 |