ichimomo / tc_tctaf22

Training Course on Reproducible science, best practices and ICES Transparent Assessment Framework

TCRSBPITAF-2022

Reproducible Science, Best Practices and the ICES Transparent Assessment Framework

• ICES Training Programme
• Instructors:
  • Iago Mosqueira, Wageningen Marine Research, Netherlands.
  • Colin Millar, ICES Secretariat.

Course goals

• Be able to create and populate a TAF repository for any analysis.
• Create all required outputs for a stock assessment and advice forecast.
• Use git for version control, development and collaboration.
• Report on the work carried out using markdown.

Requirements

• R >= 4.2.0.
• Ability to install packages from various repositories (CRAN, FLR).
• Demonstrations will be run in RStudio Desktop 2022.07.1+554. If you use Rtudio make sure it is recent version, or reinstall the very latest.
• Your own account in github.
• Optional: Rtools, to be able to reinstall packages that migt be updated.

INSTALLATION

• Please try installing the necessary packages in advance, by running:

pkgs <- c("data.table", "flextable", "officedown", "doParallel",
  "ggrepel", "patchwork", "icesdown", "icesAdvice", "icesTAF",
  "FLCore", "FLFishery", "FLasher", "FLa4a", "ggplotFL", "a4adiags")

install.packages(pkgs, repos=c(
    FLR="https://flr-project.org/R",
    ICES="https://ices-tools-prod.r-universe.dev/",
    CRAN="https://cloud.r-project.org"))

• Report any problems using the repository issue system, or by email.

• Please clone the course material repository at https://github.com/ices-eg/tc_tctaf22.

Bring

• Your own data and code for a stock assessment and forecast.