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branchingprocess

https://github.com/epiforesite/branchingprocess

Science Score: 39.0%

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

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    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
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    DOI references
    Found 4 DOI reference(s) in README
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    Low similarity (11.2%) to scientific vocabulary
Last synced: 9 months ago · JSON representation

Repository

Basic Info
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  • Stars: 0
  • Watchers: 4
  • Forks: 1
  • Open Issues: 1
  • Releases: 1
Created almost 2 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog License

README.Rmd 

---
output: github_document
---

# branchingprocess


[![CRAN status](https://www.r-pkg.org/badges/version/branchingprocess)](https://CRAN.R-project.org/package=branchingprocess)
 [![CRANlogs downloads](https://cranlogs.r-pkg.org/badges/branchingprocess)](https://cran.r-project.org/package=branchingprocess)
[![ForeSITE Group](https://github.com/EpiForeSITE/software/raw/e82ed88f75e0fe5c0a1a3b38c2b94509f122019c/docs/assets/foresite-software-badge.svg)](https://github.com/EpiForeSITE)
[![R-CMD-check](https://github.com/EpiForeSITE/branchingprocess/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/EpiForeSITE/branchingprocess/actions/workflows/R-CMD-check.yaml)
[![pkgdown](https://github.com/EpiForeSITE/branchingprocess/actions/workflows/pkgdown.yaml/badge.svg)](https://github.com/EpiForeSITE/branchingprocess/actions/workflows/pkgdown.yaml)


## Calculate Outbreak Probabilities for a Branching Process Model

The goal of `branchingprocess` is to quantify outbreak risk posed by individual 
importers of a transmissible pathogen. Input parameters of negative binomial
offspring distributions for the number of transmissions from each infected 
individual and initial number of infected. Calculate probabilities of final 
outbreak size and generations of transmission.  A full description and
derivation of the mathematical results implemented in these functions can be
found in the following manuscripts:

- Toth D, Gundlapalli A, Khader K, Pettey W, Rubin M, Adler F, Samore M (2015). Estimates of outbreak risk from new introductions of Ebola with immediate and delayed transmission control. Emerg Infect Dis, 21(8), 1402-1408. .

- Toth D, Tanner W, Khader K, Gundlapalli A (2016). Estimates of the risk of large or long-lasting outbreaks of Middle East respiratory syndrome after importations outside the Arabian Peninsula. Epidemics, 16, 27-32. 

Work to create this software tool was made possible by cooperative agreement CDC-RFA-FT-23-0069 from the CDC’s Center for Forecasting and Outbreak Analytics.

## Installation

You can install the development version of `branchingprocess` from GitHub with:

```r
devtools::install_github("EpiForeSITE/branchingprocess")
```
You can install branchingprocess from CRAN with:

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

Owner

  • Name: ForeSITE
  • Login: EpiForeSITE
  • Kind: organization
  • Email: Eric.Lofgren@wsu.edu

A collection of epidemic modeling and forecasting tools for ForeSITE, part of the CDC-funded InsightNet

GitHub Events

Total
  • Release event: 1
  • Delete event: 1
  • Push event: 15
  • Pull request event: 1
  • Create event: 1
Last Year
  • Release event: 1
  • Delete event: 1
  • Push event: 15
  • Pull request event: 1
  • Create event: 1

Packages

  • Total packages: 1
  • Total downloads:
    • cran 443 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 1
  • Total maintainers: 1
cran.r-project.org: branchingprocess

Calculate Outbreak Probabilities for a Branching Process Model

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 443 Last month
Rankings
Dependent packages count: 26.7%
Dependent repos count: 32.9%
Average: 48.8%
Downloads: 86.7%
Maintainers (1)
damon.toth@hsc.utah.edu
Last synced: 10 months ago

Dependencies

.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v4 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
DESCRIPTION cran
  • stats * imports