Science Score: 46.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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✓DOI references
Found 3 DOI reference(s) in README -
✓Academic publication links
Links to: wiley.com -
✓Committers with academic emails
5 of 19 committers (26.3%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (9.8%) to scientific vocabulary
Last synced: 7 months ago
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JSON representation
Repository
Basic Info
- Host: GitHub
- Owner: lamho86
- License: gpl-2.0
- Language: R
- Default Branch: master
- Size: 518 KB
Statistics
- Stars: 37
- Watchers: 6
- Forks: 13
- Open Issues: 11
- Releases: 0
Created almost 11 years ago
· Last pushed over 1 year ago
Metadata Files
Readme
License
README.md
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phylolm: R package for Phylogenetic Linear Regression on very large trees
The package provides functions for fitting phylogenetic linear models and phylogenetic generalized linear models. Computations use an algorithm that is linear in the number of tips in the tree. The package also provides functions for simulating continuous or binary traits along the tree. When a new version is stable, it is pushed to CRAN, so the version available here is newer than that on CRAN.
Lam Si Tung Ho and Cécile Ané (2014). Intrinsic inference difficulties for trait evolution with Ornstein-Uhlenbeck models. Methods in Ecology and Evolution 5(11):1133-1146. (link)
Lam Si Tung Ho and Cécile Ané (2014). A linear-time algorithm for Gaussian and non-Gaussian trait evolution models. Systematic Biology 63(3):397-408. (link to pdf)
Installation
Install phylolm from github:
{r}
devtools::install_github("lamho86/phylolm")
Main features
- phylogenetic signal
- phylogenetic linear, logistic and Poisson regression
- stepwise model selection (from v2.3)
- OU shift detection
- continuous and discrete trait simulators with covariates
- bootstrap-based confidence intervals for phylogenetic logistic regression (from v2.3) and phylogenetic regression (from v2.4.2)
- goodness-of-fit test of a population tree with the coalescent (from v.2.4)
- allowing measurement errors in phylogenetic linear regression (from v2.4.1)
- log likelihood of an one-dimensional Ornstein-Uhlenbeck model (from v2.5)
- bootstrapping can be parallelized (from v2.6)
- R-squared and Adjusted R-squared (from v2.6.1)
- phyloglmstep (from v2.6.2)
- mace (from v2.6.4)
- REML for phylolm (from v2.6.4)
- Compatible with visreg (from v2.6.5)
- predict.phyloglm (from v2.6.7)
Owner
- Name: Lam Ho
- Login: lamho86
- Kind: user
- Location: Canada
- Company: Dalhousie University
- Website: https://sites.google.com/site/lamho86/
- Repositories: 3
- Profile: https://github.com/lamho86
GitHub Events
Total
- Issues event: 11
- Watch event: 5
- Issue comment event: 14
- Push event: 8
- Pull request review event: 3
- Pull request event: 9
- Fork event: 1
Last Year
- Issues event: 11
- Watch event: 5
- Issue comment event: 14
- Push event: 8
- Pull request review event: 3
- Pull request event: 9
- Fork event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Lam Ho | l****6@g****m | 40 |
| Lam Ho | l****o@L****l | 12 |
| Lam Ho | l****o@L****l | 11 |
| Cecile Ane | c****e@w****u | 6 |
| Lam Ho | l****o@L****e | 6 |
| Joan Maspons | j****s@c****t | 5 |
| Paul Bastide | p****e@g****m | 4 |
| Ax3man | w****l@z****e | 3 |
| Cecile Ane | a****e@s****u | 3 |
| Lam Ho | l****o@L****e | 3 |
| Lam Ho | l****o@T****a | 2 |
| Andrea Manica | a****5@c****k | 2 |
| Qing Yu | q****7@w****u | 2 |
| Cecile Ane | c****e | 2 |
| Rutger Vos | r****o@g****m | 2 |
| jboyko | j****1@g****m | 1 |
| Paul Bastide | p****e@m****g | 1 |
| Henrik Bengtsson | hb@a****g | 1 |
| Wouter van der Bijl | w****r@z****a | 1 |
Committer Domains (Top 20 + Academic)
wisc.edu: 2
zoology.ubc.ca: 1
aroma-project.org: 1
m4x.org: 1
cam.ac.uk: 1
tb83b.wpa.dal.ca: 1
lams-mbp-2.hitronhub.home: 1
stat.wisc.edu: 1
zoologi.su.se: 1
creaf.uab.cat: 1
lams-mbp.hitronhub.home: 1
Issues and Pull Requests
Last synced: 8 months ago
All Time
- Total issues: 53
- Total pull requests: 30
- Average time to close issues: 7 months
- Average time to close pull requests: 2 days
- Total issue authors: 37
- Total pull request authors: 11
- Average comments per issue: 3.58
- Average comments per pull request: 1.0
- Merged pull requests: 29
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 6
- Pull requests: 5
- Average time to close issues: about 1 month
- Average time to close pull requests: about 20 hours
- Issue authors: 4
- Pull request authors: 1
- Average comments per issue: 2.5
- Average comments per pull request: 0.0
- Merged pull requests: 5
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- MarcRieraDominguez (4)
- AMBarbosa (4)
- rosbakh (4)
- paternogbc (3)
- Ax3man (2)
- matthieu-haudiquet (2)
- yuxin0406 (2)
- rvosa (2)
- NB-Bio (2)
- jmaspons (1)
- courtiol (1)
- wrshoemaker (1)
- GrRomas (1)
- estherdr (1)
- pbradz (1)
Pull Request Authors
- AMBarbosa (9)
- cecileane (8)
- Ax3man (4)
- pbastide (4)
- jmaspons (2)
- jboyko (2)
- yuqing19118 (1)
- HenrikBengtsson (1)
- rvosa (1)
- dramanica (1)
- lamho86 (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
-
Total downloads:
- cran 6,117 last-month
- Total docker downloads: 43,788
-
Total dependent packages: 12
(may contain duplicates) -
Total dependent repositories: 16
(may contain duplicates) - Total versions: 11
- Total maintainers: 1
cran.r-project.org: phylolm
Phylogenetic Linear Regression
- Homepage: https://github.com/lamho86/phylolm
- Documentation: http://cran.r-project.org/web/packages/phylolm/phylolm.pdf
- License: GPL-2 | GPL-3 | file LICENSE [expanded from: GPL (≥ 2) | file LICENSE]
-
Latest release: 2.6.5
published over 1 year ago
Rankings
Dependent packages count: 5.0%
Forks count: 6.9%
Dependent repos count: 7.1%
Downloads: 7.4%
Stargazers count: 10.2%
Average: 10.4%
Docker downloads count: 25.6%
Maintainers (1)
Last synced:
8 months ago
conda-forge.org: r-phylolm
- Homepage: https://github.com/lamho86/phylolm
- License: GPL-2.0-or-later
-
Latest release: 2.6.2
published over 5 years ago
Rankings
Dependent packages count: 28.8%
Dependent repos count: 34.0%
Average: 36.8%
Forks count: 40.0%
Stargazers count: 44.2%
Last synced:
7 months ago
Dependencies
DESCRIPTION
cran
- R >= 3.0 depends
- ape * depends
- future.apply * imports
- testthat * suggests