tystan / vedol_panc

Signal detection for the adverse reaction of pancreatitis in vedolizumab use

vedol_panc

Signal detection for the adverse reaction of pancreatitis in vedolizumab use

How to run code

The following steps will allow you to run analyse_vedol_panc.R to reproduce Table 2 and Figure 1 of Duszynski et al. (2022):

• Make sure you have R and RStudio installed.
• Download the vedol_panc.zip file (on the repo page: green Code button -> Download ZIP button).
• Unzip the download.
• Double click the vedol_panc.Rproj file - this should open an RStudio session.
• (only has to be performed once) Make sure the prerequisite packages are installed by running the below command in the R console:

install.packages(
  c(
    "arrow", "dplyr", "tibble", 
    "ggplot2", "knitr", "tidyr"
  )
)
# install pharmsignal package from github
# NOTE: devtools package needs to be installed - please see 
#    https://www.r-project.org/nosvn/pandoc/devtools.html
devtools::install_github('tystan/pharmsignal')

• Now the code is ready to be run:
  • Open the analyse_vedol_panc.R file by clicking on Files tab in the Files/Plots/Packages/... pane of RStudio.
  • Now to finally run the code in analyse_vedol_panc.R in the R console.

Code outputs: Table 2 and Figure 1

Table 2: Signal detection estimates and 95% confidence intervals (RSIC = 2^IC using BCPNN MCMC) of vedolizumab v other comparators for pancreatitis

|Comparator       | N vedol and panc| N vedol| N comparator and panc| N comparator|RSIC = 2^IC        |
|:----------------|----------------:|-------:|---------------------:|------------:|:------------------|
|(1) All          |              124|   19034|                 21272|      7067209|2.15 (1.79, 2.54)* |
|(2) mAbs         |              124|   19034|                  1550|       558201|2.24 (1.87, 2.63)* |
|(3) IRAs         |              124|   19034|                    78|        35486|1.75 (1.56, 1.94)  |
|(4) All IBD indi |               96|   14797|                   824|       125466|0.99 (0.81, 1.18)  |
|(4a) CD indi     |               40|    7885|                   537|        89236|0.86 (0.62, 1.12)  |
|(4b) CU indi     |               52|    6538|                   265|        35658|1.06 (0.81, 1.33)  |

Figure 1: Signal detection estimates and 95% confidence intervals (RSIC = 2^IC using BCPNN MCMC) of vedolizumab v other comparators for pancreatitis.