Set up an AI-assisted analysis project structure

Usage

airsetup(
  path,
  split = TRUE,
  skills = TRUE,
  qc_agent = FALSE,
  japanese = FALSE,
  overwrite = FALSE
)

Arguments

path: Parent directory to create or update.
split: Logical. If TRUE, create sibling ai_project and r_project folders. If FALSE, create only ai_project.
skills: Logical. If TRUE, add the context, general plan, clinical SAP, result, and M11 semantic QC skill templates under ai_project/agent_control/.
qc_agent: Logical. If TRUE, add independent QC agent specifications and Plan gate review folders.
japanese: Logical. If TRUE, generated AGENTS.md instructs Codex to write narrative output documents in Japanese by default. If FALSE, it instructs Codex to use English by default. This does not override scripts, source code, schemas, or explicit user instructions.
overwrite: Logical. If TRUE, overwrite generated files that already exist.

Value

Invisibly returns the normalized parent path.

Examples

project_dir <- file.path(tempdir(), "airsetup_example")

airsetup(project_dir)
airsetup(project_dir, qc_agent = TRUE)
airsetup(project_dir, split = FALSE)
airsetup(project_dir, skills = FALSE)

aircheck(project_dir)
#>                                                item   type
#> 1                                 ai_project/source folder
#> 2                        ai_project/ai_visible_data folder
#> 3                              ai_project/ai_output folder
#> 4                               ai_project/r_output folder
#> 5                                     ai_project/qc folder
#> 6                                    ai_project/log folder
#> 7                          ai_project/agent_control folder
#> 8                              ai_project/AGENTS.md   file
#> 9                           ai_project/QC_STATUS.md   file
#> 10               ai_project/source/initial_YYYYMMDD folder
#> 11      ai_project/ai_visible_data/initial_YYYYMMDD folder
#> 12  ai_project/agent_control/AGENT_CONTROL_INDEX.md   file
#> 13     ai_project/agent_control/QC_SKILL_CONTEXT.md   file
#> 14        ai_project/agent_control/QC_SKILL_PLAN.md   file
#> 15         ai_project/agent_control/QC_SKILL_SAP.md   file
#> 16      ai_project/agent_control/QC_SKILL_RESULT.md   file
#> 17 ai_project/agent_control/QC_SKILL_M11SEMANTIC.md   file
#> 18                         r_project/ai_hidden_data folder
#> 19                             r_project/.gitignore   file
#> 20         r_project/README_DO_NOT_SHARE_WITH_AI.md   file
#> 21                         r_project/ai_hidden_data folder
#> 22        r_project/ai_hidden_data/initial_YYYYMMDD folder
#>                                                path exists required
#> 1                                 ai_project/source   TRUE     TRUE
#> 2                        ai_project/ai_visible_data   TRUE     TRUE
#> 3                              ai_project/ai_output   TRUE     TRUE
#> 4                               ai_project/r_output   TRUE     TRUE
#> 5                                     ai_project/qc   TRUE     TRUE
#> 6                                    ai_project/log   TRUE     TRUE
#> 7                          ai_project/agent_control   TRUE     TRUE
#> 8                              ai_project/AGENTS.md   TRUE     TRUE
#> 9                           ai_project/QC_STATUS.md   TRUE     TRUE
#> 10               ai_project/source/initial_YYYYMMDD   TRUE     TRUE
#> 11      ai_project/ai_visible_data/initial_YYYYMMDD   TRUE     TRUE
#> 12  ai_project/agent_control/AGENT_CONTROL_INDEX.md   TRUE     TRUE
#> 13     ai_project/agent_control/QC_SKILL_CONTEXT.md   TRUE     TRUE
#> 14        ai_project/agent_control/QC_SKILL_PLAN.md   TRUE     TRUE
#> 15         ai_project/agent_control/QC_SKILL_SAP.md   TRUE     TRUE
#> 16      ai_project/agent_control/QC_SKILL_RESULT.md   TRUE     TRUE
#> 17 ai_project/agent_control/QC_SKILL_M11SEMANTIC.md   TRUE     TRUE
#> 18                         r_project/ai_hidden_data   TRUE     TRUE
#> 19                             r_project/.gitignore   TRUE     TRUE
#> 20         r_project/README_DO_NOT_SHARE_WITH_AI.md   TRUE     TRUE
#> 21                         r_project/ai_hidden_data   TRUE     TRUE
#> 22        r_project/ai_hidden_data/initial_YYYYMMDD   TRUE     TRUE
#>                       message
#> 1                       Found
#> 2                       Found
#> 3                       Found
#> 4                       Found
#> 5                       Found
#> 6                       Found
#> 7                       Found
#> 8                       Found
#> 9                       Found
#> 10 Found dated initial folder
#> 11 Found dated initial folder
#> 12                      Found
#> 13                      Found
#> 14                      Found
#> 15                      Found
#> 16                      Found
#> 17                      Found
#> 18                      Found
#> 19                      Found
#> 20                      Found
#> 21                      Found
#> 22                      Found