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 16 DOI reference(s) in README -
✓Academic publication links
Links to: biorxiv.org, wiley.com -
✓Committers with academic emails
2 of 7 committers (28.6%) from academic institutions -
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (14.0%) to scientific vocabulary
Keywords
Repository
Repository for the R nLTT package
Basic Info
- Host: GitHub
- Owner: thijsjanzen
- License: gpl-2.0
- Language: R
- Default Branch: master
- Size: 2.81 MB
Statistics
- Stars: 6
- Watchers: 1
- Forks: 4
- Open Issues: 2
- Releases: 7
Topics
Metadata Files
README.md
nLTT 
Branch|
|
---|---|---
master|
|
develop|
|
Repository for the R nLTT package
Installing this package
Make sure you have the package devtools installed.
Then, from within R do, for the stable version:
devtools::install_github("thijsjanzen/nLTT")
For the bleeding-edge version:
devtools::install_github("thijsjanzen/nLTT", ref = "develop")
What is the nLTT statistic?
The nLTT statistic is a likelihood free summary statistic to compare the similarity between two phylogenetic trees. It calculates the distance between the lineage through time curves of the two trees, after normalizing the lineage through time curves with respect to the maximum number of lineages obtained in each tree, and with respect to the total time between the root and the tips of the tree (see also the wiki).
A more detailed description, and a detailed analysis of the performance of the nLTT statistic can be found in the following paper:
Janzen, Thijs, Sebastian Höhna, and Rampal S. Etienne. "Approximate Bayesian computation of diversification rates from molecular phylogenies: introducing a new efficient summary statistic, the nLTT." Methods in Ecology and Evolution 6.5 (2015): 566-575. link
What else does the package do?
Apart from providing functions that calculate the nLTT statistic, the nLTT package for R also provides functions to: - plot the normalized Lineages-Through-Time plot for a single, or for multiple, trees - calculate and plot the average Lineages-Through-Time plot for multiple trees - estimate the parameters of a model for which the likelihood is known (for comparison), using MCMC (as used in the paper) - estimate the parameters of a model for which no likelihood is available, using ABC-SMC (as used in the paper)
Papers using the nLTT statistic
Shu Xie, Luis Valente, Rampal S. Etienne. A simple island biodiversity model is robust to trait dependence in diversification and colonization rates (2022) bioRxiv 2022.01.01.474685; doi: https://doi.org/10.1101/2022.01.01.474685
Francisco Richter, Thijs Janzen, Hanno Hildenbrandt, Ernst C. Wit, Rampal S. Etienne. Detecting phylodiversity-dependent diversification with a general phylogenetic inference framework (2021) bioRxiv 2021.07.01.450729; doi: https://doi.org/10.1101/2021.07.01.450729
Thijs Janzen, Folmer Bokma, Rampal S Etienne, Nucleotide Substitutions during Speciation may Explain Substitution Rate Variation, Systematic Biology (2021), syab085, https://doi.org/10.1093/sysbio/syab085
Pedro Santos Neves, Joshua W. Lambert, Luis Valente, Rampal S. Etienne. "The robustness of a simple dynamic model of island biodiversity to geological and eustatic change" bioRxiv (2021) 2021.07.26.453064; doi: https://doi.org/10.1101/2021.07.26.453064
Bilderbeek, RJC, Laudanno, G, Etienne, RS. Quantifying the impact of an inference model in Bayesian phylogenetics. Methods Ecol Evol. (2021); 12: 351– 358. https://doi.org/10.1111/2041-210X.13514
Hagen O, Flück B, Fopp F, Cabral JS, Hartig F, et al. (2021) gen3sis: A general engine for eco-evolutionary simulations of the processes that shape Earth’s biodiversity. PLOS Biology 19(7): e3001340. https://doi.org/10.1371/journal.pbio.3001340
Giardina F, Romero-Severson EO, Albert J, Britton T, Leitner T "Inference of Transmission Network Structure from HIV Phylogenetic Trees". PLOS Computational Biology (2017) 13(1): e1005316. link
Janzen, Thijs, and Rampal Etienne. "Inferring the role of habitat dynamics in driving diversification: evidence for a species pump in Lake Tanganyika cichlids." bioRxiv (2017): 085431. link
Ibeh, Neke, and Stephane Aris-Brosou. "Estimation of sub-epidemic dynamics by means of Sequential Monte Carlo Approximate Bayesian Computation: an application to the Swiss HIV Cohort Study." bioRxiv (2016): 085993. link
McCloskey, Rosemary M., Richard H. Liang, and Art FY Poon. "Reconstructing contact network parameters from viral phylogenies." Virus evolution 2.2 (2016): vew029. link
Janzen, Thijs, Sebastian Höhna, and Rampal S. Etienne. "Approximate Bayesian computation of diversification rates from molecular phylogenies: introducing a new efficient summary statistic, the nLTT." Methods in Ecology and Evolution (2015): 566-575. link
Acknowledgements
- @franciscorichter: bug reporting
I want to contribute!
See CONTRIBUTING.md
Code of Conduct
See codeofconduct.md
Owner
- Name: Thijs Janzen
- Login: thijsjanzen
- Kind: user
- Location: Netherlands
- Company: University of Groningen
- Website: www.thijsjanzen.nl
- Twitter: thijsjanzen
- Repositories: 51
- Profile: https://github.com/thijsjanzen
Scientific programmer at University of Groningen
GitHub Events
Total
- Release event: 1
- Push event: 2
- Create event: 1
Last Year
- Release event: 1
- Push event: 2
- Create event: 1
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| richelbilderbeek | r****l@r****l | 224 |
| Thijs Janzen | t****n@g****m | 71 |
| Thijs Janzen | j****n@e****e | 56 |
| Neves-P | p****s@r****l | 23 |
| Richel Bilderbeek | r****k | 2 |
| Simon J Greenhill | S****l | 1 |
| Maëlle Salmon | m****n@y****e | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 54
- Total pull requests: 6
- Average time to close issues: 2 months
- Average time to close pull requests: 5 days
- Total issue authors: 3
- Total pull request authors: 4
- Average comments per issue: 3.89
- Average comments per pull request: 3.0
- Merged pull requests: 6
- 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
Top Authors
Issue Authors
- richelbilderbeek (37)
- thijsjanzen (16)
- EvoLandEco (1)
Pull Request Authors
- Neves-P (3)
- thijsjanzen (1)
- maelle (1)
- SimonGreenhill (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- cran 678 last-month
- Total docker downloads: 21,789
- Total dependent packages: 5
- Total dependent repositories: 12
- Total versions: 14
- Total maintainers: 1
cran.r-project.org: nLTT
Calculate the NLTT Statistic
- Homepage: https://github.com/thijsjanzen/nLTT
- Documentation: http://cran.r-project.org/web/packages/nLTT/nLTT.pdf
- License: GPL-2
-
Latest release: 1.4.10
published 10 months ago
Rankings
Maintainers (1)
Dependencies
- ape * imports
- coda * imports
- testit * imports
- DAISIE * suggests
- DDD * suggests
- Hmisc * suggests
- TESS * suggests
- TreeSim * suggests
- ggplot2 * suggests
- knitr * suggests
- lintr * suggests
- microbenchmark * suggests
- plyr * suggests
- reshape2 * suggests
- rmarkdown * suggests
- testthat * suggests