MLZ (version 0.1.5)

profile_MLCR: Grid search for the mean length with catch rate estimator

Description

A grid search is performed over the time series, which can be used to identify local and global minima. A plot of the likelihood surface is also created similar to Figure 6 of Gedamke and Hoenig (2006) or Figure 3 of Huynh et al. (2017).

Usage

profile_MLCR(MLZ_data, ncp, CPUE.type = c(NA, "NPUE", "WPUE"),
  loglikeCPUE = c("normal", "lognormal"), startZ = rep(0.5, ncp + 1),
  min.time = 3, parallel = ifelse(ncp > 2, TRUE, FALSE),
  figure = TRUE, color = TRUE)

Value

A matrix of change points with the total negative log-likelihood values and values from the mean lengths and catch rates.

Arguments

MLZ_data

An object of class MLZ_data.

ncp

The number of change points.

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.

startZ

A vector of length ncp+1 as the starting value of total mortality rate used in the grid search.

min.time

The minimum number of years between change points. Only used if ncp > 1.

parallel

Whether the grid search is performed with parallel processing.

figure

If TRUE, creates a plot of the likelihood over the grid search. Only used if ncp = 1 or 2.

color

If TRUE, creates a color plot for the likelihood surface. Only used if ncp = 2.

References

Gedamke, T. and Hoenig, J.M. 2006. Estimating mortality from mean length data in nonequilibrium situations, with application to the assessment of goosefish. Transactions of the American Fisheries Society 135:476-487.

Huynh, Q.C, Gedamke, T., Hoenig, J.M, and Porch C. 2017. Multispecies Extensions to a Nonequilibrium Length-Based Mortality Estimator. Marine and Coastal Fisheries 9:68-78.

Examples

if (FALSE) {
data(MuttonSnapper)
profile_MLCR(MuttonSnapper, ncp = 1, CPUE.type = 'WPUE')
}