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osmose (version 0.1.1)

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

0.1.1

License

CeCILL

Maintainer

Nicolas Barrier

Last Published

January 9th, 2018

Functions in osmose (0.1.1)

configureCalibration

Reads calibration parameters from an osmose.config list.
getAverageMortality

Computes the average mortality.
getFishingBaseRate.linear

Get fishing base rate using a linear rate
getFishingMortality

Get fishing mortality rate.
getFishingBaseRate.byYear

Get fishing base rate using annual rates.
getFishingBaseRate.constant

Get fishing base rate using constant rate
getMortality

Get the total mortality rate.
getMortalityDeviation

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

Get fishing base rate.
getFishingBaseRate.byDt

Get fishing base rate using time-step rates.
getOsmoseParameter

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

Get size spectrum
read_osmose

Read OSMOSE outputs into an R object
osmose-package

OSMOSE: Modelling Marine Exploited Ecosystems
plot.osmose

Plot method for osmose objects
runOsmose

Run an OSMOSE configuration
print.osmose

Print informations about Osmose outputs
print.summary.osmose

Print the summary informations about Osmose outputs
writeFishingFiles

Write fishing files from osmose configuration list.
readOsmoseConfiguration

Reads Osmose configuration files.
readOsmoseFiles

Read Osmose output file
getVar

Get variable
getVar.osmose

GetVar method for osmose objects
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.