SS_makedatlist: make a list for SS data

Description

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.

Usage

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)

Arguments

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.

Description

Usage

Arguments

See Also