Description Usage Arguments Details Value References Examples
View source: R/growth_length_age.R
This function estimates growth parameters from lengthatage data. It allows to perform different methods: Gulland and Holt, Ford Walford plot, Chapman's method, Bertalanffy plot, or non linear least squares method (LSM).
1 2 3  growth_length_age(param, method, Linf_est = NA, Linf_init = 10,
K_init = 0.1, t0_init = 0, CI = FALSE, ci.level = 0.95,
age_plot = NULL, do.sim = FALSE, nsim = 10000)

param 
a list consisting of following parameters:

method 
indicating which of following methods should be applied:

Linf_est 
BertalanffyPlot requires an estimate for Linf to derive K and t0 (for more information see Details). 
Linf_init 
initital parameter of Linf for nonlinear sqaures fitting (default 10) 
K_init 
initital parameter of K for nonlinear sqaures fitting (default 0.1) 
t0_init 
initital parameter of t0 for nonlinear sqaures fitting (default 0) 
CI 
logical; Should confidence intervals be calculated? This option only works for the LSM method. Default is FALSE. 
ci.level 
required confidence level (for LSM method only) 
age_plot 
sequence with ages used for plotting (LSM method only). By default age_plot = seq(min(param$age),max(param$age),0.1) 
do.sim 
logical. Should Monte Carlo simulation be applied? Default = FALSE 
nsim 
the number of Monte Carlo simulations to be performed, minimum is 10000 (default). 
Gulland and Holt plot assumes
infinitestimal delta t (only reasonable approximation of growth parameters if delta t
is small). Ford Walford plot and Chapman assume constant time intervals between ages
(delta t). The Bertalanffy plot is a robust method, however it requires an estimate of Linf. As
long as this estimate is reasonable the resulting estimate of K is reasonable. For
a first estimate of Linf the Powell Wetherall method powell_wetherall can
be used. Otherwise, the largest fish or the average of the ten largest fish can be
used for a small or large sample, respectively. All lengths have to be smaller than
Linf as otherwise the logarithm is not defined. Oldest fish (if larger than Linf) have
to be omitted. Nonlinear least squares fitting is the preferred method to estimate
growth parameters according to Sparre and Venema (1998). If CI = TRUE
the
confidence interval of parameters is calculated and plotted. For plotting the
confidence interval the predictNLS
from the propagate package
is applied.
A list with the input parameters and following parameters:
x: independent variable used for regression analysis,
y: dependent variable used for regression analysis,
mod: (non) linear model,
Linf: infinite length for investigated species in cm [cm],
K: growth coefficent for investigated species per year [1/year],
t0: theoretical time zero, at which individuals of this species hatch (only for Bertalanffy plot and LSM method).
estimates: dataframe with growth parameters and confidence intervals (only if LSM method was applied).
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.
1 2 3 4 5 6 7 8 9 10 11 12 13  # synthetical length at age data
dat < list(age = rep(1:7,each = 5),
length = c(rnorm(5,25.7,0.9),rnorm(5,36,1.2),rnorm(5,42.9,1.5),rnorm(5,47.5,2),
rnorm(5,50.7,0.4),rnorm(5,52.8,0.5),rnorm(5,54.2,0.7)))
growth_length_age(dat, method = "GullandHolt")
# Bertalaffy plot
growth_length_age(dat, method = "BertalanffyPlot", Linf_est = 50)
# non linear least squares method
output < growth_length_age(param = dat, method = "LSM",
Linf_init = 30, CI = TRUE, age_plot=NULL)
summary(output$mod)

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