MLCR: Mean length with catch rate mortality estimator

In quang-huynh/MLZ: Mean Length-Based Estimators of Mortality using TMB

Mean length with catch rate mortality estimator

Description

Estimator of instantaneous total mortality (Z) from a time series of mean length data.

Usage

MLCR(MLZ_data, ncp, CPUE.type = c(NA, "WPUE", "NPUE"),
  loglikeCPUE = c("lognormal", "normal"), start = NULL,
  grid.search = TRUE, parallel = ifelse(ncp > 2, TRUE, FALSE),
  min.time = 3, Z.max = 5, figure = TRUE)

Arguments

MLZ_data	An object of class MLZ_data containing mean lengths and life history data of stock.
ncp	The number of change points in total mortality in the time series. ncp + 1 total mortality rates will be estimated.
CPUE.type	Indicates whether CPUE time series is abundance or biomass based.
loglikeCPUE	Indicates whether the log-likelihood for the CPUE will be lognormally or normally distributed.
start	An optional list of starting values. See details.
grid.search	If TRUE, a grid search will be performed using the profile_MLCR function to find the best starting values for the change points (the years when mortality changes). Ignored if ncp = 0 or if start is provided.
parallel	Whether grid search is performed with parallel processing. Ignored if grid.search = FALSE.
min.time	The minimum number of years between each change point for the grid search, passed to profile_MLCR. Not used if grid.search = FALSE.
Z.max	The upper boundary for Z estimates.
figure	If TRUE, a call to plot of observed and predicted mean lengths will be produced.

Details

For a model with I change points, the starting values in start is a list with the following entries: Z a vector of length = I+1. yearZ a vector of length = I.

start can be NULL, in which case, the supplied starting values depend on the value of grid.search. If grid.search = TRUE, starting values will use the values for yearZ which minimize the negative log-likelihood from the grid search. Otherwise, the starting values for yearZ evenly divide the time series.

Value

An object of class MLZ_model.

References

Huynh, Q.C., Gedamke, T., Porch, C.E., Hoenig, J.M., Walter, J.F, Bryan, M., and Brodziak, J. In revision. Estimating Total Mortality Rates from Mean Lengths and Catch Rates in Non-equilibrium Situations. Transactions of the American Fisheries Society.

See Also

profile_MLCR

Examples

## Not run: 
data(MuttonSnapper)
MLCR(MuttonSnapper, ncp = 2, CPUE.type = "WPUE", grid.search = TRUE)

## End(Not run)

quang-huynh/MLZ documentation built on April 10, 2022, 7:39 p.m.