profile: Profile likelihood of assessment models

In tcarruth/MSEtool: Management Strategy Evaluation Toolkit

Description

Profile the likelihood for parameters of assessment models.

Usage

profile(fitted, ...)

## S4 method for signature 'Assessment'
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.

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

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 <- DD_TMB(Data = DLMtool::Red_snapper)
pro <- profile(output, R0 = seq(0.75, 1.25, 0.025), h = seq(0.9, 0.99, 0.01))
pro <- profile(output, R0 = seq(0.75, 1.25, 0.025)) # Profile R0 only

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

tcarruth/MSEtool documentation built on Oct. 19, 2020, 6:09 a.m.