admiralvaccine

Vaccines extension package for ADaM in R Asset Library (admiral)

https://github.com/pharmaverse/admiralvaccine

Science Score: 26.0%

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Scientific vocabulary similarity
Low similarity (18.1%) to scientific vocabulary

Keywords

cdisc r rstats

Last synced: 6 months ago · JSON representation

Repository

Vaccines extension package for ADaM in R Asset Library (admiral)

Basic Info

Host: GitHub
Owner: pharmaverse
License: apache-2.0
Language: R
Default Branch: main
Homepage: https://pharmaverse.github.io/admiralvaccine
Size: 11.8 MB

Statistics

Stars: 6
Watchers: 4
Forks: 8
Open Issues: 7
Releases: 4

Topics

cdisc r rstats

Created over 3 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog License Codeowners

README.Rmd

---
title: "Admiral Extension for Vaccines"
output: md_document
date: '2022-06-27'
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
link <- function(text, url) {
  return(
    paste0(
      "[", text, "]",
      "(", url, ")"
    )
  )
}
dyn_link <- function(text,
                     base_url,
                     relative_url = "",
                     # Change to TRUE when admiral adopts multiversion docs
                     is_multiversion = TRUE,
                     multiversion_default_ref = "main") {
  url <- paste(base_url, relative_url, sep = "/")
  if (is_multiversion) {
    url <- paste(
      base_url,
      Sys.getenv("BRANCH_NAME", multiversion_default_ref),
      sep = "/"
    )
  }
  return(link(text, url))
}

# Other variables
admiral_homepage <- "https://pharmaverse.github.io/admiral/"
```



# Admiral Extension for Vaccines 


[](https://pharmaverse.org/)
[![CRAN status](https://www.r-pkg.org/badges/version/admiralvaccine)](https://CRAN.R-project.org/package=admiralvaccine/)
[![Test Coverage](https://raw.githubusercontent.com/pharmaverse/admiralvaccine/badges/main/test-coverage.svg)](https://github.com/pharmaverse/admiralvaccine/actions/workflows/code-coverage.yml/)


Vaccine extension package for ADaM in R Asset Library `{admiral}`

## Purpose

To provide a complementary (to `{admiral}`) toolbox that enables users to develop vaccine specific domains.

## Installation

The package is available from CRAN and can be installed by running 
`install.packages("admiralvaccine")`.

To install the latest development version of the package directly from GitHub use the following code:

```r
if (!requireNamespace("remotes", quietly = TRUE)) {
  install.packages("remotes")
}

