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genieR

genieR: An R package for inference of demographic history of phylogenies - Published in JOSS (2019)

https://github.com/xiangfstats/genier

Science Score: 93.0%

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    CITATION.cff file
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    Found 1 DOI reference(s) in JOSS metadata
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    Published in Journal of Open Source Software
Last synced: 6 months ago · JSON representation

Repository

Inference of demographic history from phylogeny

Basic Info
  • Host: GitHub
  • Owner: xiangfstats
  • License: mit
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 677 KB
Statistics
  • Stars: 1
  • Watchers: 2
  • Forks: 3
  • Open Issues: 7
  • Releases: 2
Created over 9 years ago · Last pushed almost 7 years ago
Metadata Files
Readme License

README.Rmd 

---
output: github_document
---



```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)
```
# genieR: an R package for the genealogy interval explorer
genieR  is a package for the inference of demographic history from
reconstructed molecular phylogenies. It covers a few functions designed in GENIE, Pybus and Rambaut (2002). 

# Installing the package
To install the devel version of the package, type:
```{r install, eval=FALSE}
devtools::install_github("xiangfstats/genieR")
```

Note that this requires the package *devtools* installed and a Rtools installation is necessary to build this package for the benefit of Windows users.

### Contributors (by alphabetic order):
Simon D. W. Frost (@sdwfrost)
Fei Xiang (@xiangfstats)
Maintainer : Fei Xiang (xf3087@gmail.com)

### References
Pybus O. G. , Rambaut A. (2002) GENIE: Estimating demographic history from molecular phylogenies. Bioinformatics 18:1404-5.

Owner

  • Name: Fei Xiang
  • Login: xiangfstats
  • Kind: user

JOSS Publication

genieR: An R package for inference of demographic history of phylogenies
Published
January 05, 2019
DOI
Volume 4, Issue 33, Page 634
Authors
Fei Xiang ORCID
Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
Bethany Dearlove ORCID
US Military HIV Research Program, Rockville, MD, United States
Simon Frost ORCID
Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
Editor
George Githinji
Tags
demographic history phylogeny coalescent models
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GitHub Events

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Last synced: 7 months ago

All Time
  • Total Commits: 150
  • Total Committers: 2
  • Avg Commits per committer: 75.0
  • Development Distribution Score (DDS): 0.027
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Fei Xiang x****7@g****m 146
Simon Frost s****t@g****m 4

Issues and Pull Requests

Last synced: 6 months ago

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  • Total issues: 7
  • Total pull requests: 0
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  • Total issue authors: 1
  • Total pull request authors: 0
  • Average comments per issue: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • 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
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  • pboesu (7)
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Dependencies

DESCRIPTION cran
  • R >= 3.3.0 depends
  • Rcpp * imports
  • dfoptim * imports
  • minqa * imports
  • ape * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests