growth_tagging: Growth from tagging data

In tokami/TropFishR: Tropical Fisheries Analysis

Growth from tagging data

Description

This function estimates growth parameters from tagging data. Munro plot is applied

Usage

growth_tagging(param, method, Linf_range = c(5, 600), time_unit = "year")

Arguments

param	a list consisting of following parameters: L1: length at tagging [cm], L2: length at recapture [cm], delta_t: time interval between tagging ang recapture (instead two vectors with t1 (age at tagging) and t2 (age at recapture) can be provided.
method	indicating which of following methods should be applied: "GullandHolt" or "Munro".
Linf_range	two values indicating the lower and upper limits of the range, in which the optimise searches for the Linf value with the best fit (lowest CV value ),
time_unit	indicating the unit of the time interval, either "year", "month", "week", or "day"

Details

If Munro plot is applied the optimal Linf value is found by minimizing the coefficient of variation (CV = sd(K)/mean(K)). For this iterative method the optimise function is applied. The histogram of the individual K values allows to distinguish potential differences in growth performance between individuals. t0 can not be estimated by Munro plot, neither by the Gulland Holt method.

Value

A list with the input parameters and following parameters:

• x: independent variable used for regression analysis,

• y: dependent variable used for regression analysis,

• reg_coeffs: regression coefficients,

• r2: r squared of regression analysis,

• Linf: infinite length for investigated species in cm [cm],

• K: growth coefficent for investigated species per year [1/year],

• conf_int_K: confidence intervals of K (only if Gulland Holt method was applied).

References

Sparre, P., Venema, S.C., 1998. Introduction to tropical fish stock assessment. Part 1. Manual. FAO Fisheries Technical Paper, (306.1, Rev. 2). 407 p.

Sparre, P., Venema, S.C., 1999. Introduction to tropical fish stock assessment. Part 2. Excercises. FAO Fisheries Technical Paper, (306.2, Rev. 2). 94 p.

Wolff, M., 1984. Early setback for scallop culture in Peru.

Examples

# from Wolff (1984)
dat <- list(L1 = c(40,46,29,30,18,31,48,49,59,58,61,65,57,55),
   L2 = c(85,53,55,56,25,43,70,59,62,80,72,83,65,56),
   delta_t = c(289,26,84,77,14,38,89,38,28,149,89,74,38,21))
growth_tagging(param = dat, "Munro", time_unit = "day", Linf_range=c(80,120))
growth_tagging(param = dat, "GullandHolt", time_unit = "day")


# from Sparre and Venema (1999)
dat <- list(L1 = c(9.7,10.5,10.9,11.1,12.4,12.8,14.0,16.1,16.3,17.0,17.7),
   L2 = c(10.2,10.9,11.8,12.0,15.5,13.6,14.3,16.4,16.5,17.2,18.0),
   delta_t = c(53,33,108,102,272,48,53,73,63,106,111))
growth_tagging(param = dat, "Munro", time_unit = "day", Linf_range = c(10,40))
growth_tagging(param = dat, "GullandHolt", time_unit = "day")

tokami/TropFishR documentation built on Feb. 29, 2024, 11 p.m.