Dynamic Energy Budgets

Persefone's nature module uses Kooijman's Dynamic Energy Budget theory to model energy flows within individuals.

"The standard model of the Dynamic Energy Budget theory"

The standard model of the Dynamic Energy Budget theory. (Fig. 1 from Sousa et al. (2010).)

  • Sousa et al. (2010). Dynamic energy budget theory restores coherence in biology. Philosophical Transactions of the Royal Society B: Biological Sciences, 365(1557), 3413–3428.

  • Kooijman, S. A. L. M. (2009). Dynamic energy and mass budgets in biological systems (3rd ed). Cambridge University Press.

  • Sibly et al. (2013). Representing the acquisition and use of energy by individuals in agent-based models of animal populations. Methods in Ecology and Evolution, 4(2), 151–161.

energy.jl

Persefone.DEBparametersType
DEBparameters

An immutable struct to save the parameter list for a species' Dynamic Energy Budget model. (See Sousa et al., 2010.)

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Persefone.EnergyBudgetType
EnergyBudget

This struct represents an individual's energy balance, as conceptualised by the Dynamic Energy Budget theory. Upon assimilation, energy is first stored as biomass in a reserve buffer, before being used for maintenance, growth, and reproduction. (Note that this is a simplified model form which ignores maturity as a separate buffer.)

Sources:

  • Malishev & Kramer-Schadt (2021). Movement, models, and metabolism: Individual-based energy budget models as next-generation extensions for predicting animal movement outcomes across scales. Ecological Modelling, 441, 109413. https://doi.org/10.1016/j.ecolmodel.2020.109413
  • Marques et al. (2018). The AmP project: Comparing species on the basis of dynamic energy budget parameters. PLOS Computational Biology,14(5), e1006100. https://doi.org/10.1371/journal.pcbi.1006100
  • Sibly et al. (2013). Representing the acquisition and use of energy by individuals in agent-based models of animal populations. Methods in Ecology and Evolution, 4(2), 151–161. https://doi.org/10.1111/2041-210x.12002
  • Sousa et al. (2010). Dynamic energy budget theory restores coherence in biology. Philosophical Transactions of the Royal Society B: Biological Sciences, 365(1557), 3413–3428. https://doi.org/10.1098/rstb.2010.0166
  • Kooijman, S. A. L. M. (2009). Dynamic energy and mass budgets in biological systems (3rd ed). Cambridge University Press. https://www.researchgate.net/profile/Edgar-Meza-3/post/Isthereatoxicokineticmodelfordaphniamagnaorotherzooplankton/attachment/59d62cf579197b807798b396/AS%3A348547653357569%401460111644286/download/Dynamic+Energy+Budget+theory+-+Kooijman.pdf
  • see also: Brown et al. (2004). Toward a metabolic theory of ecology. Ecology, 85(7), 1771–1789. https://doi.org/10.1890/03-9000
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Persefone.feed!Method
feed!(quantity, energybudget)

Consume a given quantity of food. Expands the energy reserve by an amount determined by the assimilation rate. Returns true if successful, false if the reserve is already full.

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Persefone.reproduce!Method
reproduce!(energybudget)

If there is sufficient energy in the offspring buffer of an adult, produce an embryo/egg, reducing the parent energy in the process. Returns the embryo's energy budget, or nothing if the conditions are not met.

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Persefone.update!Method
update!(energybudget)

Carry out a daily update of the energy budget. Mobilises reserves and allocates these to maintenance (prioritised), growth, and reproduction.

Return true if the individual has enough energy to survive, or false if the reserve is empty and it starves.

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Persefone.volumetriclengthMethod
volumetriclength(energybudget)

Calculate the structural length in cm based on an individual's weight (assuming a density of 1 g/cm³ to calculate volume, see Kooijman 2009).

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