extractSSB | R Documentation |
A number of derived quantities are available in the Report.sso file, and are useful for checking that the generated FLR objects lead to the same values. These functions are called on the list returned by readOutputss3 or r4ss::SS_output, and extract the yearly values from the following rows in the derived_quants data.frame:
extractSSB(out)
extractRec(out)
extractFbar(out)
extractZatage(out)
extractDevs(out)
out |
A list as returned by r4ss::SS_output. |
extractSSB: SSB_y
for y between startyr
and endyr
.
extractRec: Recr_y
for y between startyr
and endyr
.
extractFbar: F_y
for y between startyr
and endyr
.
extractZatage: Z_ay
for y between startyr
and endyr
and ages but last.
For 2 sex models (nsexes
), extractRec will return a two-unit FLQuant,
with the Recr_y
values split according to the recruitment sex ratio. This
is extracted from recruitment_dist[[1]][, "Frac/sex"]
.
The value returned by extractFbar
is the actual mean F over the age range,
and the value in derived_quants
is corrected according to F_report_basis
for models where F reporting basis is F/FMSY.
An FLQuant object of the requested quantity.
out <- readOutputss3(system.file("ext-data", "herring", package="ss3om"))
extractSSB(out)
extractFbar(out)
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