best_f: Best F

In ben-williams/datacall: Pull in data - then prep it for fishery stock assessments

Description

Use this year's model to recalculate the F for the previous year that would have produced the specified OFL for the previous year

Usage

best_f(data, m, last_ofl, type = 1, f_ratio = NULL, m2 = NULL)

Arguments

data	data.frame in form (age, naa, waa, saa)
m	natural mortality (for both sexes(type=1) or for sex 1 (type=2 or type=3 estimates))
last_ofl	OFL from the previous assessment
type	1 = 1 sex - 1 gear; 2 = 1 sex - 2 gear; 3 = 2 sex - 1 gear - 2m; 4 = 2 sex - 2 gear - 2m
f_ratio	is the final ratio of catch between gears in the previous year, as estimated by this year's model - only needed if using multiple gear types
m2	is the second estimate of natural mortality

Value

The estimated F_OFL

Examples

oneone <- data.frame(age = 1:9,
naa = c(15.27, 10.85, 0.24, 8.72, 2.49, 10.66, 3.92, 3.71, 2.6),
waa = c(0.69, 1.11, 1.54, 1.95, 2.32, 2.64, 2.91, 3.41, 3.33),
saa = c(0.01,	0.1	, 0.57, 0.94, 0.99, 1, 1,	1, 1))


onetwo <- data.frame(age = 1:9,
                    naa = c(15.27, 10.85, 0.24, 8.72, 2.49, 10.66, 3.92, 3.71, 2.6),
                    waa = c(0.69, 1.11, 1.54, 1.95, 2.32, 2.64, 2.91, 3.41, 3.33),
                    saa01 = c(0.01,	0.1	, 0.57, 0.94, 0.99, 1, 1,	1, 1),
                    saa01 = c(0.01, 0.06, 0.34, 0.82, 0.97, 1, 1, 1, 1))

twotwo = structure(list(age = 2:10,
                       naa1 = c(7.64, 5.43, 0.12, 4.36, 1.24,5.33, 1.96, 1.85, 1.3),
                       naa2 = c(7.64, 5.42, 0.12, 4.4, 1.27,5.44, 2, 1.89, 1.32),
                       waa1 = c(0.97, 1.46, 1.88, 2.22, 2.48, 2.67, 2.81, 2.91, 2.99),
                       waa2 = c(0.92, 1.48, 2.05, 2.6, 3.09, 3.52, 3.89, 4.19, 4.44),
                       saa11 = c(0.01, 0.1, 0.57, 0.94, 0.99, 1, 1, 1, 1),
                       saa21 = c(0.01, 0.06, 0.34, 0.82, 0.97, 1, 1, 1, 1),
                       saa12 = c(0.12, 0.37, 0.62, 0.82, 0.94, 1, 1, 0.96, 0.89),
                       saa22 = c(0.01, 0.13, 0.38, 0.66, 0.89, 1, 1, 0.92, 0.79)),
                  class = "data.frame", row.names = c(NA, -9L))

type 1
best_f(m = 0.1, last_ofl = 15, data = oneone, type = 1)
type 2
best_f(m = 0.1, last_ofl = 15, data = onetwo, type = 2, f_ratio = 0.1)
type 3
best_f(m = 0.12, last_ofl = 15, data = twotwo, type = 3, f_ratio = 0.1, m2 = 0.08)
type 4
best_f(m = 0.12, last_ofl = 15, data = twotwo, type = 4, f_ratio = 0.1, m2 = 0.08)

ben-williams/datacall documentation built on Oct. 30, 2020, 5:46 p.m.