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osmose (version 0.1.0)

Object Oriented Simulator of Marine Ecosystems

Description

The multispecies and individual-based model (IBM) 'OSMOSE' (Shin and Curry (2001) and Shin and Curry (2004) ) focuses on fish species. This model assumes opportunistic predation based on spatial co-occurrence and size adequacy between a predator and its prey (size-based opportunistic predation). It represents fish individuals grouped into schools, which are characterized by their size, weight, age, taxonomy and geographical location (2D model), and which undergo major processes of fish life cycle (growth, explicit predation, natural and starvation mortalities, reproduction and migration) and fishing exploitation. The model needs basic biological parameters that are often available for a wide range of species, and which can be found in 'FishBase' for instance (see ), and fish spatial distribution data. This package provides tools to build and run simulations using the 'OSMOSE' model.

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Version

Install

install.packages('osmose')

Monthly Downloads

21

Version

0.1.0

License

CeCILL

Maintainer

Nicolas Barrier

Last Published

December 11th, 2017

Functions in osmose (0.1.0)

osmose-package

OSMOSE: Modelling Marine Exploited Ecosystems
getFishingBaseRate.constant

Get fishing base rate using constant rate
plot.osmose

Plot method for osmose objects
getFishingBaseRate.linear

Get fishing base rate using a linear rate
print.osmose

Print informations about Osmose outputs
print.summary.osmose

Print the summary informations about Osmose outputs
getFishingMortality

Get fishing mortality rate.
getFishingBaseRate.byDt

Get fishing base rate using time-step rates.
configureCalibration

Reads calibration parameters from an osmose.config list.
getOsmoseParameter

Get a parameter from a name chain (error if not found).
getSizeSpectrum

Get size spectrum
getAverageMortality

Computes the average mortality.
writeFishingFiles

Write fishing files from osmose configuration list.
readOsmoseConfiguration

Reads Osmose configuration files.
getMortality

Get the total mortality rate.
readOsmoseFiles

Read Osmose output file
getMortalityDeviation

Computes the mortality deviation. The "proxy", which is removed, can be provided by the user in the "pars" argument.
summary.osmose

Summarizes informations about Osmose outputs
write.osmose

Write an array or dataframe in the Osmose format. The separator is ";", there are no quotes and a blank column is added for the row names column.
getFishingBaseRate

Get fishing base rate.
getVar

Get variable
getVar.osmose

GetVar method for osmose objects
read_osmose

Read OSMOSE outputs into an R object
runOsmose

Run an OSMOSE configuration
getFishingBaseRate.byYear

Get fishing base rate using annual rates.