Package 'PEcAn.SIPNET'

Merge multiple NetCDF files into one

Description

Merge multiple NetCDF files into one

Usage

mergeNC(files, outfile)

Arguments

files	character. List of filepaths, which should lead to NetCDF files.
outfile	character. Output filename of the merged data.

Value

A NetCDF file containing all of the merged data.

Source

https://github.com/RS-eco/processNC/blob/main/R/mergeNC.R

Examples

## Not run: 
files <- list.files(paste0(system.file(package="processNC"), "/extdata"), 
                    pattern="tas.*\\.nc", full.names=TRUE)
temp <- tempfile(fileext=".nc")
mergeNC(files=files, outfile=temp)
terra::rast(temp) 

## End(Not run)

---

met2model.SIPNET

Description

met2model wrapper for SIPNET

Usage

met2model.SIPNET(
  in.path,
  in.prefix,
  outfolder,
  start_date,
  end_date,
  overwrite = FALSE,
  verbose = FALSE,
  year.fragment = FALSE,
  ...
)

Arguments

in.path	location on disk where inputs are stored
in.prefix	prefix of input and output files OR the full file name if year.fragment = TRUE
outfolder	location on disk where outputs will be stored
start_date	the start date of the data to be downloaded (will only use the year part of the date)
end_date	the end date of the data to be downloaded (will only use the year part of the date)
overwrite	should existing files be overwritten
verbose	should the function be very verbose
year.fragment	the function should ignore whether or not the data is stored as a set of complete years (such as for forecasts).
...	Additional arguments, currently ignored

Author(s)

Luke Dramko, Michael Dietze, Alexey Shiklomanov, Rob Kooper

---

Convert SIPNET output to netCDF

Description

Converts all output contained in a folder to netCDF.

Usage

model2netcdf.SIPNET(
  outdir,
  sitelat,
  sitelon,
  start_date,
  end_date,
  delete.raw = FALSE,
  revision,
  prefix = "sipnet.out",
  overwrite = FALSE,
  conflict = FALSE
)

Arguments

outdir	Location of SIPNET model output
sitelat	Latitude of the site
sitelon	Longitude of the site
start_date	Start time of the simulation
end_date	End time of the simulation
delete.raw	logical: remove sipnet.out files after converting?
revision	model revision
prefix	prefix to read the output files
overwrite	Flag for overwriting nc files or not
conflict	Flag for dealing with conflicted nc files, if T we then will merge those, if F we will jump to the next.

Author(s)

Shawn Serbin, Michael Dietze

---

Read restart function for SDA with SIPNET

Description

Read Restart for SIPNET

Usage

read_restart.SIPNET(outdir, runid, stop.time, settings, var.names, params)

Arguments

outdir	Output directory
runid	Run ID
stop.time	Year that is being read
settings	PEcAn settings object
var.names	Variable names to be extracted
params	Any parameters required for state calculations

Value

X.vec vector of forecasts

Author(s)

Ann Raiho [email protected]

---

Clear out previous SIPNET config and parameter files.

Description

Clear out previous SIPNET config and parameter files.

Usage

remove.config.SIPNET(main.outdir, settings)

Arguments

main.outdir	Primary PEcAn output directory (will be depreciated)
settings	PEcAn settings file

Value

nothing, removes config files as side effect

Author(s)

Shawn Serbin, David LeBauer

---

Sample initial conditions for SIPNET

Description

Sample initial conditions for SIPNET

Usage

sample.IC.SIPNET(ne, state, year = 1)

Arguments

ne	number of ensembles
state	state variables you want to pull
year	year to pull from

Value

IC matrix of initial conditions

Author(s)

Mike Dietze and Ann Raiho

---

Convert SIPNET DOY to datetime

Description

Convert SIPNET DOY to datetime

Usage

sipnet2datetime(sipnet_tval, base_year, base_month = 1, force_cf = FALSE)

Arguments

sipnet_tval	vector of SIPNET DOY values
base_year	base year to calculate datetime from DOY
base_month	reference month for converting from DOY to datetime
force_cf	force output to follow CF convention. Default FALSE

Author(s)

Alexey Shiklomanov, Shawn Serbin

---

split_inputs.SIPNET

Description

Splits climate met for SIPNET

Usage

split_inputs.SIPNET(
  settings,
  start.time,
  stop.time,
  inputs,
  overwrite = FALSE,
  outpath = NULL
)

Arguments

settings	PEcAn settings object
start.time	start date and time for each SDA ensemble
stop.time	stop date and time for each SDA ensemble
inputs	list of model inputs to use in write.configs.SIPNET
overwrite	Default FALSE
outpath	if specified, write output to a new directory. Default NULL writes back to the directory being read

Value

file split up climate file

Author(s)

Mike Dietze and Ann Raiho

---

veg2model.SIPNET

Description

veg2model.SIPNET

Usage

veg2model.SIPNET(outfolder, poolinfo, siteid, ens)

Arguments

outfolder	location to store ncdf files
poolinfo	object passed from write_ic contains output from cohort2pool function
siteid	object passed from write_ic contains site id
ens	number of ensemble members

Value

result object with filepaths to ncdf files

Author(s)

Alexis Helgeson

---

write_restart.SIPNET

Description

Write restart files for SIPNET. WARNING: Some variables produce illegal values < 0 and have been hardcoded to correct these values!!

Usage

write_restart.SIPNET(
  outdir,
  runid,
  start.time,
  stop.time,
  settings,
  new.state,
  RENAME = TRUE,
  new.params = FALSE,
  inputs,
  verbose = FALSE
)

Arguments

outdir	output directory
runid	run ID
start.time	start date and time for each SDA ensemble
stop.time	stop date and time for each SDA ensemble
settings	PEcAn settings object
new.state	analysis state vector
RENAME	flag to either rename output file or not
new.params	list of parameters to convert between different states
inputs	list of model inputs to use in write.configs.SIPNET
verbose	decide if we want to print the outputs.

Value

NONE

Author(s)

Ann Raiho [email protected]

---

Writes a configuration files for SIPNET model

Description

Writes a configuration files for your model

Usage

write.config.SIPNET(
  defaults,
  trait.values,
  settings,
  run.id,
  inputs = NULL,
  IC = NULL,
  restart = NULL,
  spinup = NULL
)

Arguments

defaults	pft
trait.values	vector of samples for a given trait
settings	PEcAn settings object
run.id	run ID
inputs	list of model inputs
IC	initial condition
restart	In case this is a continuation of an old simulation. restart needs to be a list with name tags of runid, inputs, new.params (parameters), new.state (initial condition), ensemble.id (ensemble id), start.time and stop.time.See Details.
spinup	currently unused, included for compatibility with other models

Author(s)

Michael Dietze

---