philsf.workflow

Scripts to automate Statistical Analysis Reports (SAR)

The scripts in this repository standardize and automate the creation of individual git repositories for the creation of a Statistical Analysis Report (SAR). They also simplify the synchronization between repo remotes, regardless of location (github/gitlab/etc, USB or network drive).

Management of a SAR repo

Creation of a SAR repo

Essential scripts:

• SAR-new - Creates a new SAR dir (argument) in a sub-dir of the current dir
• SAR-remote-set - defines a remote for a SAR repo (in current dir)

Accessory scripts:

• SAR-rename - Renames a SAR repo
• SAR-remote-set - Creates and configures a SAR remote in a local/network dir

Used internally:

• SAR-init - Initiates the SAR repo
• SAR-basedirs - Creates the standardized dir structure for the SAR repo
• SAR-basefiles - Creates the stardardized file structure for the SAR repo

Maintenance of a SAR repo

Essencial scripts:

• SAR-sync - Syncs all remotes in the current dir (no arguments)
• SAR-sync-all - Syncs all remotes in all dirs (dirs as arguments)

Accessory scripts:

• SAR-remote-rename - Rename a git remote, and update its reference (also renames remote dir)
• SAR-remote-set-all - Batch creation and configuration of several SAR remotes

Document templates

A few R Markdown templates are provided suitable for SAR, SAP and general study protocols.

• SAR_pt - Statistical Analysis Report (pt)
• SAR_en - Statistical Analysis Report (en)
• SAP_pt - Analytical Plan (pt)
• SAP_en - Analytical Plan (en)

It includes a reference docx with pre-formatted styles for easy creation of professional reports or SAPs, in brazilian portuguese (pt) and english (en). These reference styles docx includes a template URL pointing to a philsf-biostat organization repository.

The SAP template was elaborated following recommendations on the structure for Statistical Analysis Plans for better transparency and clarity.

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