remotes::install_github("pharmaverse/admiraldev", ref = "devel") # This is a required dependency of {admiralvaccine}
remotes::install_github("pharmaverse/admiral", ref = "devel") # This is a required dependency of {admiralvaccine}
remotes::install_github("pharmaverse/admiralvaccine", ref = "devel")
```

### Dependencies

The latest version of the package works with the latest versions of the packages
stated in `DESCRIPTION`.

If a previous version of the package should be used, it is recommended to use
latest version of the dependencies at the point of time when the previous
version of {admiralvaccine} was released.

## Scope

* Build a toolbox of re-usable functions and utilities to create vaccine-specific ADaM datasets in R in a modular manner.
* All functions are created based upon the ADaM Implementation Guide and aim to facilitate the programming of ADaM dataset standards.
* Initially the package will focus on creating the reactogenicity and immunogenicity domain following flat model as per Center for Biologics Evaluation and Research (CBER) guidelines.In future we will make enhancements as we get updates on Center for Biologics Evaluation and Research (CBER).

## Expectations

`{admiralvaccine}` is expected to complement `{admiral}` and provide functions to help with the creation of the efficacy endpoints required for vaccine ADaMs.

## References and Documentation

* Please refer to the [{admiral} References and Documentation](https://pharmaverse.github.io/admiral/)

## R Versions

Here's a summary of our strategy for this package related to R versions:

* R versions for developers and users will follow the same as `{admiral}` core package.
* For development the `devel` branch of `{admiral}` core is used as a dependency. For releasing a new `{admiralvaccine}` version it must run using the latest released `{admiral}` core version, i.e., `main` branch of `{admiral}` core.

## Contact

We use the following for support and communications between user and developer community:

* [Slack](https://pharmaverse.slack.com/) - for informal discussions, Q&A and building our user community. If you don't have access, use this [link](https://join.slack.com/t/pharmaverse/shared_invite/zt-yv5atkr4-Np2ytJ6W_QKz_4Olo7Jo9A/) to join the pharmaverse Slack workspace
* [GitHub Issues](https://github.com/pharmaverse/admiralvaccine/issues/) - for direct feedback, enhancement requests or raising bugs

## {admiralvaccine} R Package Collaboration: Pfizer, GSK and J&J

- Project Lead & Contributor: Neetu Sangari

- Maintainer: Sukalpo Saha

- Developers: Vikram S, Arjun Rubalingam, Dhivya Kanagaraj, Federico Baratin, Yamini Purna Bollu, Ilse Augustyns, Kalyani Bodicherla

- Support lead & Reviewer: Ben Straub

- Other Reviewers: Stefan Bundfuss, Edoardo Mancini

- Other Contributors: Ross Farrugia, Abdul Khayat, Jayashree V, Jagadish Katam, Ankur Jindal, Andrea Pammolli, Daniele Bottigliengo, Ranya Ben Hsain, Lee Armishaw, Hilde Delanghe, Marleen Nijs, Mandy Peng, Tina Zhai

Owner

Name: pharmaverse
Login: pharmaverse
Kind: organization
Location: Switzerland

Repositories: 25
Profile: https://github.com/pharmaverse

GitHub Events

Total

Create event: 5
Release event: 1
Issues event: 8
Delete event: 4
Issue comment event: 13
Push event: 47
Pull request review event: 13
Pull request review comment event: 10
Pull request event: 6

Last Year

Create event: 5
Release event: 1
Issues event: 8
Delete event: 4
Issue comment event: 13
Push event: 47
Pull request review event: 13
Pull request review comment event: 10
Pull request event: 6

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 69
Total pull requests: 63
Average time to close issues: 4 months
Average time to close pull requests: 12 days
Total issue authors: 16
Total pull request authors: 12
Average comments per issue: 0.48
Average comments per pull request: 1.9
Merged pull requests: 33
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 6
Pull requests: 6
Average time to close issues: about 2 months
Average time to close pull requests: 23 days
Issue authors: 4
Pull request authors: 4
Average comments per issue: 1.0
Average comments per pull request: 0.67
Merged pull requests: 2
Bot issues: 0
Bot pull requests: 0

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Top Authors

Issue Authors

bms63 (23)
federicobaratin (7)
arjoon-r (7)
vikrams95 (6)
manciniedoardo (5)
YaminiBollu (4)
rossfarrugia (3)
vizdhivi (3)
iaugu (3)
ap765541 (2)
ahasoplakus (1)
Fanny-Gautier (1)
lorenzwalthert (1)
jwang-lilly (1)
jsrivj (1)

Pull Request Authors

arjoon-r (16)
federicobaratin (14)
bms63 (9)
ahasoplakus (5)
vikrams95 (5)
manciniedoardo (3)
YaminiBollu (3)
arkadiuszbeer (2)
dgrassellyb (2)
larmisha22 (2)
rossfarrugia (1)
pharmaverse-bot (1)

Top Labels

Issue Labels

enhancement (24) documentation (20) good first issue (6) bug (2) question (1)

Pull Request Labels

enhancement (20) documentation (11) help wanted (7) final review (4)

Packages

Total packages: 1
Total downloads:
- cran 280 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 4
Total maintainers: 1

cran.r-project.org: admiralvaccine

Vaccine Extension Package for ADaM in 'R' Asset Library

Homepage: https://pharmaverse.github.io/admiralvaccine/
Documentation: http://cran.r-project.org/web/packages/admiralvaccine/admiralvaccine.pdf
License: Apache License (≥ 2)
Latest release: 0.4.0
published about 1 year ago

Versions: 4
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 280 Last month

Rankings

Forks count: 8.2%

Dependent packages count: 29.1%

Dependent repos count: 34.8%

Stargazers count: 35.2%

Average: 39.4%

Downloads: 89.6%

Maintainers (1)

sukalpo.saha@pfizer.com