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align readme with other nest pkgs (#704)
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as we approach open-sourcing it would be good to clean-up readme a
little

changes includes:
- update logo
- added "Catalog" in the top menu to promote it more
- explain the package content more - give a lot of examples with
references to the catalog. Those references uses `/latest-tag/` endpoint
so as to avoid promoting development version
- update installation instructions (align with other pkgs - here: teal)
- add references to `rtables` and `tern` on which this package is built
- remove "how to request new tlg" vigniette and added link to the readme
instead. Some parts of it has been outdated and this doesn't fit into
"how to use the package" it's more process oriented - hence: readme.
- remove dates from vignettes as this looks bad when it's old (but still
correct)
- add missing entries to DESCRIPTION

Caveat: some of the links (e.g. r-universe.dev, stargazers) won't work
until we fully open source. Similar to the badges that are already
there.

PS. You can see README rendered here:
https://github.com/insightsengineering/chevron/tree/readme#readme

If you have any comments and/or ideas please shout!
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@pawelru
pawelru authored Dec 4, 2023
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6 changes: 3 additions & 3 deletions .github/CONTRIBUTING.md
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Expand Up @@ -130,7 +130,7 @@ The package maintainer also reserves the right to adjust the criteria to recogni
If you have further questions regarding the contribution guidelines, please contact the package/repository maintainer.

<!-- urls -->
[docs]: https://insightsengineering.github.io/chevron/index.html
[articles]: https://insightsengineering.github.io/chevron/main/articles/index.html
[license]: https://insightsengineering.github.io/chevron/main/LICENSE-text.html
[docs]: https://insightsengineering.github.io/chevron/latest-tag/index.html
[articles]: https://insightsengineering.github.io/chevron/latest-tag/articles/index.html
[license]: https://insightsengineering.github.io/chevron/latest-tag/LICENSE-text.html
[insights]: https://github.com/insightsengineering/chevron/pulse
3 changes: 3 additions & 0 deletions DESCRIPTION
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Expand Up @@ -17,6 +17,9 @@ Authors@R: c(
Description: Standard Table, Listings, and Graphs (TLG) library used in
clinical trials.
License: Apache License 2.0 | file LICENSE
URL: https://insightsengineering.github.io/chevron/,
https://github.com/insightsengineering/chevron/
BugReports: https://github.com/insightsengineering/chevron/issues
Depends:
R (>= 4.0.0)
Imports:
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151 changes: 108 additions & 43 deletions README.md
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<!-- markdownlint-disable MD033 -->

# Chevron: Standard TLGs for clinical trials reporting <a href='https://github.com/insightsengineering/chevron'><img src="man/figures/chevron.png" align="right" height="139" style="max-width: 100%;"/></a>
# `chevron`: Standard TLGs for clinical trials reporting <a href='https://insightsengineering.github.io/chevron/'><img src="man/figures/chevron.png" align="right" height="139" style="max-width: 100%; max-height: 139px;"/></a>

<!-- start badges -->
[![Check 🛠](https://github.com/insightsengineering/chevron/actions/workflows/check.yaml/badge.svg)](https://insightsengineering.github.io/chevron/main/unit-test-report/)
Expand All @@ -21,18 +19,64 @@
[![Open Issues](https://img.shields.io/github/issues-raw/insightsengineering/chevron?color=red\&label=open%20issues)](https://github.com/insightsengineering/chevron/issues?q=is%3Aissue+is%3Aopen+sort%3Aupdated-desc)
<!-- end badges -->

<!-- markdownlint-enable MD033 -->
`chevron` is a collection of high-level functions to create standard outputs for clinical trials reporting with limited parameterisation. These outputs includes:

<!-- markdownlint-disable MD007 MD030 -->

- [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)

<!-- markdownlint-enable MD007 MD030 -->

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).

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

It is recommended that you [create and use a GitHub PAT](https://docs.github.com/en/github/authenticating-to-github/keeping-your-account-and-data-secure/creating-a-personal-access-token) to install the latest version of this package. Once you have the PAT, run the following:
```r
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.

```r
Sys.setenv(GITHUB_PAT = "your_access_token_here")
if (!require("remotes")) install.packages("remotes")
remotes::install_github("insightsengineering/chevron@*release")
install.packages("chevron", repos = c("https://pharmaverse.r-universe.dev", getOption("repos")))

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

## Usage
Expand All @@ -48,39 +92,60 @@ which returns

```text
MedDRA System Organ Class A: Drug X B: Placebo C: Combination
MedDRA Preferred Term (N=134) (N=134) (N=132)
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%)
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

[![Stargazers over time](https://starchart.cc/insightsengineering/chevron.svg)](https://starchart.cc/insightsengineering/chevron)

### Stargazers

[![Stargazers repo roster for chevron](https://reporoster.com/stars/insightsengineering/chevron)](https://github.com/insightsengineering/chevron/stargazers)

[![Forkers repo roster for chevron](https://reporoster.com/forks/insightsengineering/chevron)](https://github.com/insightsengineering/chevron/network/members)
8 changes: 5 additions & 3 deletions _pkgdown.yaml
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---
url: https://go.roche.com/nest-docs/releases/latest/api-reference/chevron
url: https://insightsengineering.github.io/chevron

template:
package: nesttemplate

navbar:
structure:
left: [intro, reference, articles, tutorials, news, reports]
left: [intro, reference, articles, catalog, tutorials, news, reports]
right: [search, github]
components:
catalog:
text: Catalog
href: articles/chevron_catalog.html
reports:
text: Reports
menu:
Expand All @@ -24,7 +27,6 @@ articles:
- title: All vignettes
contents:
- chevron
- adding_new_tlgs_to_chevron
- script_generator
- chevron_catalog

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2 changes: 1 addition & 1 deletion inst/WORDLIST
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Expand Up @@ -3,6 +3,7 @@ Agresti
CTC
Clopper
Coull
Forkers
Haenszel
Hauck
Hoffmann
Expand All @@ -22,7 +23,6 @@ postprocessing
pre
preprocess
repo
reproducibility
responder
responders
unstratified
9 changes: 9 additions & 0 deletions man/chevron-package.Rd
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