fluxweb

An R package to easily estimate energy fluxes in food webs

Benoit Gauzens, Andrew D. Barnes, Darren P. Giling, Jes Hines, Malte Jochum, Jonathan S. Lefcheck, Benjamin Rosenbaum, Shaopeng Wang, Ulrich Brose

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Understanding how changes in biodiversity will impact the stability and functioning of ecosystems is a central challenge in ecology. Food web approaches have been advocated to link community composition with ecosystem functioning by describing the fluxes of energy among species or trophic groups. However, estimating such fluxes remain problematic because current methods become unmanageable as network complexity increases. We developed a generalization of previous indirect estimation methods assuming a steady-state system (Hunt et al.,); the model estimates energy fluxes in a top-down manner assuming system equilibrium; each node's losses (consumption and physiological) balances its consumptive gains. Jointly, we provide theoretical and practical guidelines to use the fluxweb R package (available on CRAN at https://cran.rproject.org/web/packages/fluxweb/index.html). We also present how the framework can merge with the allometric theory of ecology (Brown, Gillooly, Allen, Savage, & West,; to calculate fluxes based on easily obtainable organism-level data (i.e., body masses and species groups—e.g., plants, animals), opening its use to food webs of all complexities. Physiological losses (metabolic losses or losses due to death other than from predation within the food web) may be directly measured or estimated using allometric relationships based on the metabolic theory of ecology, and losses and gains due to predation are a function of ecological efficiencies that describe the proportion of energy that is used for biomass production. The primary output is a matrix of fluxes among the nodes of the food web. These fluxes can be used to describe the role of a species, a function of interest (e.g., predation; total fluxes to predators), multiple functions, or total energy flux (system throughflow or multitrophic functioning). Additionally, the package includes functions to calculate network stability based on the Jacobian matrix, providing insight into how resilient the network is to small perturbations at steady state. Overall, fluxweb provides a flexible set of functions that greatly increase the feasibility of implementing food web energetic approaches to more complex systems. As such, the package facilitates novel opportunities for mechanistically linking quantitative food webs and ecosystem functioning in real and dynamic natural landscapes.

Original languageEnglish
Pages (from-to)270-279
Number of pages10
JournalMethods in Ecology and Evolution
Volume10
Issue number2
DOIs
Publication statusPublished - Feb 2019
Externally publishedYes

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energy flux
food webs
food web
energy
predation
ecology
ecosystems
ecosystem
throughflow
matrix
ecological function
estimation method
body mass
community composition
biomass production
energetics
perturbation
loss
predator
biodiversity

Cite this

Gauzens, B., Barnes, A. D., Giling, D. P., Hines, J., Jochum, M., Lefcheck, J. S., ... Brose, U. (2019). fluxweb: An R package to easily estimate energy fluxes in food webs. Methods in Ecology and Evolution, 10(2), 270-279. https://doi.org/10.1111/2041-210X.13109
Gauzens, Benoit ; Barnes, Andrew D. ; Giling, Darren P. ; Hines, Jes ; Jochum, Malte ; Lefcheck, Jonathan S. ; Rosenbaum, Benjamin ; Wang, Shaopeng ; Brose, Ulrich. / fluxweb : An R package to easily estimate energy fluxes in food webs. In: Methods in Ecology and Evolution. 2019 ; Vol. 10, No. 2. pp. 270-279.
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Gauzens, B, Barnes, AD, Giling, DP, Hines, J, Jochum, M, Lefcheck, JS, Rosenbaum, B, Wang, S & Brose, U 2019, 'fluxweb: An R package to easily estimate energy fluxes in food webs', Methods in Ecology and Evolution, vol. 10, no. 2, pp. 270-279. https://doi.org/10.1111/2041-210X.13109

fluxweb : An R package to easily estimate energy fluxes in food webs. / Gauzens, Benoit; Barnes, Andrew D.; Giling, Darren P.; Hines, Jes; Jochum, Malte; Lefcheck, Jonathan S.; Rosenbaum, Benjamin; Wang, Shaopeng; Brose, Ulrich.

In: Methods in Ecology and Evolution, Vol. 10, No. 2, 02.2019, p. 270-279.

Research output: Contribution to journalArticle

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T1 - fluxweb

T2 - An R package to easily estimate energy fluxes in food webs

AU - Gauzens, Benoit

AU - Barnes, Andrew D.

