Get ADMB Hessian — getADMBHessian • FLa4a

Reads the hessian file from any ADMB fit. Used here with the a4a model.

getADMBHessian(wkdir)

getADMBCovariance(wkdir)

Arguments

wkdir: the location of the admb output

Value

a list with the following elements

Note

getADMBHessian is intended to be used internally

Examples

# load some data
data(ple4)
data(ple4.indices)
# choose a working directory
wkdir <- tempfile()
# do an 'assessment' fit with default settings (not recomended!) and keep results in wkdir
fit <- sca(stock=ple4,indices=ple4.indices,wkdir=wkdir)
#> Warning: *** ~te(age, year, k = c(6, 30), bs = "tp") + s(age, k = 6) has 4 too many parameter(s)!!
#>     i will remove the redundant ones:
#> 	s(age).2
#> 	s(age).3
#> 	s(age).4
#> 	s(age).5
#> Model and results are stored in working directory [/tmp/Rtmp8T7ruQ/file1685a1210552d0]
hessInfo <- getADMBHessian(wkdir)
str(hessInfo)
#> List of 4
#>  $ num.pars           : int 287
#>  $ hes                : num [1:287, 1:287] 1442752 28482 23352 28406 27457 ...
#>  $ hybrid_bounded_flag: int 0
#>  $ scale              : num [1:287] 1 1 1 1 1 1 1 1 1 1 ...
# calculate covariance matrix
Sigma <- solve(hessInfo$hes)