SS_makedatlist: make a list for SS data
In r4ss: R code for Stock Synthesis

Description Usage Arguments Author(s) See Also

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.

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`	months per seasons
`spawn_seas`	spawning season
`Nfleet`	number of fishing fleets
`Nsurveys`	number of surveys
`N_areas`	number of areas
`fleetnames`	names of fleets
`surveytiming`	vector of survey timings
`areas`	area definitions for each fleet or survey
`units_of_catch`	units of catch for each fleet
`se_log_catch`	Uncertainty in catch (standard error in log space).
`Ngenders`	Number of genders.
`Nages`	Number of ages.
`init_equil`	Initial equilibrium catch.
`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.
`do_tags`	Include tag data? NOT IMPLEMENTED YET.
`morphcomp_data`	Morph composition data. NOT IMPLEMENTED YET.