process_nutrient_data

Interpolates N and P time series from <code>bio_obj$nutrient_data</code> to
daily values aligned with <code>target_days</code>. Returns <code>NULL</code> when
no nutrient data is present.
Expected structure of <code>bio_obj$nutrient_data</code>:<dl>
 <dt>prey_n_concentrations</dt>
<dd>data.frame with Day + one column per prey (g N/g wet wt)</dd> <dt>prey_p_concentrations</dt>
<dd>data.frame with Day + one column per prey (g P/g wet wt)</dd> <dt>predator_n_concentration</dt>
<dd>data.frame with Day + value column (g N/g wet wt)</dd> <dt>predator_p_concentration</dt>
<dd>data.frame with Day + value column (g P/g wet wt)</dd> <dt>n_assimilation_efficiency</dt>
<dd>data.frame with Day + one column per prey (fraction 0-1)</dd> <dt>p_assimilation_efficiency</dt>
<dd>data.frame with Day + one column per prey (fraction 0-1)</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_nutrient_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 N and P time series from <code>bio_obj$nutrient_data</code> to
daily values aligned with <code>target_days</code>. Returns <code>NULL</code> when
no nutrient data is present.
Expected structure of <code>bio_obj$nutrient_data</code>:<dl>
 <dt>prey_n_concentrations</dt>
<dd>data.frame with Day + one column per prey (g N/g wet wt)</dd>

 <dt>prey_p_concentrations</dt>
<dd>data.frame with Day + one column per prey (g P/g wet wt)</dd>

 <dt>predator_n_concentration</dt>
<dd>data.frame with Day + value column (g N/g wet wt)</dd>

 <dt>predator_p_concentration</dt>
<dd>data.frame with Day + value column (g P/g wet wt)</dd>

 <dt>n_assimilation_efficiency</dt>
<dd>data.frame with Day + one column per prey (fraction 0-1)</dd>

 <dt>p_assimilation_efficiency</dt>
<dd>data.frame with Day + one column per prey (fraction 0-1)</dd>


</dl>

Process nutrient regeneration data — process_nutrient_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_nutrient_data: Process nutrient regeneration data

Description

Usage

Value

Arguments