The cardinal R package contains table-generating functions to implement standard FDA Safety Tables according to the guidelines published in the FDA Safety Tables and Figures Integrated Guide. The cardinal project aims to build and open-source a catalog of harmonized templates for generating tables, listings, and graphs (TLGs) in clinical study reporting. Details on package usage and the variety of functions currently available in the package are available on the cardinal website.
You can install the latest development version of cardinal directly from GitHub and its dependencies from CRAN by running the following:
if (!require("formatters")) install.packages("formatters")
if (!require("rtables")) install.packages("rtables")
if (!require("rlistings")) install.packages("rlistings")
if (!require("tern")) install.packages("tern")
if (!require("remotes")) install.packages("remotes")
remotes::install_github("pharmaverse/cardinal")See the Getting Started page on the cardinal website for additional details on getting started with the cardinal package.
In the following example, Table 2 (Baseline Demographic and Clinical Characteristics) from the FDA Safety Tables and Figures Integrated Guide is generated using the make_table_02 function from the cardinal package.
First we will load the cardinal package and use the random.cdisc.data package to load an example ADSL dataset. The cardinal package works with standard CDISC datasets and variable names while allowing users to set custom variable names & labels where necessary.
library(cardinal)
adsl <- random.cdisc.data::cadslWith data now loaded, the make_table_02 function can be used to generate the FDA standard table.
make_table_02(
df = adsl,
vars = c("SEX", "AGE", "RACE"),
lbl_vars = c("Sex", "Age, years", "Race")
) A: Drug X B: Placebo C: Combination Total Population
Characteristic (N=134) (N=134) (N=132) (N=400)
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
Sex
F 79 (59%) 82 (61.2%) 70 (53%) 231 (57.8%)
M 55 (41%) 52 (38.8%) 62 (47%) 169 (42.2%)
Age, years
Mean (SD) 33.8 (6.6) 35.4 (7.9) 35.4 (7.7) 34.9 (7.4)
Median (Min - Max) 33.0 (21.0 - 50.0) 35.0 (21.0 - 62.0) 35.0 (20.0 - 69.0) 34.0 (20.0 - 69.0)
Race
ASIAN 68 (50.7%) 67 (50%) 73 (55.3%) 208 (52%)
BLACK OR AFRICAN AMERICAN 31 (23.1%) 28 (20.9%) 32 (24.2%) 91 (22.8%)
WHITE 27 (20.1%) 26 (19.4%) 21 (15.9%) 74 (18.5%)
AMERICAN INDIAN OR ALASKA NATIVE 8 (6%) 11 (8.2%) 6 (4.5%) 25 (6.2%)
MULTIPLE 0 1 (0.7%) 0 1 (0.2%)
NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER 0 1 (0.7%) 0 1 (0.2%)
For more information on the make_table_02 function and parameters you can use to customize the output table, see the FDA Table 2 page on the cardinal website.
tern- analysis functions used to build standard tables.rtables- table engine used for standard tables.rlistings- listing engine used for standard listings.gtsummary- table functions used to build select non-standard tables.Tplyr- table functions used to build select non-standard tables.
We are reachable via the following channels for inquiries and support:
- Slack - Use this channel to message the cardinal team directly with questions & feedback on the package. If you don't have access, use this link to join the Pharmaverse Slack workspace
- GitHub Issues - To report a bug, request a new feature or table, or ask a question, open a new issue on GitHub.
This package is a result of an industry collaboration across several different companies. We would like to thank all of the developers and users who have contributed so far!
