Man pages for osmose-model/osmose
Object Oriented Simulator of Marine Ecosystems

configureCalibrationReads calibration parameters from an osmose.config list.
correct_ltl_fileCreates a NetCDF file containing the new format for LTL...
existOsmoseParameterCheck if a parameter exists
extract_grid_maskExtracts the model grid file from the LTL forcing file.
extract_grid_paramComputes the Osmose grid parameters by using the LTL forcing...
find_species_indexReturns the index of a species within the configuration.
getAverageMortalityComputes the average mortality.
getFishingBaseRateGet fishing base rate.
getFishingBaseRate.byDtGet fishing base rate using time-step rates.
getFishingBaseRate.byYearGet fishing base rate using annual rates.
getFishingBaseRate.constantGet fishing base rate using constant rate
getFishingBaseRate.linearGet fishing base rate using a linear rate
getFishingMortalityGet fishing mortality rate.
getMortalityGet the total mortality rate.
getMortalityDeviationComputes the mortality deviation. The "proxy", which is...
getOsmoseParameterGet a parameter from a name chain (error if not found).
getSizeSpectrumGet size spectrum
getVarGet variable
getVar.osmoseGetVar method for osmose outputs objects
getVar.osmose.configGetVar method for osmose configuration objects
make_movement_netcdfConverts the movement CSV settings into a set of NetCDF files...
osmose-packageOSMOSE: Modelling Marine Exploited Ecosystems
plot.osmosePlot method for osmose objects
plot.osmose.abundancePlot function for abundance
plot.osmose.biomassPlot function for biomass
plot.osmose.configTitle
plot.osmose.yieldPlot function for yield
plot.osmose.yieldNPlot function for yield
print.osmosePrint informations about Osmose outputs
print.summary.osmosePrint the summary informations about Osmose outputs
read_osmoseRead OSMOSE outputs into an R object
readOsmoseConfigurationReads Osmose configuration files.
readOsmoseFilesRead Osmose output file
reportReport method
report.osmoseReport method for osmose objects
run_osmoseRun an OSMOSE configuration
runOsmoseTitle
summary.osmoseSummarizes informations about Osmose outputs
summary.osmose.dietMatrixTitle
summary.osmose.mortalityRateTitle
writeFishingFilesWrite fishing files from osmose configuration list.
write_osmoseWrite data in osmose format
osmose-model/osmose documentation built on Dec. 13, 2018, 8:09 a.m.