Description Usage Arguments Author(s) See Also

View source: R/SS_makedatlist.R

create a list similar to those built by `SS_readdat`

which can
be written to a Stock Synthesis data file using `SS_writedat`

.
In hindsight, this function doesn't seem very useful and I haven't taken
time to describe the arguments below.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | ```
SS_makedatlist(styr = 1971, endyr = 2001, nseas = 1,
months_per_seas = 12, spawn_seas = 1, Nfleet = 1, Nsurveys = 1,
N_areas = 1, fleetnames = c("fishery1", "survey1"),
surveytiming = 0.5, areas = 1, units_of_catch = 1,
se_log_catch = 0.01, Ngenders = 2, Nages = 40, init_equil = 0,
catch = NULL, CPUE = NULL, N_discard_fleets = 0,
discard_data = NULL, meanbodywt = NULL, DF_for_meanbodywt = 30,
lbin_method = 2, binwidth = 2, minimum_size = 2,
maximum_size = 90, comp_tail_compression = -1e-04,
add_to_comp = 1e-04, max_combined_lbin = 0, lbin_vector = seq(22,
90, 2), lencomp = NULL, agebin_vector = 1:25,
ageerror = data.frame(rbind(0:40 + 0.5, 0.001, 0:40 + 0.5, seq(0.525,
2.525, 0.05))), agecomp = NULL, Lbin_method = 3,
max_combined_age = 1, MeanSize_at_Age_obs = NULL,
N_environ_variables = 0, N_environ_obs = 0, N_sizefreq_methods = 0,
do_tags = 0, morphcomp_data = 0)
``` |

`styr` |
start year of the model |

`endyr` |
end year of the model |

`nseas` |
number of seasons |

`months_per_seas` |
vector of months per season |

`spawn_seas` |
spawning season |

`Nfleet` |
number of fishing fleets |

`Nsurveys` |
number of surveys |

`N_areas` |
number of areas |

`fleetnames` |
names of fleets and surveys (alphanumeric only, no spaces or special characters) |

`surveytiming` |
vector of survey timings |

`areas` |
area definitions for each fleet and survey |

`units_of_catch` |
units of catch for each fleet |

`se_log_catch` |
Uncertainty in catch (standard error in log space) for each fleet |

`Ngenders` |
Number of genders. |

`Nages` |
Number of ages. |

`init_equil` |
Initial equilibrium catch for each fleet |

`catch` |
Catch data |

`CPUE` |
Indices of abundance (if present). |

`N_discard_fleets` |
Number of fleets with discard data. |

`discard_data` |
Discard data (if exists). |

`meanbodywt` |
Mean body weight data (if exists) |

`DF_for_meanbodywt` |
Degrees of freedom for mean body weight t-distribution. |

`lbin_method` |
Method for entering length bins. (1=use databins; 2=generate from binwidth,min,max below; 3=read vector). Not sure if all options implemented. |

`binwidth` |
Bin width for length bins. |

`minimum_size` |
Lower bound of length bins. |

`maximum_size` |
Upper bound of length bins. |

`comp_tail_compression` |
Value below which tails of composition data will be compressed (negative to turn off). |

`add_to_comp` |
Robustifying constant added to multinomial composition likelihoods. |

`max_combined_lbin` |
Maximum length bin below which length composition data will have genders combined. |

`lbin_vector` |
Vector of length bins. |

`lencomp` |
Length composition data (if exists). |

`agebin_vector` |
Vector of age bins. |

`ageerror` |
Ageing error matrices. |

`agecomp` |
Age composition data (if exists). |

`Lbin_method` |
Method of specifying length bins in conditional age-at-length data. |

`max_combined_age` |
Maximum age below which age composition data will have genders combined. |

`MeanSize_at_Age_obs` |
Data on mean size at age (if exists). |

`N_environ_variables` |
Number of environmental variables. |

`N_environ_obs` |
Number of environmental observations. |

`N_sizefreq_methods` |
Number of size frequency methods. NOT IMPLEMENTED YET. |

`do_tags` |
Include tag data? NOT IMPLEMENTED YET. |

`morphcomp_data` |
Morph composition data. NOT IMPLEMENTED YET. |

Ian Taylor

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