profile_ML {MLZ} | R Documentation |
Grid search for the mean length 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_ML(MLZ_data, ncp, startZ = rep(0.5, ncp + 1), min.time = 3,
parallel = ifelse(ncp > 2, TRUE, FALSE), figure = TRUE,
color = TRUE)
Arguments
MLZ_data |
An object of class |
ncp |
The number of change points. |
startZ |
A vector of length |
min.time |
The minimum number of years between change points. Only used if |
parallel |
Whether grid search is performed using parallel processing. |
figure |
If |
color |
If |
Value
A matrix of change points with the negative log-likelihood values.
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
## Not run:
data(Goosefish)
profile_ML(Goosefish, ncp = 1)
profile_ML(Goosefish, ncp = 2)
## End(Not run)