Profile the likelihood for parameters of assessment models.

profile(fitted, ...)

# S4 method for Assessment
profile(fitted, figure = TRUE, ...)

# S4 method for RCModel
profile(fitted, figure = TRUE, ...)

Arguments

fitted, Assessment

An object of class Assessment.

...

A sequence of values of the parameter(s) for the profile. See details and example below. See details for name of arguments to be passed on.

figure

Logical, indicates whether a figure will be plotted.

Value

An object of class prof that contains a data frame of negative log-likelihood values from the profile and, optionally, a figure of the likelihood surface.

Details

For the following assessment models, possible sequence of values for profiling are:

  • DD_TMB and DD_SS: R0 and h

  • SP and SP_SS: FMSY and MSY

  • DD and cDD_SS: R0 and h

  • SCA and SCA_Pope: R0 and h

  • SCA2: meanR

  • VPA: F_term

  • SSS: R0

For RCM: D (spawning biomass depletion), R0, and h are used.

Author

Q. Huynh

Examples

# \donttest{
output <- SCA(Data = MSEtool::SimulatedData)

# Profile R0 only
pro <- profile(output, R0 = seq(1000, 2000, 50))


# Profile both R0 and steepness
pro <- profile(output, R0 = seq(1000, 2000, 100), h = seq(0.8, 0.95, 0.025))


# Ensure your grid is of proper resolution. A grid that is too coarse
# will likely distort the shape of the likelihood surface.
# }