Standard TLGs for Clinical Trials Reporting

Provide standard tables, listings, and graphs (TLGs) libraries used in clinical trials. This package implements a structure to reformat the data with 'dunlin', create reporting tables using 'rtables' and 'tern' with standardized input arguments to enable quick generation of standard outputs. In addition, it also provides comprehensive data checks and script generation functionality.

chevron: Standard TLGs for clinical trials reporting

chevron is a collection of high-level functions to create standard outputs for clinical trials reporting with limited parameterisation. These outputs includes:

• Tables:
  • safety table, e.g.
    • Safety Summary (AET01)
  • adverse events table, e.g.
    • Adverse Events (AET02)
    • Adverse Events by Greatest Intensity (AET03)
    • Most Common (>=5%) Adverse Events (AET10)
  • demographic table, e.g.
    • Demographics and Baseline Characteristics (DMT01)
  • ECG table, e.g.
    • ECG Results and Change from Baseline by Visit (EGT01)
    • ECG Abnormalities (Regardless of Abnormality at Baseline) (EGT02_1)
    • ECG Abnormalities (Among Subject Without Abnormality at Baseline) (EGT02_2)
  • lab results table, e.g.
    • Laboratory Test Results and Change from Baseline by Visit (LBT01)
    • Laboratory Abnormalities (LBT04)
    • Laboratory Abnormalities with Single and Replicated Marked (LBT05)
  • medical history table, e.g.
    • Medical History (MHT01)
  • response table, e.g.
    • Best Overall Response (RSPT01)
  • time to event table, e.g.
    • Time-to-event Summary (TTET01)
  • vital signs, e.g.
    • Vital Signs (VST01)
    • Vital Signs Abnormalities (Regardless of Abnormality at Baseline) (VST02_1)
    • Vital Signs Abnormalities (Among Subject Without Abnormality at Baseline) (VST02_2)
• Listings
• Graphs:
  • Kaplan-Meier Plot (KMG01)
  • Mean Plot (MNG01)

Please visit the catalog to see full list of available outputs. If you want a new output, please create an issue.

If you need more flexibility please refer to tern with its TLG Catalog.

Installation

chevron is available on CRAN and you can install the latest released version with:

install.packages("chevron")

Alternatively, you might also use the development version.

# install.packages("pak")
pak::pak("insightsengineering/chevron")

Usage

To understand how to use this package, please refer to the Introduction to chevron article, which provides multiple examples of code implementation.

Below is the showcase of the example usage.

library(chevron)

data(syn_data)
run(aet02, syn_data)

which returns

  MedDRA System Organ Class                                     A: Drug X    B: Placebo    C: Combination
    MedDRA Preferred Term                                        (N=134)       (N=134)        (N=132)
  ———————————————————————————————————————————————————————————————————————————————————————————————————————
  Total number of patients with at least one adverse event     122 (91.0%)   123 (91.8%)    120 (90.9%)
  Overall total number of events                                   609           622            703
  cl A.1
    Total number of patients with at least one adverse event   78 (58.2%)    75 (56.0%)      89 (67.4%)
    Total number of events                                         132           130            160
    dcd A.1.1.1.1                                              50 (37.3%)    45 (33.6%)      63 (47.7%)
    dcd A.1.1.1.2                                              48 (35.8%)    48 (35.8%)      50 (37.9%)
  cl B.2
    Total number of patients with at least one adverse event   79 (59.0%)    74 (55.2%)      85 (64.4%)
    Total number of events                                         129           138            143
    dcd B.2.2.3.1                                              48 (35.8%)    54 (40.3%)      51 (38.6%)
    dcd B.2.1.2.1                                              49 (36.6%)    44 (32.8%)      52 (39.4%)
  cl D.1
    Total number of patients with at least one adverse event   79 (59.0%)    67 (50.0%)      80 (60.6%)
    Total number of events                                         127           106            135
    dcd D.1.1.1.1                                              50 (37.3%)    42 (31.3%)      51 (38.6%)
    dcd D.1.1.4.2                                              48 (35.8%)    42 (31.3%)      50 (37.9%)
  cl D.2
    Total number of patients with at least one adverse event   47 (35.1%)    58 (43.3%)      57 (43.2%)
    Total number of events                                         62            72              74
    dcd D.2.1.5.3                                              47 (35.1%)    58 (43.3%)      57 (43.2%)
  cl B.1
    Total number of patients with at least one adverse event   47 (35.1%)    49 (36.6%)      43 (32.6%)
    Total number of events                                         56            60              62
    dcd B.1.1.1.1                                              47 (35.1%)    49 (36.6%)      43 (32.6%)
  cl C.2
    Total number of patients with at least one adverse event   35 (26.1%)    48 (35.8%)      55 (41.7%)
    Total number of events                                         48            53              65
    dcd C.2.1.2.1                                              35 (26.1%)    48 (35.8%)      55 (41.7%)
  cl C.1
    Total number of patients with at least one adverse event   43 (32.1%)    46 (34.3%)      43 (32.6%)
    Total number of events                                         55            63              64
    dcd C.1.1.1.3                                              43 (32.1%)    46 (34.3%)      43 (32.6%)

Related

• rtables - table engine used
• tern - analysis function used

Acknowledgment

This package is a result of a joint efforts by many developers and stakeholders. We would like to thank everyone who has contributed so far!