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Chevron: Standard TLGs for clinical trials reporting

chevron is a collection of function to create standard tables, listings, and graphs for clinical trials reporting.

Installation

Clone and install manually

  1. Clone the repository

  2. Install staged.dependencies with

    devtools::install_github("openpharma/staged.dependencies")

    and setup your GitHub tokens following the instructions on the staged.dependencies website. Make sure that you enable SSO for the token.

  3. Install the chevron package dependencies with (make sure the working directory is set to the root of chevron)

    library(staged.dependencies)
   x <- dependency_table(
   project = "insightsengineering/chevron",
   project_type = "repo@host",
   ref = "main",
   verbose = 1
)

install_deps(x, install_direction = "upstream", install_project = TRUE)

Usage 

library(chevron)

db <- syn_test_data()
run(aet02_1, db)

which returns

Adverse Events: {Specify Population}
Protocol: {{protocol}}, Snapshot: {{snapshot}}, Snapshot Date: {{snapshot-date}}, Cutoff Date: {{cutoff-date}}

—————————————————————————————————————————————————————————————————————————————————————————————————————
MedDRA System Organ Class                                    A: Drug X    B: Placebo   C: Combination
  MedDRA Preferred Term                                       (N=122)      (N=123)        (N=120)
—————————————————————————————————————————————————————————————————————————————————————————————————————
Total number of patients with at least one adverse event     122 (100%)   123 (100%)     120 (100%)
Overall total number of events                                  609          622            703
cl A.1
  Total number of patients with at least one adverse event   78 (63.9%)    75 (61%)      89 (74.2%)
  Total number of events                                        132          130            160
  dcd A.1.1.1.1                                               50 (41%)    45 (36.6%)     63 (52.5%)
  dcd A.1.1.1.2                                              48 (39.3%)    48 (39%)      50 (41.7%)
cl B.2
  Total number of patients with at least one adverse event   79 (64.8%)   74 (60.2%)     85 (70.8%)
  Total number of events                                        129          138            143
  dcd B.2.2.3.1                                              48 (39.3%)   54 (43.9%)     51 (42.5%)
  dcd B.2.1.2.1                                              49 (40.2%)   44 (35.8%)     52 (43.3%)
cl D.1
  Total number of patients with at least one adverse event   79 (64.8%)   67 (54.5%)     80 (66.7%)
  Total number of events                                        127          106            135
  dcd D.1.1.1.1                                               50 (41%)    42 (34.1%)     51 (42.5%)
  dcd D.1.1.4.2                                              48 (39.3%)   42 (34.1%)     50 (41.7%)
cl D.2
  Total number of patients with at least one adverse event   47 (38.5%)   58 (47.2%)     57 (47.5%)
  Total number of events                                         62           72             74
  dcd D.2.1.5.3                                              47 (38.5%)   58 (47.2%)     57 (47.5%)
cl C.2
  Total number of patients with at least one adverse event   35 (28.7%)    48 (39%)      55 (45.8%)
  Total number of events                                         48           53             65
  dcd C.2.1.2.1                                              35 (28.7%)    48 (39%)      55 (45.8%)
cl B.1
  Total number of patients with at least one adverse event   47 (38.5%)   49 (39.8%)     43 (35.8%)
  Total number of events                                         56           60             62
  dcd B.1.1.1.1                                              47 (38.5%)   49 (39.8%)     43 (35.8%)
cl C.1
  Total number of patients with at least one adverse event   43 (35.2%)   46 (37.4%)     43 (35.8%)
  Total number of events                                         55           63             64
  dcd C.1.1.1.3                                              43 (35.2%)   46 (37.4%)     43 (35.8%)
—————————————————————————————————————————————————————————————————————————————————————————————————————

Investigator text for AEs encoded using MedDRA version xx.x.  Percentages are based on N in the column headings. For frequency counts by preferred term, multiple occurrences of the same AE in an individual are counted only once.  For frequency counts of "Total number of events" rows, multiple occurrences of the same AE in an individual are counted separately. Standard footnote defining AEs included in table (e.g., includes AEs with onset from first dose of study drug through 7 days after last dose of study drug).                                         48 (39.3%)   54 (43.9%)     51 (42.5%)