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c212

c212: An R Package for the Detection of Safety Signals in Clinical Trials Using Body-Systems (System Organ Classes) - Published in JOSS (2020)

https://github.com/rcarragh/c212

Science Score: 93.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in JOSS metadata
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software
Last synced: 10 months ago · JSON representation

Repository

Methods for detecting safety signals in clinical trials using groupings of adverse events by body-system or system organ class.

Basic Info
  • Host: GitHub
  • Owner: rcarragh
  • License: gpl-3.0
  • Language: R
  • Default Branch: master
  • Size: 621 KB
Statistics
  • Stars: 0
  • Watchers: 0
  • Forks: 3
  • Open Issues: 0
  • Releases: 5
Created about 7 years ago · Last pushed over 1 year ago
Metadata Files
Readme Contributing License Code of conduct

README.Rmd 

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# c212: Methods for Detecting Safety Signals in Clinical Trials Using Body-Systems (System Organ Classes) 




The goal of c212 is to provide a self-contained set of methods, which use groupings of adverse events, to aid clinical trial safety investigators, statisticians and researchers, in the early detection of adverse events.

## Installation

You can install the released version of c212 from [CRAN](https://CRAN.R-project.org) with:

``` r
install.packages("c212")
```

And the development version from [GitHub](https://github.com/) with:

``` r
# install.packages("devtools")
devtools::install_github("rcarragh/c212")
```

## Example

This is a basic example which shows how to apply the Double False Discovery Rate to a set of multiple hypotheses:

```{r example1}
library(c212)
data(c212.FDR.data)
c212.err.cntrl(c212.FDR.data, method="DFDR", alpha = 0.05)
```

This is an example of how to apply the Berry and Berry model:

```{r example2}
library(c212)
data(c212.trial.data)
mod.BB <- c212.BB(c212.trial.data, burnin = 100, iter = 200)
```

Owner

  • Login: rcarragh
  • Kind: user

JOSS Publication

c212: An R Package for the Detection of Safety Signals in Clinical Trials Using Body-Systems (System Organ Classes)
Published
December 04, 2020
DOI
Volume 5, Issue 56, Page 2706
Authors
Raymond Carragher ORCID
Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK, Department of Mathematics and Statistics, University of Strathclyde, Glasgow, UK, Health Data Research (UK), University of Strathclyde, Glasgow, UK
Chris Robertson
Department of Mathematics and Statistics, University of Strathclyde, Glasgow, UK, Health Protection Scotland, NHS National Services Scotland, Glasgow, UK
Editor
Charlotte Soneson ORCID
Tags
Adverse event Safety Pharmacovigilance Clinical trials False Discovery Rate Body-systems System organ classes Bayesian hierarchy Multiple comparisons.
View PDF Review Thread Software Archive

GitHub Events

Total
  • Release event: 2
  • Push event: 2
  • Fork event: 1
  • Create event: 2
Last Year
  • Release event: 2
  • Push event: 2
  • Fork event: 1
  • Create event: 2

Committers

Last synced: 11 months ago

All Time
  • Total Commits: 36
  • Total Committers: 3
  • Avg Commits per committer: 12.0
  • Development Distribution Score (DDS): 0.139
Past Year
  • Commits: 2
  • Committers: 1
  • Avg Commits per committer: 2.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Raymond Carragher r****h@g****m 31
Raoul r****w 4
Charlotte Soneson c****n@g****m 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 8
  • Total pull requests: 2
  • Average time to close issues: 12 days
  • Average time to close pull requests: about 20 hours
  • Total issue authors: 2
  • Total pull request authors: 2
  • Average comments per issue: 2.88
  • Average comments per pull request: 1.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • rrrlw (5)
  • rcarragh (3)
Pull Request Authors
  • csoneson (1)
  • rrrlw (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 666 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 7
  • Total maintainers: 1
cran.r-project.org: c212

Methods for Detecting Safety Signals in Clinical Trials Using Body-Systems (System Organ Classes)

  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 666 Last month
Rankings
Dependent repos count: 23.9%
Dependent packages count: 28.7%
Average: 30.9%
Downloads: 40.1%
Maintainers (1)
rcarragh@gmail.com
Last synced: 10 months ago

Dependencies

DESCRIPTION cran
  • coda >= 0.19 depends