Package 'PEcAn.workflow'

Create a PEcAn XML file and use it to run a PEcAn workflow

Description

Create a PEcAn XML file and use it to run a PEcAn workflow

Usage

create_execute_test_xml(
  model_id,
  met,
  site_id,
  start_date,
  end_date,
  dbfiles_folder,
  user_id,
  output_folder = "batch_test_output",
  pecan_path = getwd(),
  pft = NULL,
  ensemble_size = 1,
  sensitivity_variable = "NPP",
  sensitivity = FALSE,
  db_bety_username = NULL,
  db_bety_password = NULL,
  db_bety_hostname = NULL,
  db_bety_port = NULL,
  db_bety_driver = "Postgres"
)

Arguments

model_id	(numeric) Model ID (from 'models' table)
met	(character) Name of meteorology input source (e.g. '"CRUNCEP"')
site_id	(numeric) Site ID (from 'sites' table)
start_date	(character or date) Run start date
end_date	(character or date) Run end date
dbfiles_folder	(character) Path to 'dbfiles' directory
user_id	(numeric) User ID to associate with the workflow
output_folder	(character) Path to root directory for storing outputs. Default = '"batch_test_output"'
pecan_path	(character) Path to PEcAn source code. Default is current working directory.
pft	(character) Name of PFT to run. If 'NULL' (default), use the first PFT in BETY associated with the model.
ensemble_size	(numeric) Number of ensembles to run. Default = 1.
sensitivity_variable	(character) Variable for performing sensitivity analysis. Default = '"NPP"'
sensitivity	(logical) Whether or not to perform a sensitivity analysis (default = 'FALSE')
db_bety_username, db_bety_password, db_bety_hostname, db_bety_port	(character) BETY database connection options. Default values for all of these are pulled from '<pecan_path>/web/config.php'.
db_bety_driver	(character) BETY database connection driver (default = '"Postgres"')

Value

A list with two entries: * 'sys': Exit value returned by the workflow (0 for sucess). * 'outdir': Path where the workflow results are saved

Author(s)

Alexey Shiklomanov, Tony Gardella

---

do_conversions

Description

Input conversion workflow

Usage

do_conversions(
  settings,
  overwrite.met = FALSE,
  overwrite.fia = FALSE,
  overwrite.ic = FALSE
)

Arguments

settings	PEcAn settings list
overwrite.met, overwrite.fia, overwrite.ic	logical

Author(s)

Ryan Kelly, Rob Kooper, Betsy Cowdery, Istem Fer

---

model_specific_tags

Description

model_specific_tags

Usage

model_specific_tags(settings, model.info)

Arguments

settings	pecan xml settings
model.info	model info extracted from bety

Value

updated settings list

---

Write model-specific run scripts and configuration files

Description

Generates run scripts and configuration files for all analyses specified in the provided settings. Most of the heavy lifting is done by the write.config.* function for your specific ecosystem model (e.g. write.config.ED2, write.config.SIPNET).

Usage

run.write.configs(
  settings,
  write = TRUE,
  ens.sample.method = "uniform",
  posterior.files = rep(NA, length(settings$pfts)),
  overwrite = TRUE
)

Arguments

settings	a PEcAn settings list
write	should the runs be written to the database?
ens.sample.method	how to sample the ensemble members('halton' sequence or 'uniform' random)
posterior.files	Filenames for posteriors for drawing samples for ensemble and sensitivity analysis (e.g. post.distns.Rdata, or prior.distns.Rdata)
overwrite	logical: Replace output files that already exist?

Details

The default value for posterior.files is NA, in which case the most recent posterior or prior (in that order) for the workflow is used. When specified, posterior.files should be a vector of filenames with one entry for each PFT. Specify filenames with no path; PFT outdirs will be appended. This forces use of only files within this workflow, to avoid confusion.

Value

an updated settings list, which includes ensemble IDs for SA and ensemble analysis

Author(s)

David LeBauer, Shawn Serbin, Ryan Kelly, Mike Dietze

---

Get trait data for all PFTs in a settings list

Description

Get trait data for all PFTs in a settings list

Usage

runModule.get.trait.data(settings)

Arguments

settings

PEcAn configuration list. Must have class 'Settings' or 'MultiSettings'

---

Generate model-specific run configuration files for one or more PEcAn runs

Description

Generate model-specific run configuration files for one or more PEcAn runs

Usage

runModule.run.write.configs(settings, overwrite = TRUE)

Arguments

settings	a PEcAn Settings or MultiSettings object
overwrite	logical: Replace config files if they already exist?

Value

A modified settings object, invisibly

---

Start selected ecosystem model runs within PEcAn workflow

Description

Start selected ecosystem model runs within PEcAn workflow

Usage

start_model_runs(settings, write = TRUE, stop.on.error = TRUE)

runModule_start_model_runs(settings, stop.on.error = TRUE)

Arguments

settings	pecan settings object
write	(logical) Whether or not to write to the database. Default TRUE.
stop.on.error	Throw error if _any_ of the runs fails. Default TRUE.

Functions

• runModule_start_model_runs(): A lightweight wrapper around 'start_model_runs' that takes 'write' from 'settings' instead of as a separate argument.

Author(s)

Shawn Serbin, Rob Kooper, David LeBauer, Alexey Shiklomanov

Examples

## Not run: 
  start_model_runs(settings)

## End(Not run)

---