SSS: This file contails all the SSS code

In shcaba/SSS: Simple Stock Synthesis

This file contails all the SSS code

Description

This file contails all the SSS code

Usage

SSS(filepath, file.name, reps = 1000, seed.in = 19, Dep.in = c(1, 0.4,
  0.1), M.in = c(3, 0.1, 0.4, 3, 0.1, 0.4), SR_type = 3, h.in = c(1, 0.6,
  0.2), FMSY_M.in = c(1, 0.5, 0.1), BMSY_B0.in = c(1, 0.5, 0.1),
  L1.in = c(0, 0, 0, 0), Linf.in = c(0, 0, 0, 0), k.in = c(0, 0, 0, 0),
  Zfrac.Beta.in = c(-99, 0.2, 0.6, -99, 0.5, 2), R_start = c(0, 8),
  doR0.loop = c(1, 4.1, 12.1, 0.5), sum_age = 0, sb_ofl_yrs = c(2010,
  2011, 2012), f_yr = 2012, year0 = 1916, genders = F, BH_FMSY_comp = F)

Arguments

filepath	location where the SSS will look for model files and run the executable
file.name	vector of file names for the data and control file where the expected input is c("data file", "control file")
reps	number of mcmc draws to perform
seed.in	seed number
Dep.in	vector defining distribution, mean, sd, and bounds for depletion prior. Expected input is c(distribution shape, mean, sd). The distribution options are 2 = 1 - beta, 4 = uniform, 10 = truncated normal.
M.in	vector defining natural mortality distribuition, mean, and . Expected input is c(distrbution shape for females, mean for females, sd for females, distribution shape for males, mean for males, sd for males). The distibution options are 0 = normal, 3 = lognormal, and 4 = uniform.
SR_type	The shape of the stock-recruitment curve. Options are based on SS stock-recruit options. Option 3 = Beverton-holt, 8 = Shepherd 3-parameter, 9 = Ricker 3-parameter
h.in	vector defining the steepness distribution, mean, and sd. Expected input is c(distribution, mean, sd). Distribution options are 2 = truncated beta, 10 = truncated normal, 30 = truncated lognormal, 4 = uniform.
FMSY_M.in	vector defining the Fmsy/M ratio distribution, mean, and sd. Expected input is c(distribution, mean, sd). Distribution options are; negative value = ?, 2 = truncated beta, 10 = truncated normal, 30 = truncated lognormal, 4 = uniform.
BMSY_B0.in	vector defining the Bmsy/B0 ratio distribution, mean, and sd. Expected input is c(distribution, mean, sd). Distribution options are; negative value = ?, 2 = truncated beta, 10 = truncated normal, 30 = truncated lognormal, 4 = uniform.
L1.in	vector defining the minimum length. This is an optional feature. A vector of zeros will not draw values for this value. Expected input values are c(female mean, female sd, male mean, male sd)
Linf.in	vector defining the maximum length. This is an optional feature. A vector of zeros will not draw values for this value. Expected input values are c(female mean, female sd, male mean, male sd)
k.in	vector defining the growth coefficient k. This is an optional feature. A vector of zeros will not draw values for this value. Expected input values are c(female mean, female sd, male mean, male sd)
R_start	vector allowing the user to control the starting R0 value in the control file. Expected value is c( switch option, input value) where the switch optionas are 1= draw from a random draw from a truncated lognormal distribution based on the input value and 0 = start from the input value.
sum_age	summary age for total biomass calculation used by SS
sb_ofl_yrs	the years for which OFL values should be calculated
f_yr	final model year
year0	initial model year
genders	TRUE/FALSE allows for the user to specify whether or not sexes should have the same values from drawn parameters (e.g., natural mortality, L1, Linf)

Author(s)

Jason Cope and Chantel Wetzel

See Also

Opt_s_prof, Change_SSfiles, rbeta, rbeta_solve, rtlnorm, Run_SS,

shcaba/SSS documentation built on Jan. 26, 2024, 5:10 a.m.