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

install.packages("chevron", repos = c("https://insightsengineering.r-universe.dev", getOption("repos")))

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

Alternatively, you might also use the development version.

install.packages("chevron", repos = c("https://pharmaverse.r-universe.dev", getOption("repos")))

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

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!

Stargazers and Forkers

Stargazers over time

Stargazers