assign_energy_components

Internal helper that populates the <code>estimate</code> and <code>se</code> slots of
several energy components inside a budget result list. Avoids repeating the
same assignment pattern across population, individual, and TMB branches of
<code>get_energy_budget_uncertainty()</code>.

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

assign_energy_components function

<dl><dt>budget</dt>
<dd>Named list with one sub-list per energy component, each
containing at least <code>estimate</code> and <code>se</code> slots.</dd>
<dt>src</dt>
<dd>Named list (or data frame column) that holds the raw
<code>&lt;prefix&gt;_est</code> / <code>&lt;prefix&gt;_se</code> values.</dd>
<dt>mapping</dt>
<dd>Named character vector mapping component names (keys) to
source field prefixes (values), e.g.
<code>c(consumption_energy = "mean_total_consumption", ...)</code>.</dd>
<dt>idx</dt>
<dd>Integer index used for vector extraction (individual branch).
<code>NULL</code> for scalar extraction (population / TMB branches).</dd></dl>

Arguments

Fill energy budget components from a named source list — assign_energy_components

<dl>

<dt>budget</dt>
<dd>Named list with one sub-list per energy component, each
containing at least <code>estimate</code> and <code>se</code> slots.</dd>


<dt>src</dt>
<dd>Named list (or data frame column) that holds the raw
<code>&lt;prefix&gt;_est</code> / <code>&lt;prefix&gt;_se</code> values.</dd>


<dt>mapping</dt>
<dd>Named character vector mapping component names (keys) to
source field prefixes (values), e.g.
<code>c(consumption_energy = "mean_total_consumption", ...)</code>.</dd>


<dt>idx</dt>
<dd>Integer index used for vector extraction (individual branch).
<code>NULL</code> for scalar extraction (population / TMB branches).</dd>

</dl>

assign_energy_components: Fill energy budget components from a named source list

Description

Usage

Value

Arguments