contaminant_model_3

Complete model with uptake from water and food, elimination proportional to respiration

internal

An implementation of the 'Fish Bioenergetics 4.0' framework
described in Deslauriers et al. (2017)
<doi:10.1080/03632415.2017.1377558>. Provides automated parameter
optimization, multi-prey diet modeling, and comprehensive energy budget
simulations for fisheries research and aquaculture applications. An
optional 'TMB' (Template Model Builder) backend delivers 10-50x speedup
in maximum likelihood estimation while maintaining full backward
compatibility. Includes species-specific parameter databases and tools
for modeling fish growth, consumption, and metabolism under varying
environmental conditions.

Hans Ttito

fb4package

'Fish Bioenergetics 4.0' Model Implementation with
High-Performance 'TMB' Backend

contaminant_model_3 function

<dl><dt>respiration_o2</dt>
<dd>Respiration (g O2/g/day)</dd>
<dt>consumption</dt>
<dd>Vector of consumption by prey (g/day)</dd>
<dt>weight</dt>
<dd>Fish weight (g)</dd>
<dt>temperature</dt>
<dd>Water temperature (deg C)</dd>
<dt>prey_concentrations</dt>
<dd>Vector of concentrations in prey (ug/g)</dd>
<dt>assimilation_efficiency</dt>
<dd>Vector of assimilation efficiencies</dd>
<dt>current_burden</dt>
<dd>Current body burden (ug)</dd>
<dt>gill_efficiency</dt>
<dd>Gill uptake efficiency</dd>
<dt>fish_water_partition</dt>
<dd>Fish:water partition coefficient</dd>
<dt>water_concentration</dt>
<dd>Total concentration in water (mg/L)</dd>
<dt>dissolved_fraction</dt>
<dd>Dissolved fraction</dd>
<dt>do_saturation</dt>
<dd>Dissolved oxygen saturation (fraction)</dd></dl>

Arguments

Contaminant model 3 - Arnot &amp; Gobas (2004) (Low-level) — contaminant_model_3

<dl>

<dt>respiration_o2</dt>
<dd>Respiration (g O2/g/day)</dd>


<dt>consumption</dt>
<dd>Vector of consumption by prey (g/day)</dd>


<dt>weight</dt>
<dd>Fish weight (g)</dd>


<dt>temperature</dt>
<dd>Water temperature (deg C)</dd>


<dt>prey_concentrations</dt>
<dd>Vector of concentrations in prey (ug/g)</dd>


<dt>assimilation_efficiency</dt>
<dd>Vector of assimilation efficiencies</dd>


<dt>current_burden</dt>
<dd>Current body burden (ug)</dd>


<dt>gill_efficiency</dt>
<dd>Gill uptake efficiency</dd>


<dt>fish_water_partition</dt>
<dd>Fish:water partition coefficient</dd>


<dt>water_concentration</dt>
<dd>Total concentration in water (mg/L)</dd>


<dt>dissolved_fraction</dt>
<dd>Dissolved fraction</dd>


<dt>do_saturation</dt>
<dd>Dissolved oxygen saturation (fraction)</dd>

</dl>

contaminant_model_3: Contaminant model 3 - Arnot & Gobas (2004) (Low-level)

Description

Usage

Value

Arguments