Description Usage Arguments Details Value Author(s) Examples
Profile the likelihood for parameters of assessment models.
1 2 3 4 |
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. |
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
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.
Q. Huynh
1 2 3 4 5 6 | 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.
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