SS_makedatlist: make a list for SS data

Description Usage Arguments Author(s) See Also

View source: R/SS_makedatlist.R

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

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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

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.

Author(s)

Ian Taylor

See Also

SS_readdat, SS_writedat


r4ss documentation built on May 29, 2017, 2:24 p.m.