run_osmose: Run an OSMOSE configuration

In roliveros-ramos/osmose: Object Oriented Simulator of Marine Ecosystems

Run an OSMOSE configuration

Description

This function create a valid configuration by several input files from user input parameters.

Usage

runOsmose(
  input,
  parameters = NULL,
  output = "output",
  log = "osmose.log",
  version = "4.1.0",
  osmose = NULL,
  java = "java",
  options = NULL,
  verbose = TRUE,
  clean = TRUE
)

run_osmose(
  input,
  parameters = NULL,
  output = NULL,
  log = "osmose.log",
  version = NULL,
  osmose = NULL,
  java = "java",
  options = NULL,
  verbose = TRUE,
  clean = TRUE,
  force = FALSE
)

Arguments

input	Filename of the main configuration file
parameters	Parameters to be passed to osmose (version 4 or higher).
output	Output directory. If NULL, the value set in the configuration file is used.
log	File to save OSMOSE execution messages.
version	OSMOSE version. Integer (2, 3, etc.) or releases ('v3r2') are accepted.
osmose	Path to a OSMOSE .jar executable. By default (NULL), uses the stable jar for the current version.
java	Path to the java executable. The default assumes 'java' is on the search path.
options	Java options (e.g. -Xmx2048m to increase memory limit).
verbose	Show messages? (output in the log file if FALSE).
clean	TRUE if the output directory should be cleaned before running OSMOSE.
force	TRUE if an outdated configuration can be run without being updated.

Details

Basic configurations may not need the use of buildConfiguration, but it is required for configuration using interannual inputs or fishing selectivity.

Author(s)

Ricardo Oliveros-Ramos

Examples

{
  ## Not run: 
    path = cacheManager("eec-4.3.0")
    filename = file.path(path, "osm_all-parameters.csv")
    run_osmose(filename)
  
## End(Not run)
}

roliveros-ramos/osmose documentation built on Feb. 19, 2023, 8:19 a.m.