View source: R/SSS_code_newSRs.r

SSS | R Documentation |

This file contails all the SSS code

```
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)
```

`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) |

Jason Cope and Chantel Wetzel

`Opt_s_prof`

, `Change_SSfiles`

, `rbeta`

, `rbeta_solve`

, `rtlnorm`

, `Run_SS`

,

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