An R package implementation of Fish Bioenergetics 4.0 (FB4), a widely used approach for modelling energy allocation in fish. The model partitions consumed energy into three fundamental components: metabolism (respiration + activity + specific dynamic action), waste losses (egestion + excretion), and growth (somatic + gonadal). The package provides multiple estimation strategies (binary search, direct, bootstrap, maximum likelihood) and an optional C++ backend via TMB for high-performance MLE.
Maintainer: Hans Ttito kvttitos@gmail.com
The bioenergetics energy balance implemented here follows Kitchell et al. (1977):
$$C = R + A + \mathrm{SDA} + F + U + G$$
where \(C\) = consumption, \(R\) = standard respiration, \(A\) = active metabolism, \(\mathrm{SDA}\) = specific dynamic action, \(F\) = egestion, \(U\) = excretion, and \(G\) = growth (somatic + gonadal).
Consumption is modelled as \(C = C_{\max} \cdot p \cdot F(T)\), where \(C_{\max} = CA \cdot W^{CB}\) (Hartman and Hayward 2007) and \(F(T)\) is one of four temperature-dependence functions (CEQ 1–4; Kitchell et al. 1977; Thornton and Lessem 1978).
Respiration is modelled as \(R = RA \cdot W^{RB} \cdot F(T) \cdot \mathrm{ACT}\), with \(F(T)\) following Kitchell et al. (1977) or a simple Q10 exponential (REQ 1–2).
Egestion and excretion follow Elliott (1976) or Stewart et al. (1983) (EGEQ/EXEQ 1–4).
Predator energy density can be modelled as weight-dependent or constant (PREDEDEQ 1–2; Hanson et al. 1997).
This package extends Fish Bioenergetics 4.0 (Deslauriers et al. 2017), itself an R-based re-implementation of Fish Bioenergetics 3.0 (Hanson et al. 1997) and its predecessors (Hewett and Johnson 1987, 1992).
Deslauriers, D., Chipps, S.R., Breck, J.E., Rice, J.A. and Madenjian, C.P. (2017). Fish Bioenergetics 4.0: An R-based modeling application. Fisheries, 42(11), 586–596. tools:::Rd_expr_doi("10.1080/03632415.2017.1377558")
Hanson, P.C., Johnson, T.B., Schindler, D.E. and Kitchell, J.F. (1997). Fish Bioenergetics 3.0. University of Wisconsin Sea Grant Institute, Madison, WI. WISCU-T-97-001.
Kitchell, J.F., Stewart, D.J. and Weininger, D. (1977). Applications of a bioenergetics model to yellow perch (Perca flavescens) and walleye (Stizostedion vitreum vitreum). Journal of the Fisheries Research Board of Canada, 34(10), 1922–1935. tools:::Rd_expr_doi("10.1139/f77-258")
Thornton, K.W. and Lessem, A.S. (1978). A temperature algorithm for modifying biological rates. Transactions of the American Fisheries Society, 107(2), 284–287.
Elliott, J.M. (1976). Energy losses in the waste products of brown trout (Salmo trutta L.). Journal of Animal Ecology, 45(2), 561–580.
Stewart, D.J., Weininger, D., Rottiers, D.V. and Edsall, T.A. (1983). An energetics model for lake trout, Salvelinus namaycush: application to the Lake Michigan population. Canadian Journal of Fisheries and Aquatic Sciences, 40(6), 681–698.
Hartman, K.J. and Hayward, R.S. (2007). Bioenergetics. In C.S. Guy and M.L. Brown (eds.), Analysis and Interpretation of Freshwater Fisheries Data. American Fisheries Society, Bethesda, MD.
Hewett, S.W. and Johnson, B.L. (1987). A Generalized Bioenergetics Model of Fish Growth for Microcomputers. University of Wisconsin Sea Grant Institute, Madison, WI.
Hewett, S.W. and Johnson, B.L. (1992). Fish Bioenergetics 2.0. University of Wisconsin Sea Grant Institute, Madison, WI.
Winberg, G.G. (1956). Rate of metabolism and food requirements of fishes. Fisheries Research Board of Canada Translation Series No. 194.
Breck, J.E. (2014). Body composition in fishes: body size matters. Aquaculture, 433, 40–49. tools:::Rd_expr_doi("10.1016/j.aquaculture.2014.05.049")
Arnot, J.A. and Gobas, F.A.P.C. (2004). A food web bioaccumulation model for organic chemicals in aquatic ecosystems. Environmental Toxicology and Chemistry, 23(10), 2343–2355. tools:::Rd_expr_doi("10.1897/03-438")
Bioenergetic, run_fb4, fish4_parameters