dBdt

Compute system of differential equations representing EcoState dynamics
derived from EcoSim.

Fits a state-space mass-balance model for marine ecosystems,
which implements dynamics derived from
'Ecopath with Ecosim' <https://ecopath.org/>
while fitting to time-series of fishery catch, biomass indices,
age-composition samples, and weight-at-age data. Package
'ecostate' fits biological parameters (e.g., equilibrium mass)
and measurement parameters (e.g., catchability coefficients)
jointly with residual variation in process errors, and can include
Bayesian priors for parameters.

James Thorson

ecostate

State-Space Mass-Balance Model for Marine Ecosystems

dBdt function

<dl><dt>Time</dt>
<dd>not used</dd>
<dt>State</dt>
<dd>vector of state variables to integrate</dd>
<dt>Pars</dt>
<dd>list of parameters governing the ODE</dd>
<dt>type_i</dt>
<dd>type for each taxon</dd>
<dt>n_species</dt>
<dd>number of species</dd>
<dt>F_type</dt>
<dd>whether to integrate catches along with biomass (<code>"integrated"</code>)
or calculate catches from the Baranov catch equation applied to average
biomass (<code>"averaged"</code>)</dd>
<dt>what</dt>
<dd>what output to produce</dd></dl>

Arguments

Dynamics from EcoSim — dBdt

<dl>

<dt>Time</dt>
<dd>not used</dd>


<dt>State</dt>
<dd>vector of state variables to integrate</dd>


<dt>Pars</dt>
<dd>list of parameters governing the ODE</dd>


<dt>type_i</dt>
<dd>type for each taxon</dd>


<dt>n_species</dt>
<dd>number of species</dd>


<dt>F_type</dt>
<dd>whether to integrate catches along with biomass (<code>"integrated"</code>)
or calculate catches from the Baranov catch equation applied to average
biomass (<code>"averaged"</code>)</dd>


<dt>what</dt>
<dd>what output to produce</dd>

</dl>

dBdt: Dynamics from EcoSim

Description

Usage

Value

Arguments

Details