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.
Arni Magnusson and Mark Maunder.
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) |
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. 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. 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. 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. tools:::Rd_expr_doi("10.1139/f02-069").
Useful links: