Data

Tools

Indexes

Applications

Experiments

Open Source Science

apex

Phylogenetic Methods for Multiple Gene Data

https://github.com/thibautjombart/apex

Science Score: 46.0%

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
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    3 of 6 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (5.3%) to scientific vocabulary
Last synced: 7 months ago · JSON representation

Repository

Phylogenetic Methods for Multiple Gene Data

Basic Info
  • Host: GitHub
  • Owner: thibautjombart
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 3.46 MB
Statistics
  • Stars: 5
  • Watchers: 8
  • Forks: 3
  • Open Issues: 4
  • Releases: 2
Created about 11 years ago · Last pushed 9 months ago
Metadata Files
Readme Changelog

README.Rmd 

[![R-CMD-check](https://github.com/thibautjombart/apex/workflows/R-CMD-check/badge.svg)](https://github.com/thibautjombart/apex/actions)
[![DOI](https://zenodo.org/badge/11430/thibautjombart/apex.svg)](http://dx.doi.org/10.5281/zenodo.16822)



```{r compileVignette, results="hide",echo=FALSE,message=FALSE}
## recompile vignette
setwd("vignettes")
library(knitr)
knitr::knit("apex.Rmd", output = "apex.md")
setwd("../")
```

```{r include, results="asis", echo=FALSE, warning=FALSE}
## read md of the vignette
mdInput <- readLines("vignettes/apex.md")

## remove vignette-specific headers
toRemove <- 1:10
mdInput <- mdInput[-toRemove]

## restore right path for figures
mdInput <- gsub("figs/","vignettes/figs/",mdInput)
cat(paste(mdInput,collapse="\n"), file = "README.md")
```

Owner

  • Name: Thibaut Jombart
  • Login: thibautjombart
  • Kind: user
  • Location: France
  • Company: Data.Org / Imperial College London

Software Design Lead for Epiverse at Data.org. Senior Lecturer in outbreak analytics Imperial College London. R geek. Muay Thai enthusiast. Grindcore vocalist.

GitHub Events

Total
Last Year

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 202
  • Total Committers: 6
  • Avg Commits per committer: 33.667
  • Development Distribution Score (DDS): 0.257
Past Year
  • Commits: 3
  • Committers: 1
  • Avg Commits per committer: 3.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Thibaut Jombart t****t@g****m 150
Klaus Schliep k****p@g****m 29
Eric Archer e****r@n****v 11
Zhian Kamvar k****z@s****u 9
RBHarris r****s@u****u 2
Yihui Xie x****e@y****e 1
Committer Domains (Top 20 + Academic)
yihui.name: 1 uw.edu: 1 science.oregonstate.edu: 1 noaa.gov: 1

Issues and Pull Requests

Last synced: 8 months ago

All Time
  • Total issues: 64
  • Total pull requests: 19
  • Average time to close issues: 27 days
  • Average time to close pull requests: 2 months
  • Total issue authors: 7
  • Total pull request authors: 4
  • Average comments per issue: 2.7
  • Average comments per pull request: 2.0
  • Merged pull requests: 15
  • 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
  • thibautjombart (29)
  • EricArcher (4)
  • KlausVigo (2)
  • zkamvar (2)
  • mprous1 (1)
  • gustavo-miranda (1)
  • Wesleyhattingh (1)
Pull Request Authors
  • zkamvar (5)
  • EricArcher (3)
  • KlausVigo (2)
  • yihui (1)
Top Labels
Issue Labels
enhancement (16) Priority (6) documentation (5) bug (3) Warnings / NOTES (2) question (1) help wanted (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 1,386 last-month
  • Total docker downloads: 21,206
  • Total dependent packages: 0
  • Total dependent repositories: 4
  • Total versions: 7
  • Total maintainers: 1
cran.r-project.org: apex

Phylogenetic Methods for Multiple Gene Data

  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 4
  • Downloads: 1,386 Last month
  • Docker Downloads: 21,206
Rankings
Forks count: 14.5%
Dependent repos count: 15.0%
Average: 20.7%
Stargazers count: 22.1%
Downloads: 23.0%
Dependent packages count: 28.7%
Maintainers (1)
klaus.schliep@gmail.com
Last synced: 7 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.1.3 depends
  • ape * depends
  • methods * depends
  • phangorn * depends
  • adegenet * imports
  • graphics * imports
  • stats * imports
  • utils * imports
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact main composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite