Package 'PEcAn.BASGRA'

Read restart function for SDA with BASGRA

Description

Read Restart for BASGRA

Usage

read_restart.BASGRA(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)

Istem Fer

---

run BASGRA model

Description

BASGRA wrapper function. Runs and writes model outputs in PEcAn standard.

Usage

run_BASGRA(
  run_met,
  run_params,
  site_harvest,
  site_fertilize,
  start_date,
  end_date,
  outdir,
  sitelat,
  sitelon,
  co2_file = NULL,
  write_raw_output = FALSE
)

Arguments

run_met	path to CF met
run_params	parameter vector
site_harvest	path to harvest file
site_fertilize	path to fertilizer application file
start_date	start time of the simulation
end_date	end time of the simulation
outdir	where to write BASGRA output
sitelat	latitude of the site
sitelon	longitude of the site
co2_file	path to daily atmospheric CO2 concentration file, optional, defaults to 350 ppm when missing
write_raw_output	write raw output in csv or not

Details

BASGRA is written in fortran is run through R by wrapper functions written by Marcel Van Oijen. This function makes use of those wrappers but gives control of datastream in and out of the model to PEcAn. With this function we skip model2netcdf, we can also skip met2model but keeping it for now. write.config.BASGRA modifies args of this function through template.job then job.sh runs calls this function to run the model

Author(s)

Istem Fer, Julius Vira

---

write_restart.SIPNET

Description

Write restart files for BASGRA

Usage

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

Arguments

outdir	outout directory
runid	run id
start.time	Time of current assimilation step
stop.time	Time of next assimilation step
settings	pecan settings list
new.state	Analysis state matrix returned by sda.enkf
RENAME	flag to either rename output file or not
new.params	optional, additionals params to pass write.configs that are deterministically related to the parameters updated by the analysis
inputs	new input paths updated by the SDA workflow, will be passed to write.configs

Value

TRUE if successful

Author(s)

Istem Fer

---

Write BASGRA configuration files

Description

Writes a BASGRA config file.

Usage

write.config.BASGRA(defaults, trait.values, settings, run.id, IC = NULL)

Arguments

defaults	list of defaults to process
trait.values	vector of samples for a given trait
settings	list of settings from pecan settings file
run.id	id of run
IC	initial conditions list

Details

Requires a pft xml object, a list of trait values for a single model run, and the name of the file to create

Value

configuration file for BASGRA for given run

Author(s)

Istem Fer

---