data-raw/project_template.R

In ddsjoberg/bstfun: Functions for the MSK Biostatistics Department

## code to prepare project template goes here

# bstfun project template ------------------------------------------------------
## base template--this is the same for all bst tempaltes -----------------------
project_template_base <-
  list(
    readme = rlang::expr(list(
      template_filename = fs::path_package("project_templates/readme.md", package = "bstfun"),
      filename = "README.md",
      copy = FALSE
    )),
    gitignore = rlang::expr(list(
      template_filename = fs::path_package("project_templates/gitignore.txt", package = "bstfun"),
      filename = ".gitignore",
      copy = TRUE
    )),
    data_date = rlang::expr(list(
      template_filename = fs::path_package("project_templates/data_date.txt", package = "bstfun"),
      filename = "data_date.txt",
      copy = FALSE
    )),
    rproj = rlang::expr(list(
      template_filename = fs::path_package("project_templates/default_rproj.Rproj", package = "bstfun"),
      filename = glue::glue("_rstudio_project.Rproj"),
      copy = TRUE
    )),
    derived_vars = rlang::expr(list(
      template_filename = fs::path_package("project_templates/derived_variables.xlsx", package = "bstfun"),
      filename = glue::glue("scripts/derived_variables.xlsx"),
      copy = TRUE
    )),
    sap = rlang::expr(list(
      template_filename = fs::path_package("project_templates/sap.docx", package = "bstfun"),
      filename = glue::glue("SAP - {folder_name}.docx"),
      copy = TRUE
    )),
    # only add Rprofile if renv was used
    rprofile =
      rlang::expr(switch(renv,
                         list(
                           template_filename =
                             fs::path_package(package = "starter", "project_templates/default_rprofile.R"),
                           filename = stringr::str_glue(".Rprofile"),
                           glue = TRUE
                         )
      )),
    csl = rlang::expr(list(
      template_filename = fs::path_package("project_templates/european-urology.csl", package = "bstfun"),
      filename = "scripts/templates/european-urology.csl",
      copy = TRUE
    ))
  )

## default bst template (scripts/results in folder) ----------------------------
project_template_default <-
  c(
    project_template_base,
    list(
      setup = rlang::expr(list(
        template_filename = fs::path_package("project_templates/setup.qmd", package = "bstfun"),
        filename = glue::glue("scripts/10-setup_{folder_first_word}.qmd"),
        copy = FALSE
      )),
      analysis = rlang::expr(list(
        template_filename = fs::path_package("project_templates/analysis.qmd", package = "bstfun"),
        filename = glue::glue("scripts/20-analysis_{folder_first_word}.qmd"),
        copy = FALSE
      )),
      report = rlang::expr(list(
        template_filename = fs::path_package("project_templates/report.qmd", package = "bstfun"),
        filename = glue::glue("scripts/30-report_{folder_first_word}.qmd"),
        copy = FALSE
      )),
      doc_template = rlang::expr(list(
        template_filename = fs::path_package("project_templates/doc_template.docx", package = "bstfun"),
        filename = "scripts/templates/doc_template.docx",
        copy = TRUE
      )),
      references = rlang::expr(list(
        template_filename = fs::path_package("project_templates/references.bib", package = "bstfun"),
        filename = glue::glue("scripts/templates/references.bib"),
        copy = TRUE
      ))
    )
  )
attr(project_template_default, "script_path") <-
  expression(fs::path_package("project_templates/script_phi_private.R", package = "bstfun"))
attr(project_template_default, "label") <- "Biostatistics Project Template (Quarto)"

## scripts+results in separate folders -----------------------------------------
project_template_results_folder <- project_template_default
project_template_results_folder[["setup"]] <-
  rlang::expr(list(
    template_filename = fs::path_package("project_templates/results_scripts_folders/setup.Rmd", package = "bstfun"),
    filename = glue::glue("scripts/10-setup_{folder_first_word}.Rmd"),
    copy = FALSE
  ))
project_template_results_folder[["analysis"]] <-
  rlang::expr(list(
    template_filename = fs::path_package("project_templates/results_scripts_folders/analysis.Rmd", package = "bstfun"),
    filename = glue::glue("scripts/20-analysis_{folder_first_word}.Rmd"),
    copy = FALSE
  ))
project_template_results_folder[["report"]] <-
  rlang::expr(list(
    template_filename = fs::path_package("project_templates/results_scripts_folders/report.Rmd", package = "bstfun"),
    filename = glue::glue("scripts/30-report_{folder_first_word}.Rmd"),
    copy = FALSE
  ))
attr(project_template_results_folder, "script_path") <-
  rlang::expr(fs::path_package("project_templates/results_scripts_folders/results_scripts_folders.R", package = "bstfun"))
attr(project_template_results_folder, "label") <- "Biostatistics Project Template (Rmd)"


