Reproducible Research

Under construction

Use version control (git or svn)

  • Do not track model development in git, it is too messy, which messes with the git history.
    • Use rsync if needed
    • Track the Rmd-file for the report
    • This tracks the models. The models are still in the “messy” folder.
      • base_model <- run25.mod
      • covariate_model <- run63.mod
      • final_model <- run67.mod
      • simulation_model <- run68.mod
    • Runrecord
      • runno
      • based on
      • OFV
      • dOFV
      • Condition number (CN)
  • Do not track produced PDFs in git

File/folder naming

  • Name files/folders using only A-Z, a-z, 0-9, -, _.
    • Start folder names with a number for sorting purposes.
  • In general, use kebab-case for naming (easier to read than snake_case).
    • If there are multiple parts to a name (e.g., a description, a date, and an author), use snake_case to separate between parts, and kebab-case within the parts (e.g., descriptive-name_2025-01-08_viktor-rognas.ext)

Folder structure:

  • model
    • pk
      • .mod
    • pd
      • .mod
  • report
    • 1a
      • .tex
      • .pdf
    • 1b
      • .tex
      • .pdf
    • 1
      • .tex
      • .pdf
  • data
    • raw_data
    • dat1.R
    • dat1.csv
    • dat2.R
    • dat2.csv
  • presentation
    • slides.pptx

Coding

R

  • Script all plots.
  • Quarto-scripted report.
    • R.version
    • rstudioapi::versionInfo()
    • .packages()
    • devtools::session_info(pkgs = "attached")

NONMEM

When using Monte-Carlo estimation methods (e.g., SAEM, IMP, or FOCE MCETA)), always specify the SEED option and RANMETHOD=P. Also, it is recommended to specify the RANMETHOD option accordingy: * For SAEM and IMP: RANMETHOD=3S2P * For MCETA:RANMETHOD=4P($SIMULATION` uses this method by default)