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Logging for an ADSL dataset

Source: vignettes/articles/adsl_demo.Rmd
adsl_demo.Rmd

In this section, we will axecute() an R script that creates and ADSL to get a log file. This file was taken from the admiral::use_ad_template("adsl") with a few changes to its contents to showcase certain features of the logrx package’s log file.

Users wishing to run a similar script will need to do the following:

  • Install the logrx package
  • Copy the below script or use admiral::use_ad_template("adsl") to generate it.
  • Note this script differs from the template with a call to diffdf to do a compare, a simple custom message is used and results are manipulated for illustrative purposes.
  • Users will also need to make the decision on whether they want to use the Addin of logrx or use the aexcute() directly in a script or in the console to get a log file.

axecute the adsl.R script

Below is a simple adsl.R script generated from the admiral package. Notable features of the script are as follows:

  • Calls for getting SDTM datasets, e.g. DM, EX, DS
  • Converting SAS blanks to NAs
  • Typical derivations you would need to get treatment groups, start/end dates, duration
  • Typical derivation for Screen Failures, Screen Flags, Death Flags
  • Creating numeric variables with custom format functions
  • A call to diffdf::diffdf() to do a simple compare between two datasets
    • Note: The compare will create a warning that the two objects being compared have different columns. This warning will appear in the log
  • Simple message inserted for illustration. This message will appear in the log.
  • Manipulated results that will appear in the log file.

Inspect adsl.R script

Feel free to explore the script. The next section showcases the output for log file for the this script.


NOTE: Users can do the following to axecute their script:

  1. Use the Addin
  2. Use logrx::axecute("file.R") directly in their script [See Vignette TODO]
  3. Use logrx::axecute("file.R") in the console
  4. Use logrx::axecute("file.R") in a batch script [See Vignette TODO]

Log Output adsl.R

  1. logrx Metadata and User and File Information, of the log contains information about the version of logrx used to create this log as well as user and file information.
  2. Session Information, Packages , External software, Masked Functions, Used Package and Functions and Program Run Time Information of the log file contains information for everything used to run the R script. We believe this information suffices to re-create the environment needed for re-running the script.
  3. Errors and Warnings and Messages, Output, and Result are the final sections of the log file. Please note the following
    • Warning from the comparison file.
    • Message sent from the script to the log file
    • Results appended to the file

Comparison between Production and QC datasets

For illustrative purposes, we have included the comparison file between the two datasets. Here we can see that diffdf::diffdf() correctly picked up the differences in the dataset. The log file picked up the warning from diffdf::diffdf() and placed it in the appropriate section of the above log file.