profile,Assessment-method {SAMtool}

Profile likelihood of assessment models

Description

Profile the likelihood for parameters of assessment models.

Usage

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

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

Arguments

fitted, Assessment

An object of class Assessment.

figure

Logical, indicates whether a figure will be plotted.

...

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.

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. If the Mesnil-Rochet stock-recruit function is used, can also profile MRRmax and MRgamma.

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.

Author(s)

Q. Huynh

Examples

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.