AU - Giling, Darren P.

AU - Hines, Jes

AU - Jochum, Malte

AU - Lefcheck, Jonathan S.

AU - Rosenbaum, Benjamin

AU - Wang, Shaopeng

AU - Brose, Ulrich

PY - 2019/2

Y1 - 2019/2

N2 - Understanding how changes in biodiversity will impact the stability and functioning of ecosystems is a central challenge in ecology. Food web approaches have been advocated to link community composition with ecosystem functioning by describing the fluxes of energy among species or trophic groups. However, estimating such fluxes remain problematic because current methods become unmanageable as network complexity increases. We developed a generalization of previous indirect estimation methods assuming a steady-state system (Hunt et al.,); the model estimates energy fluxes in a top-down manner assuming system equilibrium; each node's losses (consumption and physiological) balances its consumptive gains. Jointly, we provide theoretical and practical guidelines to use the fluxweb R package (available on CRAN at https://cran.rproject.org/web/packages/fluxweb/index.html). We also present how the framework can merge with the allometric theory of ecology (Brown, Gillooly, Allen, Savage, & West,; to calculate fluxes based on easily obtainable organism-level data (i.e., body masses and species groups—e.g., plants, animals), opening its use to food webs of all complexities. Physiological losses (metabolic losses or losses due to death other than from predation within the food web) may be directly measured or estimated using allometric relationships based on the metabolic theory of ecology, and losses and gains due to predation are a function of ecological efficiencies that describe the proportion of energy that is used for biomass production. The primary output is a matrix of fluxes among the nodes of the food web. These fluxes can be used to describe the role of a species, a function of interest (e.g., predation; total fluxes to predators), multiple functions, or total energy flux (system throughflow or multitrophic functioning). Additionally, the package includes functions to calculate network stability based on the Jacobian matrix, providing insight into how resilient the network is to small perturbations at steady state. Overall, fluxweb provides a flexible set of functions that greatly increase the feasibility of implementing food web energetic approaches to more complex systems. As such, the package facilitates novel opportunities for mechanistically linking quantitative food webs and ecosystem functioning in real and dynamic natural landscapes.

AB - Understanding how changes in biodiversity will impact the stability and functioning of ecosystems is a central challenge in ecology. Food web approaches have been advocated to link community composition with ecosystem functioning by describing the fluxes of energy among species or trophic groups. However, estimating such fluxes remain problematic because current methods become unmanageable as network complexity increases. We developed a generalization of previous indirect estimation methods assuming a steady-state system (Hunt et al.,); the model estimates energy fluxes in a top-down manner assuming system equilibrium; each node's losses (consumption and physiological) balances its consumptive gains. Jointly, we provide theoretical and practical guidelines to use the fluxweb R package (available on CRAN at https://cran.rproject.org/web/packages/fluxweb/index.html). We also present how the framework can merge with the allometric theory of ecology (Brown, Gillooly, Allen, Savage, & West,; to calculate fluxes based on easily obtainable organism-level data (i.e., body masses and species groups—e.g., plants, animals), opening its use to food webs of all complexities. Physiological losses (metabolic losses or losses due to death other than from predation within the food web) may be directly measured or estimated using allometric relationships based on the metabolic theory of ecology, and losses and gains due to predation are a function of ecological efficiencies that describe the proportion of energy that is used for biomass production. The primary output is a matrix of fluxes among the nodes of the food web. These fluxes can be used to describe the role of a species, a function of interest (e.g., predation; total fluxes to predators), multiple functions, or total energy flux (system throughflow or multitrophic functioning). Additionally, the package includes functions to calculate network stability based on the Jacobian matrix, providing insight into how resilient the network is to small perturbations at steady state. Overall, fluxweb provides a flexible set of functions that greatly increase the feasibility of implementing food web energetic approaches to more complex systems. As such, the package facilitates novel opportunities for mechanistically linking quantitative food webs and ecosystem functioning in real and dynamic natural landscapes.

KW - ecosystem function

KW - energy fluxes

KW - food web

KW - interaction strength

KW - stability

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U2 - 10.1111/2041-210X.13109

DO - 10.1111/2041-210X.13109

M3 - Article

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JO - Methods in Ecology and Evolution

JF - Methods in Ecology and Evolution

SN - 2041-210X

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