## SAS project template ---------------------------------------------------------
project_template_sas <-
  project_template_default[c("gitignore", "data_date","sap","derived_vars")] |>
  purrr::list_modify(
    readme = rlang::expr(list(
      template_filename = fs::path_package("project_templates/SASgeneral_template_files/readme.md", package = "bstfun"),
      filename = "README.md",
      copy = FALSE
    )),
    setupSAS = rlang::expr(list(
      template_filename = fs::path_package("project_templates/SASgeneral_template_files/010-data-setup.sas", package = "bstfun"),
      filename = glue::glue("010-data-setup.sas"),
      copy = FALSE
    )),
    formatsSAS = rlang::expr(list(
      template_filename = fs::path_package("project_templates/SASgeneral_template_files/_formats.sas", package = "bstfun"),
      filename = glue::glue("_formats.sas"),
      copy = FALSE
    )),
    analysisSAS = rlang::expr(list(
      template_filename = fs::path_package("project_templates/SASgeneral_template_files/020-analysis.sas", package = "bstfun"),
      filename = glue::glue("020-analysis.sas"),
      copy = FALSE
    )),
    reportSAS = rlang::expr(list(
      template_filename = fs::path_package("project_templates/SASgeneral_template_files/030-report1.sas", package = "bstfun"),
      filename = glue::glue("030-report1.sas"),
      copy = FALSE
    )),
    prepSAS = rlang::expr(list(
      template_filename = fs::path_package("project_templates/SASgeneral_template_files/_prep.sas", package = "bstfun"),
      filename = glue::glue("_prep.sas"),
      copy = FALSE
    ))
  )
attr(project_template_sas, "label") <- "Biostatistics SAS Template"
attr(project_template_sas, "arg_override") <- list(renv = FALSE, open = FALSE)

# hot template -----------------------------------------------------------------
hot_project_template <-
  project_template_default[c("readme", "gitignore", "data_date", "doc_template", "rproj", "rprofile", "csl")] |>
  purrr::list_modify(
    setup = rlang::expr(list(
      template_filename = fs::path_package("project_templates/hot_template_files/hot_setup.qmd", package = "bstfun"),
      filename = glue::glue("scripts/10-setup_{folder_first_word}.qmd"),
      copy = FALSE
    )),
    analysis = rlang::expr(list(
      template_filename = fs::path_package("project_templates/hot_template_files/hot_analysis.qmd", package = "bstfun"),
      filename = glue::glue("scripts/20-analysis_{folder_first_word}.qmd"),
      copy = FALSE
    )),
    report = rlang::expr(list(
      template_filename = fs::path_package("project_templates/hot_template_files/hot_report.qmd", package = "bstfun"),
      filename = glue::glue("scripts/30-report_{folder_first_word}.qmd"),
      copy = FALSE
    )),
    sap = rlang::expr(list(
      template_filename = fs::path_package("project_templates/sap.docx", package = "bstfun"),
      filename = glue::glue("SAP - {folder_name}.docx"),
      copy = TRUE
    )),
    derived_vars = rlang::expr(list(
      template_filename = fs::path_package("project_templates/derived_variables.xlsx", package = "bstfun"),
      filename = glue::glue("scripts/derived_variables_{folder_first_word}.xlsx"),
      copy = TRUE
    )),
    doc_template = rlang::expr(list(
      template_filename = fs::path_package("project_templates/hot_template_files/doc_template.docx", package = "bstfun"),
      filename = "scripts/templates/doc_template.docx",
      copy = TRUE
    )),
    references = rlang::expr(list(
      template_filename = fs::path_package("project_templates/references.bib", package = "bstfun"),
      filename = "scripts/templates/references.bib",
      copy = TRUE
    ))
  )

attr(hot_project_template, "script_path") <-
  expression(fs::path_package("project_templates/script_phi_private.R", package = "bstfun"))
attr(hot_project_template, "label") <- "H.O.T. Project Template"

# whitingk template ------------------------------------------------------------
whitingk_project_template <-
  project_template_default[c("readme", "gitignore", "rproj", "rprofile")] |>
  purrr::list_modify(
    setup = rlang::expr(list(
      template_filename = fs::path_package("project_templates/whitingk_template_files/01_clean-data.R", package = "bstfun"),
      filename = glue::glue("scripts/01_clean-data.R"),
      copy = FALSE
    )),
    analysis = rlang::expr(list(
      template_filename = fs::path_package("project_templates/whitingk_template_files/02_analysis.Rmd", package = "bstfun"),
      filename = glue::glue("scripts/02_analysis.Rmd"),
      copy = FALSE
    ))
  )

attr(whitingk_project_template, "script_path") <-
  expression(fs::path_package("project_templates/whitingk_template_files/write_directories.R", package = "bstfun"))
attr(whitingk_project_template, "label") <- "Karissa's Project Template"


