utilscognigen

Overview

utilscognigen provides utility functions for R and RStudio at Cognigen. This package facilitates creation, execution, and review of R files. This package also provides an interface for interacting with the Cognigen file system and sponsor directory structure.

Load it with:

library(utilscognigen)

Functionality

Creating R Files

• Create, update, and open R files with QMS approved headers with Redit() and Rcopy().
• Information can be retrieved from existing headers using the get_header_* family of functions.

Executing R Files

• Execute R scripts with rcb(). This will produce a log file (.Rout).
• Render R Markdown with render(). This produces an R script to render the Rmd file, which also results in an associated .Rout file.

Recording Input and Output Files

• record_input() and record_output() store IO information in a dedicated environment.
• Summarize the collected IO information with recorded_io().

Reviewing R and Rout Files

• Review warnings and errors with scanlogs(), which is run automatically after rcb() and render().
• Review recorded input and output files of an executed R file with get_recorded_io().
• Check if an R file meets Cognigen standards with check_standards().
• Review the entire .Rout file (as well as other logfiles) with logfile().

Interacting with the Cognigen File System

• Many functions require a path argument in this package. Generally, the open file in RStudio will be used when no other path is provided. See get_source_file().
• Convert file paths between their Unix and Windows representations with path_to_unix() and path_to_windows().
  • Also see the Toggle File Path Selection RStudio Addin.
• Navigate Outlook and SharePoint project resources with browse_project_email() and browse_project_sharepoint().
• Build file paths based on Cognigen's file system and directory structure with path_sponsor(), path_drug(), and path_project().
• Interact with the Cognigen shared-code repository and quickly identify and copy files with browse_shared_code(), list_files_shared_code(), and Rcopy_shared_code().
• Copy snippets (including shared-code snippets) with set_rstudio_snippets().
• Interact with Cognigen's zfs snapshots with file_snapshots(), diff_snapshot(), and restore_snapshot().