Data

Tools

Indexes

Applications

Experiments

Open Source Science

secsse

Several Examined and Concealed States-dependent Speciation and Extinction

https://github.com/rsetienne/secsse

Science Score: 59.0%

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 9 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    2 of 8 committers (25.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.9%) to scientific vocabulary

Keywords from Contributors

genome
Last synced: 6 months ago · JSON representation

Repository

Several Examined and Concealed States-dependent Speciation and Extinction

Basic Info
Statistics
  • Stars: 1
  • Watchers: 4
  • Forks: 2
  • Open Issues: 2
  • Releases: 2
Created about 7 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog License Zenodo

README.md

SecSSE: Several Examined and Concealed States-Dependent Speciation and Extinction

CRAN status DOI

| Branch | GitHub Actions logo | Codecov logo | |------------|------------------------------------------------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------| | master | R-CMD-check | codecov.io | | develop | R-CMD-check | codecov.io |

What is SecSSE?

SecSSE is an R package designed for multistate data sets under a concealed state and speciation (hisse) framework. In this sense, it is parallel to the 'MuSSE' functionality implemented in diversitree, but it accounts for finding possible spurious relationships between traits and diversification rates ("false positives", Rabosky & Goldberg 2015) by testing against a "hidden trait" (Beaulieu et al. 2013), which is responsible for more variation in diversification rates than the trait being investigated.

Installing secsse

The secsse package has a stable version on CRAN and a development version on GitHub.

From CRAN

From within R, do:

r install.packages("secsse")

From GitHub

Install secsse from this GitHub repository by running:

r install.packages("remotes") remotes::install_github("rsetienne/secsse")

Using secsse as a package dependency

From CRAN

To your DESCRIPTION file, add secsse as any normal package.

If your package directly uses secsse:

Imports: secsse

If your package uses secsse in its peripherals (e.g. vignettes and tests):

Suggests: secsse

From GitHub

Remotes: rsetienne/secsse

Cite

If you use secsse in your publications, please cite:

  • Herrera-Alsina, Leonel et al. "Detecting the Dependence of Diversification on Multiple Traits from Phylogenetic Trees and Trait Data." Systematic biology vol. 68,2 (2019): 317-328. https://doi.org/10.1093/sysbio/syy057

References

  • Beaulieu, Jeremy M et al. "Identifying hidden rate changes in the evolution of a binary morphological character: the evolution of plant habit in campanulid angiosperms." Systematic biology vol. 62,5 (2013): 725-37. https://doi.org/.1093/sysbio/syt034

  • Beaulieu, Jeremy M, and Brian C O'Meara. "Detecting Hidden Diversification Shifts in Models of Trait-Dependent Speciation and Extinction." Systematic biology vol. 65,4 (2016): 583-601. https://doi.org/10.1093/sysbio/syw022

  • Rabosky, Daniel L., and Emma E. Goldberg. "Model inadequacy and mistaken inferences of trait-dependent speciation." Systematic biology 64.2 (2015): 340-355. https://doi.org/10.1093/sysbio/syu131

Owner

  • Name: Rampal S. Etienne
  • Login: rsetienne
  • Kind: user
  • Location: Groningen, The Netherlands
  • Company: University of Groningen

GitHub Events

Total
  • Issues event: 2
  • Issue comment event: 8
  • Push event: 90
  • Pull request event: 7
  • Create event: 2
Last Year
  • Issues event: 2
  • Issue comment event: 8
  • Push event: 90
  • Pull request event: 7
  • Create event: 2

Committers

Last synced: 8 months ago

All Time
  • Total Commits: 563
  • Total Committers: 8
  • Avg Commits per committer: 70.375
  • Development Distribution Score (DDS): 0.558
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Thijs Janzen t****n@g****m 249
Neves-P p****s@r****l 151
rsetienne r****e@g****m 93
= = 30
Hanno Hildenbrandt h****t@r****l 16
rsetienne r****e@g****m 16
leonelhalsina l****a@g****m 7
Jeroen Ooms j****s@g****m 1
Committer Domains (Top 20 + Academic)
rug.nl: 2 gmail.om: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 5
  • Total pull requests: 32
  • Average time to close issues: over 1 year
  • Average time to close pull requests: 11 days
  • Total issue authors: 5
  • Total pull request authors: 5
  • Average comments per issue: 3.2
  • Average comments per pull request: 0.5
  • Merged pull requests: 25
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 9.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • XuWeiEvo (1)
  • rafmarcondes (1)
  • cecileane (1)
  • padpadpadpad (1)
  • elizeng (1)
Pull Request Authors
  • rsetienne (21)
  • thijsjanzen (10)
  • Neves-P (7)
  • richelbilderbeek (1)
  • jeroen (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 507 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 12
  • Total maintainers: 1
cran.r-project.org: secsse

Several Examined and Concealed States-Dependent Speciation and Extinction

  • Versions: 12
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 507 Last month
Rankings
Dependent packages count: 29.8%
Average: 34.4%
Dependent repos count: 35.5%
Downloads: 37.9%
Maintainers (1)
r.s.etienne@rug.nl
Last synced: 6 months ago

Dependencies

.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
DESCRIPTION cran
  • R >= 3.5.0 depends
  • DDD >= 4.0 imports
  • Rcpp * imports
  • RcppParallel * imports
  • ape * imports
  • geiger * imports
  • utils * imports
  • diversitree * suggests
  • knitr * suggests
  • phytools * suggests
  • rmarkdown * suggests
  • testit * suggests
  • testthat * suggests
.github/workflows/cpp_lint.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v2 composite
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.4.1 composite
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/test-coverage.yaml actions
  • actions/checkout v3 composite
  • actions/upload-artifact v3 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite