osmose (version 3.3.4)

runOsmose: 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 = "3.3.3",
  osmose = NULL,
  java = "java",
  options = NULL,
  verbose = TRUE,
  clean = TRUE
)

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.

Details

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

Examples

# NOT RUN {
{
  
# }
# NOT RUN {
    path = cacheManager("gog")
    filename = file.path(path, "osm_all-parameters.csv")
    run_osmose(filename)
  
# }
# NOT RUN {
}
# }