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

configureCalibrationReads calibration parameters from an osmose.config list.
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.osmose.outputGetVar method for osmose outputs objects
osmose.barplotPlots a barplot, with xlabels rotated with a 45degree angle
osmose.nc.extract_grid_maskExtracts the model grid file from the LTL forcing file.
osmose.nc.extract_grid_paramComputes the Osmose grid parameters by using the LTL forcing...
osmose.openfigureOpens a figure file.
osmose-packageOSMOSE: Modelling Marine Exploited Ecosystems
osmose.stackedpcentPlot a stacked percent plot.
plot.osmose.outputPlot method for osmose objects
plot.osmose.output.abundancePlots abundance time-series
plot.osmose.output.biomassPlots biomass.
plot.osmose.output.biomassDistribByAgePlots biomass by age class
plot.osmose.output.biomassDistribBySizePlots biomass by size class
plot.osmose.output.biomassDistribByTLPlots the biomass distribution by trophic level
plot.osmose.output.biomassPredPreyIniPlots the prey biomass before the mortality rate is applied
plot.osmose.output.dietMatrixPlots diet matrix
plot.osmose.output.meanSizePlots mean size.
plot.osmose.output.meanSizeCatchPlots mean size catch.
plot.osmose.output.meanTLPlots mean trophic level
plot.osmose.output.meanTLCatchPlots mean trophic level catch
plot.osmose.output.mortalityRatePlots mortality rates
plot.osmose.output.mortalityRateDistribByAgePlots mortality rates by age class.
plot.osmose.output.mortalityRateDistribBySizePlots mortality rates by size class.
plot.osmose.output.predatorPressurePlots predator pressure.
plot.osmose.output.yieldPlots yield time-series
plot.osmose.output.yieldNPlots yieldN
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
reportBuild an OSMOSE configuration
report.osmoseReport method for osmose objects
runOsmoseRun an OSMOSE configuration
summary.osmoseSummarizes informations about Osmose outputs
summary.osmose.output.dietMatrixTitle
summary.osmose.output.mortalityRateTitle
writeFishingFilesWrite fishing files from osmose configuration list.
write.osmoseWrite an array or dataframe in the Osmose format. The...
osmose-model/osmose documentation built on April 23, 2018, 3:23 a.m.