Every step has its own command, its products in a folder of out/ named like it, and one verdict line. A step that needs something older or missing says which command to run first, or makes it with --with-deps. Details of each are in Omakase.
From protocol to a plan#
| Command | What it does |
|---|
sapling new <study> --protocol F [--sdtm DIR] | A study folder with a first sap.qmd. F is a CDISC USDM JSON file, or a protocol document (PDF or its text) for a skeleton of open decisions. |
sapling generate <thing> ... | One conventional block (a population, a table, a multiplicity block) in its section of the plan. |
sapling ai "<plain English>" | Your AI drafts a block; it is compiled in its place and written only when you say so. |
sapling check [--strict] [--json] | The compiler's passes. SAPLING CHECK PASS / FAIL. |
sapling review | Every finding of the guideline rules, with its fix and source. |
sapling decide | Records a person's answer to an open decision, with the person's name. An agent never runs it in its own name. |
sapling dummy | Dummy SDTM data of a study that has no data yet, for testing a plan. Never use it in a folder with real data. |
sapling doctor | Checks the machine and prints the fix of each problem. |
From the plan to outputs#
| Command | Products |
|---|
sapling build | The SAP (structured, JSON, PDF), the ADaM and TLF specifications, programs, shells. |
sapling run | The ADaM data, the tables and the results (the ARD). |
sapling sap pdf, sapling sap html | The typeset SAP (Quarto). |
sapling export docx, sapling import docx | Word out and in. |
sapling adam spec, sapling adam programs, sapling adam data, sapling adam check | The ADaM specification, programs and data. |
sapling adam conform | The ADaM data against rules of the ADaM IG v1.2. |
sapling tlf spec, tlf shells, tlf programs, tlf run, tlf check | The analysis contract, the shells, the programs and the tables. |
sapling define, sapling package | The define file and the submission package. |
sapling status | Each step as fresh, stale, missing, edited or failed, with the next command. |
R, SAS and dashboards#
| Command | Products |
|---|
sapling r programs, sapling r run, sapling r check | The readable R programs, their run, and their numbers against the engine's. |
sapling sas programs, sapling sas run, sapling sas check | The SAS programs, their run through DataStep Studio, and every number of R against SAS. |
sapling dashboard [--check] | The study dashboard of the R engine. |
sapling sas dashboard [--check] [--no-subjects] | The dashboard of a SAS run in plain HTML. |
Design before the protocol#
| Command | What it does |
|---|
sapling design new <study> [--kind continuous|tte] | A study folder with a made-up design to change. |
sapling design check, sapling design simulate [--refine] | The design against itself; the simulation. |
sapling design export [--docx] | The statistical section of the protocol. |
sapling design to-sap <folder> | A SAP that starts with the blocks of the design. |
Commands of the editor#
In VS Code and Positron, run these from the Command Palette: Sapling: Open the Sample Study, New SAP from Protocol (USDM)..., Work Through the Open Decisions, What Is Missing (proposals from templates), Add an Analysis from a Template, Build PDF, Export Word (.docx) for Review, Edit the House Rules, What the Assistant Has Learned, Check What Sapling Needs, Data and AI Statement, Give Feedback.