In BenWilliams-NOAA/groundfishr: What the Package Does (One Line, Title Case)

knitr::opts_chunk$set(
  collapse = TRUE,
  eval = F,
  comment = "#>"
)

The goal of groundfishr is to create a clear workflow for cleaning data (and running models) for fishery stock assessments based upon the ADMB rockfish assessment framework It utilizes a "project oriented workflow" via RStudio (base R is ok, though you must use here::here()). You must be able to have a connection to the AFSC & AKFIN (Answers) data servers (e.g., VPN if offsite), and have usernames/passwords setup. This package is linked with the gfdata package, the functions herein will be looking for the folder layout and file names generated by the gfdata package.

Installation

The groundfishr package can be installed from github with:

# install.packages("devtools")
devtools::install_github("BenWilliams-NOAA/groundfishr")

library(groundfishr)

A consistent directory format is probably the most important aspect of this package. The first function creates a number of directories within your R project folder. The setup is organized by year within a folder. The setup() function creates the following folders and files:

# setup folders -----

setup(2020)

project
|__2020
    |__data
        |__models
        |    |__ageage
        |    |     AGEAGE.tpl
        |    |__allometric
        |    |     allometric.tpl
        |    |__length_sd
        |    |     lengthSD.tpl
        |    |__VBL
        |    |      VBL.tpl
        |    |__wVBL
        |    |      wVBL.tpl
        |    |      lvb.ctl
        |
        |__output
        |__raw
        |__SARA
        |__user_input

This can then be updated for each year.

# setup folders -----

setup(2021)

Which would create a duplication of the folders for the given year

project
|__2020
|   |__data
|       |__models
|       |    |__ageage
|       |    |     AGEAGE.tpl
|       |    |__allometric
|       |    |     allometric.tpl
|       |    |__length_sd
|       |    |     lengthSD.tpl
|       |    |__VBL
|       |    |      VBL.tpl
|       |    |__wVBL
|       |    |      wVBL.tpl
|       |    |      lvb.ctl
|       |
|       |__output
|       |__raw
|       |__SARA
|       |__user_input
|__2021
    |__data
        |__models
        |    |__ageage
        |    |     AGEAGE.tpl
        |    |__allometric
        |    |     allometric.tpl
        |    |__length_sd
        |    |     lengthSD.tpl
        |    |__VBL
        |    |      VBL.tpl
        |    |__wVBL
        |    |      wVBL.tpl
        |    |      lvb.ctl
        |
        |__output
        |__raw
        |__SARA
        |__user_input        

The SSC accepted model can then be added from the last assessment as the current year's "base model".

accepted_model(base_year = 2020, base_model = "m18.2b", year = 2021)

This creates a duplication of the folders for the given year

project
|__2020
    |__data
    |__base    # last accepted model
    |__m18.2a  # model variant a
    |__m18.2b  # model variant b
|__2021
    |__data
    |__base   # dupication of m18.2b
        |__ base_model_2020_m18.2b.txt"

BenWilliams-NOAA/groundfishr documentation built on May 11, 2022, 7:41 p.m.