runOsmose | R Documentation |
This function create a valid configuration by several input files from user input parameters.
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 )
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TRUE if an outdated configuration can be run without being updated. |
Basic configurations may not need the use of buildConfiguration
,
but it is required for configuration using interannual inputs or fishing selectivity.
Ricardo Oliveros-Ramos
{ ## Not run: path = cacheManager("eec-4.3.0") filename = file.path(path, "osm_all-parameters.csv") run_osmose(filename) ## End(Not run) }
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