Logging for Summary Display Table • logrx

In this section, we write a script to create a risk-difference table from the PHUSE Test Data Factory ADaM dataset, using the Typlr package. We use the logrx package to generate a log upon the script execution for reproducibility and traceability.

1. Load the packages

First, we load the packages that we will use to generate the risk-difference table.

library(haven)
library(magrittr)
library(Tplyr)

2. Load the data

Then we load the Adverse Event Analysis Dataset from the PHUSE Test Data Factory ADaM dataset. The data are stored in a transport file format and we use the haven package to load them.

adae <- read_xpt("adae.xpt")

3. Build the risk-difference table

Finally, we write a script (risk_diff.R) to build the risk-difference table, using the Typlr package.

t <- tplyr_table(adae, TRTA) %>% 
  add_layer(
    group_count(RACE) %>% 
      set_distinct_by(USUBJID) %>% 
      add_risk_diff(
        c("Xanomeline High Dose", "Placebo"),
        c("Xanomeline Low Dose", "Placebo")
      )
  )

build(t)

4. Axecute the script

We will axecute the following script.

axecute(file.path(dir,"risk_diff.R"))

Below is the log. Pay special attention to the Warnings and Result sections.