logrxpackage
In logrx: A Logging Utility Focus on Clinical Trial Programming Workflows

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(logrx)

Generating a log

The purpose of the logrx package is to generate a log upon execution of an R script which enables traceability and reproducibility of the executed code. Generating a log with {logrx} can be as simple as running one line of code as seen in the below example of how to use the axecute() function.. However, {logrx} has much more advanced capabilities to meet the demands of Clinical Reporting. To learn additional techniques about executing code with {logrx} please visit our Execution Vignette.

`axecute()`

axecute() enables the command line submission of a program. A log is set-up around the program, and its code is run safely and loudly (using safely() from the purrr package). The log will be generated in the same folder as the script unless you specify differently.

axecute("my_script.R")

`logrx` addin:

A log can be generated using the {logrx} addin, which is a simple point and click interface that allows you to run a single program. The Addin ships with the package and is available once you use install the package. The gif on the Get Started page gives a quick snapshot of its intended use.

Log attributes

We have compiled a brief overview of the information that we capture in the log file generated by {logrx}. We allow users to customize sections of the log based on their needs for a log, e.g. you can toggle on/off the messages, outputs, errors and messages. You can also build into your log approved and unapproved packages used in your R script - see Logging Unapproved Package and Function Use for additional guidance

The following attributes are recorded in the log:

Metadata: {logrx} package information
Version of the package
Type of build
Link to the GitHub repository
User and File Information
User that generated the log
Name and path of the script for which the log was generated
hash_sum: A unique hashsum is created for the log file
Session Information: The R session information
R version
OS and system
GUI
Language and timezone
Packages - List of all available packages in the environment
External Software - List of all external software
Masked Functions - List of all functions masked by packages
Program Run Time Information - Start, end, and run times
Used Package and Functions (optional) - List of all packages and functions used in the script for which the log was generated
Unapproved Package and Functions (optional) - List of all packages and functions used in the script for which the log was generated that are not part of the approved list of packages and functions
Errors and Warnings - List of Errors and Warnings from the Script
Messages, Output and Results (optional) - List Messages, Outputs and Results
Log Output File - Name and path of the log