process_contaminant_data

Interpolates contaminant time series from <code>bio_obj$contaminant_data</code>
to daily values aligned with <code>target_days</code>. Returns <code>NULL</code> when
no contaminant data is present.
Expected structure of <code>bio_obj$contaminant_data</code>:<dl>
 <dt>CONTEQ</dt>
<dd>Integer 1, 2 or 3 (bioaccumulation model)</dd> <dt>initial_concentration</dt>
<dd>Initial predator concentration (ug/g)</dd> <dt>prey_concentrations</dt>
<dd>data.frame Day + one column per prey (ug/g)</dd> <dt>transfer_efficiency</dt>
<dd>data.frame Day + one per prey — used by CONTEQ 1</dd> <dt>assimilation_efficiency</dt>
<dd>data.frame Day + one per prey — used by CONTEQ 2, 3</dd> <dt>gill_efficiency, fish_water_partition, water_concentration,
 dissolved_fraction, do_saturation</dt>
<dd>Scalars required by CONTEQ 3</dd>
</dl>

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

process_contaminant_data function

<dl><dt>bio_obj</dt>
<dd>Bioenergetic object</dd>
<dt>target_days</dt>
<dd>Target simulation days</dd>
<dt>prey_names</dt>
<dd>Character vector of prey names</dd></dl>

Arguments

Interpolates contaminant time series from <code>bio_obj$contaminant_data</code>
to daily values aligned with <code>target_days</code>. Returns <code>NULL</code> when
no contaminant data is present.
Expected structure of <code>bio_obj$contaminant_data</code>:<dl>
 <dt>CONTEQ</dt>
<dd>Integer 1, 2 or 3 (bioaccumulation model)</dd>

 <dt>initial_concentration</dt>
<dd>Initial predator concentration (ug/g)</dd>

 <dt>prey_concentrations</dt>
<dd>data.frame Day + one column per prey (ug/g)</dd>

 <dt>transfer_efficiency</dt>
<dd>data.frame Day + one per prey — used by CONTEQ 1</dd>

 <dt>assimilation_efficiency</dt>
<dd>data.frame Day + one per prey — used by CONTEQ 2, 3</dd>

 <dt>gill_efficiency, fish_water_partition, water_concentration,
 dissolved_fraction, do_saturation</dt>
<dd>Scalars required by CONTEQ 3</dd>


</dl>

Process contaminant accumulation data — process_contaminant_data

<dl>

<dt>bio_obj</dt>
<dd>Bioenergetic object</dd>


<dt>target_days</dt>
<dd>Target simulation days</dd>


<dt>prey_names</dt>
<dd>Character vector of prey names</dd>

</dl>

process_contaminant_data: Process contaminant accumulation data

Description

Usage

Value

Arguments