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https://github.com/insightsengineering/chevron
Standard TLGs For Clinical Trials Reporting
https://github.com/insightsengineering/chevron
clinical-trials graphs listings nest r reporting tables
Last synced: 2 months ago
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Standard TLGs For Clinical Trials Reporting
- Host: GitHub
- URL: https://github.com/insightsengineering/chevron
- Owner: insightsengineering
- License: other
- Created: 2021-07-22T16:28:34.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2024-05-23T08:56:55.000Z (8 months ago)
- Last Synced: 2024-05-23T08:59:07.041Z (8 months ago)
- Topics: clinical-trials, graphs, listings, nest, r, reporting, tables
- Language: R
- Homepage: https://insightsengineering.github.io/chevron/
- Size: 121 MB
- Stars: 6
- Watchers: 7
- Forks: 0
- Open Issues: 39
-
Metadata Files:
- Readme: README.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
- Codeowners: .github/CODEOWNERS
- Security: SECURITY.md
Awesome Lists containing this project
README
# `chevron`: Standard TLGs for clinical trials reporting 
[](https://insightsengineering.github.io/chevron/main/unit-test-report/)
[](https://insightsengineering.github.io/chevron/)
[](https://insightsengineering.github.io/chevron/main/coverage-report/)
[](https://www.repostatus.org/#active)
[](https://github.com/insightsengineering/chevron/tree/main)
[](https://github.com/insightsengineering/chevron/issues?q=is%3Aissue+is%3Aopen+sort%3Aupdated-desc)
`chevron` is a collection of high-level functions to create standard outputs for clinical trials reporting with limited parameterisation. These outputs includes:
- [Tables](https://insightsengineering.github.io/chevron/latest-tag/articles/chevron_catalog.html#tables):
- safety table, e.g.
- [Safety Summary (`AET01`)](https://insightsengineering.github.io/chevron/latest-tag/articles/chevron_catalog.html#safety-summary-aet01)
- adverse events table, e.g.
- [Adverse Events (`AET02`)](https://insightsengineering.github.io/chevron/latest-tag/articles/chevron_catalog.html#adverse-events-aet02)
- [Adverse Events by Greatest Intensity (`AET03`)](https://insightsengineering.github.io/chevron/latest-tag/articles/chevron_catalog.html#adverse-events-by-greatest-intensityaet03)
- [Most Common (>=5%) Adverse Events (`AET10`)](https://insightsengineering.github.io/chevron/latest-tag/articles/chevron_catalog.html#most-common-5-adverse-events-aet10)
- demographic table, e.g.
- [Demographics and Baseline Characteristics (`DMT01`)](https://insightsengineering.github.io/chevron/latest-tag/articles/chevron_catalog.html#demographics-and-baseline-characteristics-dmt01)
- ECG table, e.g.
- [ECG Results and Change from Baseline by Visit (`EGT01`)](https://insightsengineering.github.io/chevron/latest-tag/articles/chevron_catalog.html#ecg-results-and-change-from-baseline-by-visit-egt01)
- [ECG Abnormalities (Regardless of Abnormality at Baseline) (`EGT02_1`)](https://insightsengineering.github.io/chevron/latest-tag/articles/chevron_catalog.html#ecg-abnormalities-regardless-of-abnormality-at-baseline-egt02_1)
- [ECG Abnormalities (Among Subject Without Abnormality at Baseline) (`EGT02_2`)](https://insightsengineering.github.io/chevron/latest-tag/articles/chevron_catalog.html#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`)](https://insightsengineering.github.io/chevron/latest-tag/articles/chevron_catalog.html#laboratory-test-results-and-change-from-baseline-by-visit-lbt01)
- [Laboratory Abnormalities (`LBT04`)](https://insightsengineering.github.io/chevron/latest-tag/articles/chevron_catalog.html#laboratory-abnormalities-lbt04)
- [Laboratory Abnormalities with Single and Replicated Marked (`LBT05`)](https://insightsengineering.github.io/chevron/latest-tag/articles/chevron_catalog.html#laboratory-abnormalities-with-single-and-replicated-marked-lbt05)
- medical history table, e.g.
- [Medical History (`MHT01`)](https://insightsengineering.github.io/chevron/latest-tag/articles/chevron_catalog.html#medical-history-mht01)
- response table, e.g.
- [Best Overall Response (`RSPT01`)](https://insightsengineering.github.io/chevron/latest-tag/articles/chevron_catalog.html#best-overall-response-rspt01)
- time to event table, e.g.
- [Time-to-event Summary (`TTET01`)](https://insightsengineering.github.io/chevron/latest-tag/articles/chevron_catalog.html#time-to-event-summary-ttet01)
- vital signs, e.g.
- [Vital Signs (`VST01`)](https://insightsengineering.github.io/chevron/latest-tag/articles/chevron_catalog.html#vital-signs-vst01)
- [Vital Signs Abnormalities (Regardless of Abnormality at Baseline) (`VST02_1`)](https://insightsengineering.github.io/chevron/latest-tag/articles/chevron_catalog.html#vital-signs-abnormalities-regardless-of-abnormality-at-baseline-vst02_1)
- [Vital Signs Abnormalities (Among Subject Without Abnormality at Baseline) (`VST02_2`)](https://insightsengineering.github.io/chevron/latest-tag/articles/chevron_catalog.html#vital-signs-abnormalities-among-subject-without-abnormality-at-baseline-vst02_2)
- [Listings](https://insightsengineering.github.io/chevron/latest-tag/articles/chevron_catalog.html#listings)
- [Graphs](https://insightsengineering.github.io/chevron/latest-tag/articles/chevron_catalog.html#graphics):
- [Kaplan-Meier Plot (`KMG01`)](https://insightsengineering.github.io/chevron/latest-tag/articles/chevron_catalog.html#kaplan-meier-plot-kmg01)
- [Mean Plot (`MNG01`)](https://insightsengineering.github.io/chevron/latest-tag/articles/chevron_catalog.html#mean-plot-mng01)
Please visit [the catalog](https://insightsengineering.github.io/chevron/latest-tag/articles/chevron_catalog.html) to see full list of available outputs. If you want a new output, please [create an issue](https://github.com/insightsengineering/chevron/issues/new?template=new_table.yml).
If you need more flexibility please refer to [`tern`](https://insightsengineering.github.io/tern/) with its [TLG Catalog](https://insightsengineering.github.io/tlg-catalog/).
## Installation
`chevron` is available on CRAN and you can install the latest released version with:
```r
install.packages("chevron")
```
Alternatively, you might also use the development version.
```r
# install.packages("pak")
pak::pak("insightsengineering/chevron")
```
## Usage
To understand how to use this package, please refer to the [Introduction to `chevron`](https://insightsengineering.github.io/chevron/latest-tag/articles/chevron.html) article, which provides multiple examples of code implementation.
Below is the showcase of the example usage.
```r
library(chevron)
data(syn_data)
run(aet02, syn_data)
```
which returns
```text
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`](https://insightsengineering.github.io/rtables/) - table engine used
- [`tern`](https://insightsengineering.github.io/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
[](https://starchart.cc/insightsengineering/chevron)
### Stargazers
[](https://github.com/insightsengineering/chevron/stargazers)
[](https://github.com/insightsengineering/chevron/network/members)