Object Oriented Simulator of Marine Ecosystems


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Documentation for package ‘osmose’ version 3.3.4

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osmose-package OSMOSE: Modelling Marine Exploited Ecosystems
.osmose.barplot Plots a barplot, with xlabels rotated with a 45degree angle
.osmose.format_data_stacked Reformat the data into the ggplot2 stacked plot format. It returns a dataframe with specie, time and predation rate in the columns.
.plot_osmose_dietMatrix Plots diet matrix
.read_2D Generic function to read 2D output files (dietMatrix, sizeSpectrum, etc). If no file is found, it returns NULL.
.read_osmose_ncdf Function to read osmose netcdf files
cacheManager Manage the cache
configureCalibration Reads calibration parameters from an osmose.config list.
getVar Get variable from an 'osmose'-like object.
get_var Get variable from an 'osmose'-like object.
get_var.osmose get_var method for osmose outputs objects
get_var.osmose.config get_var method for osmose configuration objects
osmose OSMOSE: Modelling Marine Exploited Ecosystems
osmose2R Read OSMOSE outputs into an R object
osmose_demo Generates required OSMOSE configuration files to run a demo.
plot.osmose Plot method for osmose objects
plot.osmose.abundance Plot method for osmose objects
plot.osmose.abundanceByAge Plot method for osmose objects
plot.osmose.abundanceBySize Plot method for osmose objects
plot.osmose.abundanceByTL Plot method for osmose objects
plot.osmose.biomass Plot method for osmose objects
plot.osmose.biomassByAge Plot method for osmose objects
plot.osmose.biomassBySize Plot method for osmose objects
plot.osmose.biomassByTL Plot method for osmose objects
plot.osmose.config Plot method for 'osmose.config' objects
plot.osmose.config.predation Plot method for 'osmose.config' objects
plot.osmose.config.reproduction Plot method for 'osmose.config' objects
plot.osmose.config.species Plot method for 'osmose.config' objects
plot.osmose.yield Plot method for osmose objects
plot.osmose.yieldByAge Plot method for osmose objects
plot.osmose.yieldBySize Plot method for osmose objects
plot.osmose.yieldN Plot method for osmose objects
plot.osmose.yieldNByAge Plot method for osmose objects
plot.osmose.yieldNBySize Plot method for osmose objects
print.osmose Print information for an 'osmose' object
print.summary.osmose Print the summary informations about Osmose outputs
readOsmoseConfiguration Reads Osmose configuration files.
readOsmoseFiles Read Osmose output file
read_osmose Read OSMOSE outputs into an R object
report Report method
report.osmose Report method for 'osmose' objects
runOsmose Run an OSMOSE configuration
run_osmose Run an OSMOSE configuration
summary.osmose 'osmose' object summaries
summary.osmose.dietMatrix Title
summary.osmose.mortalityRate Title
updateCache Update the cache for the different function
write.osmose Write data in osmose format
write_osmose Write data in osmose format