fishgrowth-package: Fit Growth Curves to Fish Data

In fishgrowth: Fit Growth Curves to Fish Data

Fit Growth Curves to Fish Data

Description

Fit growth models to otoliths and/or tagging data, using the RTMB package and maximum likelihood.

The otoliths (or similar measurements of age) provide direct observed coordinates of age and length. The tagging data provide information about the observed length at release and length at recapture at a later time, where the age at release is unknown and estimated as a vector of parameters.

The growth models provided by this package can be fitted to otoliths only, tagging data only, or a combination of the two. Growth variability can be modelled as constant or increasing with length.

Details

Growth models:

gcm	growth cessation
gompertz	Gompertz
gompertzo	Gompertz (old style)
richards	Richards
richardso	Richards (old style)
schnute3	Schnute Case 3
vonbert	von Bertalanffy
vonberto	von Bertalanffy (old style)

Utilities:

pred_band

prediction band

Example data:

otoliths_had	otoliths (haddock)
otoliths_skj	otoliths (skipjack)
tags_skj	tags (skipjack)

Note

The parameter estimation method follows the statistical approach of Maunder et al. (2018), which stems from Aires-da-Silva et al. (2015), Eveson et al. (2004), and Laslett et al. (2002), collectively called the Laslett-Eveson-Polacheck approach.

Author(s)

Arni Magnusson and Mark Maunder.

References

Aires-da-Silva, A.M., Maunder, M.N., Schaefer, K.M., and Fuller, D.W. (2015). Improved growth estimates from integrated analysis of direct aging and tag-recapture data: An illustration with bigeye tuna (Thunnus obesus) of the eastern Pacific Ocean with implications for management. Fisheries Research, 163, 119–126. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.fishres.2014.04.001")}.

Maunder, M.N., Deriso, R.B., Schaefer, K.M., Fuller, D.W., Aires-da-Silva, A.M., Minte-Vera, C.V., and Campana, S.E. (2018). The growth cessation model: a growth model for species showing a near cessation in growth with application to bigeye tuna (Thunnus obesus). Marine Biology, 165, 76. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1007/s00227-018-3336-9")}.

Eveson, J.P., Laslett, G.M., and Polacheck, T. (2004). An integrated model for growth incorporating tag-recapture, length-frequency, and direct aging data. Canadian Journal of Fisheries and Aquatic Sciences, 61, 292–306. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1139/f03-163")}.

Laslett, G.M., Eveson, J.P., and Polacheck, T. (2002). A flexible maximum likelihood approach for fitting growth curves to tag-recapture data. Canadian Journal of Fisheries and Aquatic Sciences, 59, 976–986. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1139/f02-069")}.

See Also

Useful links:

• https://github.com/arni-magnusson/fishgrowth

fishgrowth documentation built on April 11, 2025, 5:52 p.m.