MLZ (version 0.1.1)

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)

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.

Value

An object of class '>MLZ_model.

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

# NOT RUN {
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])
# }