report.osmose

Object of <code>osmose</code> class.

The R Markdown output format to convert to (check 
<a rd-options="rmarkdown" href="/link/render?package=osmose&version=3.3.4&to=rmarkdown" data-mini-rdoc="rmarkdown::render">render</a>).

format

The output directory for the rendered the output file.

output

Boolean; whether to tangle the R code from the input file 
(check <a rd-options="rmarkdown" href="/link/render?package=osmose&version=3.3.4&to=rmarkdown" data-mini-rdoc="rmarkdown::render">render</a>).

tangle

Do you want to open the output file at the end? (only useful for 
MS Windows environment).

open

Extra arguments pased to <a rd-options="rmarkdown" href="/link/render?package=osmose&version=3.3.4&to=rmarkdown" data-mini-rdoc="rmarkdown::render">render</a>.

Build and export a report of <code>osmose</code> objects using
R markdown.

The multispecies and individual-based model (IBM) 'OSMOSE'
(Shin and Curry (2001) <doi:10.1016/S0990-7440(01)01106-8> and Shin and Curry
(2004) <doi:10.1139/f03-154>) 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 <http://www.fishbase.org/search.php>), and fish spatial
distribution data. This package provides tools to build and run simulations
using the 'OSMOSE' model.

Nicolas Barrier

osmose

Object Oriented Simulator of Marine Ecosystems

Yunne-Jai Shin

Travers Morgane

Verley Philippe

Ricardo Oliveros-Ramos

Laure Velez

Criscely Lujan

Michael Hurtado

Wencheng Lau-Medrano

report.osmose function

The R Markdown output format to convert to (check 
<a rd-options='rmarkdown' href='render'>render</a>).

Boolean; whether to tangle the R code from the input file 
(check <a rd-options='rmarkdown' href='render'>render</a>).

Extra arguments pased to <a rd-options='rmarkdown' href='render'>render</a>.

report.osmose: Report method for `osmose` objects

Description

Usage

Arguments