ICES2SS: Convert ICES input files to Stock Synthesis (SS) input files

Description Usage Arguments Author(s) Examples

View source: R/ICES2SS.R

Description

A series of files are used as input to ICES models. These files are standard input files for many types of models. This code acts as a standardized way to convert these ICES files to files that can be used in a Stock Synthesis (SS) model.

Usage

1
2
3
4
5
6
7
8
9
ICES2SS(
  user.wd,
  user.od,
  ices.id = "",
  slx = 26,
  tvslx = TRUE,
  ages = c(1, 2),
  forN = 1
)

Arguments

user.wd

A file path to the directory containing the ICES files.

user.od

A file path to a directory where the resulting files will be saved.

ices.id

A character value to set the ices.id because, sometimes, there is no stock id at the beginning of the file names

slx

A numerical value specifying the age-based selectivity type that will be used in Stock Synthesis.

tvslx

A logical value specifying whether or not to implement time-varying selectivity.

ages

Two values, a min and max age used for reporting fishing mortality estimates for each year. These values will be placed in the Stock Synthesis starter file for F std report ages.

forN

An integer value specifying the number of forecast years for the projections.

Author(s)

Kelli Faye Johnson

Examples

1
2
3
4
5
ICES2SS(user.wd = "c:/stockAssessment/MGWG/state-space/NScod", 
  user.od = "c:/stockAssessment/MGWG/state-space/NScod/SS",
  slx = 17, tvslx = FALSE, ages = c(2,4))
output <- r4ss::SS_output(getwd(), covar = FALSE)
r4ss::SS_plots(output, uncertainty = FALSE)

kellijohnson-NOAA/saconvert documentation built on Jan. 23, 2022, 7:57 p.m.