MLZ (version 0.1.5)

MLeffort: Mean length with effort mortality estimator

Description

Estimator of fishing and natural mortality from a time series of mean length and effort data.

Usage

MLeffort(MLZ_data, start, n_age, estimate.M = TRUE, log.par = FALSE,
  eff_init = 0, n_season = 1L, obs_season = 1L, timing = 0,
  figure = TRUE)

Value

An object of class MLZ_model.

Arguments

MLZ_data

An object of class MLZ_data containing mean lengths and life history data of stock.

start

A list of starting values. Names of start list must contain q and M.

n_age

The number of ages above age tc in the model.

estimate.M

If TRUE, natural mortality (M) will be estimated. Otherwise, the value of M is obtained from slot MLZ_data@M.

log.par

Whether parameters are estimated in logspace (TRUE) or untransformed space (FALSE).

eff_init

The assumed equilibrium effort prior to the first year of the model (0 = virgin conditions).

n_season

The number of seasons modeled in a year.

obs_season

The season corresponding to the observed mean lengths.

timing

The fraction of time (i.e., between 0 - 1) within obs_season that mean lengths are observed.

figure

If TRUE, a call to plot of observed and predicted mean lengths will be produced.

References

Then, A.Y, Hoenig, J.M, and Huynh, Q.C. In revision. Estimating fishing and natural mortality rates, and catchability coefficient, from a series of observations on mean length and fishing effort. ICES Journal of Marine Science.

Examples

if (FALSE) {
data(Nephrops)
Nephrops <- calc_ML(Nephrops, sample.size = FALSE)
res <- MLeffort(Nephrops, start = list(q = 0.1, M = 0.2),
                n_age = 24, eff_init = Nephrops@Effort[1])
}