# leej22 template ------------------------------------------------------------
leej22_project_template <-
  project_template_default[c("readme", "gitignore", "data_date", "rproj", "rprofile")] |>
  purrr::list_modify(
    setup = rlang::expr(list(
      template_filename = fs::path_package("project_templates/leej22_template_files/01_data_setup.Rmd", package = "bstfun"),
      filename = glue::glue("code/{folder_name}_01_data_setup.Rmd"),
      copy = FALSE
    )),
    data_checks = rlang::expr(list(
      template_filename = fs::path_package("project_templates/leej22_template_files/02_data_checks.Rmd", package = "bstfun"),
      filename = glue::glue("code/{folder_name}_02_data_checks.Rmd"),
      copy = FALSE
    )),
    analysis = rlang::expr(list(
      template_filename = fs::path_package("project_templates/leej22_template_files/03_analysis.Rmd", package = "bstfun"),
      filename = glue::glue("code/{folder_name}_03_analysis.Rmd"),
      copy = FALSE
    )),
    report = rlang::expr(list(
      template_filename = fs::path_package("project_templates/leej22_template_files/04_report.Rmd", package = "bstfun"),
      filename = glue::glue("code/{folder_name}_04_report.Rmd"),
      copy = FALSE
    ))
  )
attr(leej22_project_template, "script_path") <-
  expression(fs::path_package("project_templates/leej22_template_files/write_directories.R", package = "bstfun"))
attr(leej22_project_template, "label") <- "Jasme Lee Project Template"


# lobaughs template ------------------------------------------------------------
lobaughs_project_template <-
  project_template_default[c("gitignore", "data_date", "rproj", "rprofile")] |>
  purrr::list_modify(
    readme = rlang::expr(list(
      template_filename = fs::path_package("project_templates/lobaughs_template_files/readme.md", package = "bstfun"),
      filename = "README.md",
      copy = FALSE
    )),
    setupSAS = rlang::expr(list(
      template_filename = fs::path_package("project_templates/lobaughs_template_files/010-data-setup.sas", package = "bstfun"),
      filename = glue::glue("010-data-setup.sas"),
      copy = FALSE
    )),
    formatsSAS = rlang::expr(list(
      template_filename = fs::path_package("project_templates/lobaughs_template_files/_formats.sas", package = "bstfun"),
      filename = glue::glue("_formats.sas"),
      copy = FALSE
    )),
    analysisSAS = rlang::expr(list(
      template_filename = fs::path_package("project_templates/lobaughs_template_files/020-analysis.sas", package = "bstfun"),
      filename = glue::glue("020-analysis.sas"),
      copy = FALSE
    )),
    reportSAS = rlang::expr(list(
      template_filename = fs::path_package("project_templates/lobaughs_template_files/030-report1.sas", package = "bstfun"),
      filename = glue::glue("030-report1.sas"),
      copy = FALSE
    )),
    prepSAS = rlang::expr(list(
      template_filename = fs::path_package("project_templates/lobaughs_template_files/_prep.sas", package = "bstfun"),
      filename = glue::glue("_prep.sas"),
      copy = FALSE
    )),
    setup = rlang::expr(list(
      template_filename = fs::path_package("project_templates/lobaughs_template_files/010-data-setup.Rmd", package = "bstfun"),
      filename = glue::glue("010-data-setup.Rmd"),
      copy = FALSE
    )),
    analysis = rlang::expr(list(
      template_filename = fs::path_package("project_templates/lobaughs_template_files/020-analysis.Rmd", package = "bstfun"),
      filename = glue::glue("020-analysis.Rmd"),
      copy = FALSE
    )),
    report = rlang::expr(list(
      template_filename = fs::path_package("project_templates/lobaughs_template_files/030-report1.Rmd", package = "bstfun"),
      filename = glue::glue("030-report1.Rmd"),
      copy = FALSE
    )),
  )
attr(lobaughs_project_template, "label") <- "Stephanie Lobaugh Project Template"

# Create template object -----

project_templates <- list()
project_templates[["default"]] <- project_template_default
project_templates[["results_folder"]] <- project_template_results_folder
project_templates[["hot"]] <- hot_project_template
project_templates[["sas"]] <- project_template_sas
project_templates[["whitingk"]] <- whitingk_project_template
project_templates[["kwhiting"]] <- whitingk_project_template
project_templates[["leej22"]] <- leej22_project_template
project_templates[["lobaughs"]] <- lobaughs_project_template

usethis::use_data(project_templates, overwrite = TRUE)