Science Score: 49.0%
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○CITATION.cff file
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✓DOI references
Found 12 DOI reference(s) in README -
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1 of 3 committers (33.3%) from academic institutions -
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○Scientific vocabulary similarity
Low similarity (13.6%) to scientific vocabulary
Repository
R Package growthrates
Basic Info
- Host: GitHub
- Owner: tpetzoldt
- License: gpl-2.0
- Language: R
- Default Branch: master
- Homepage: http://tpetzoldt.github.io/growthrates/
- Size: 25.2 MB
Statistics
- Stars: 27
- Watchers: 5
- Forks: 7
- Open Issues: 1
- Releases: 0
Metadata Files
README.md
R package growthrates
Estimate Growth Rates from Experimental Data
The population growth rate is the main indicator of population fitness. This R package provides a collection of methods to determine growth rates from experimental data, in particular from batch experiments and microwell plate reader trials.
Overview
The package contains basically three methods:
fit a linear regression to a subset of data with the steepest log-linear increase (a method, similar to Hall et al., 2014),
fit parametric nonlinear models to the complete data set, where the model functions can be given either in closed form or as numerically solved (system of) differential equation(s),
use maximum of the 1st derivative of a smoothing spline with log-transformed y-values (similar to Kahm et al., 2010).
The package can fit data sets of single experiments or complete series containing multiple data sets. Included are functions for extracting estimates and for plotting. The package supports growth models given as numerically solved differential equations. Multi-core computation is used to speed up fitting of parametric models.
Documentation
Download and Installation
Release version (recommended)
The package is available on CRAN. Install it from within R or RStudio as usual or with:
R
install.packages("growthrates")
Development version
Install with package devtools:
R
install.packages("devtools")
library(devtools)
install_github("tpetzoldt/growthrates")
References
Hall, B. G., H. Acar, A. Nandipati, and M. Barlow. 2014. Growth Rates Made Easy. Mol. Biol. Evol. 31: 232-38. https://dx.doi.org/10.1093/molbev/mst187
Kahm, Matthias, Guido Hasenbrink, Hella Lichtenberg-Frate, Jost Ludwig, and Maik Kschischo. 2010. grofit: Fitting Biological Growth Curves with R. Journal of Statistical Software 33 (7): 1-21. https://dx.doi.org/10.18637/jss.v033.i07
R Core Team. 2015. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing. https://www.R-project.org/
Soetaert, Karline, and Thomas Petzoldt. 2010. Inverse Modelling, Sensitivity and Monte Carlo Analysis in R Using Package FME. Journal of Statistical Software 33 (3): 1-28. https://dx.doi.org/10.18637/jss.v033.i03
Soetaert, Karline, Thomas Petzoldt, and R. Woodrow Setzer. 2010. Solving Differential Equations in R: Package deSolve. Journal of Statistical Software 33 (9): 1-25. https://dx.doi.org/10.18637/jss.v033.i09
Author
Owner
- Name: Thomas Petzoldt
- Login: tpetzoldt
- Kind: user
- Location: Dresden 51.02718 13.74699
- Company: TU Dresden
- Website: http://tu-dresden.de/Members/thomas.petzoldt
- Repositories: 7
- Profile: https://github.com/tpetzoldt
limnology and ecological modelling, member of scientific staff
GitHub Events
Total
- Watch event: 1
- Push event: 7
- Create event: 1
Last Year
- Watch event: 1
- Push event: 7
- Create event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| thpe | t****t@t****e | 226 |
| michbur | m****z@g****m | 2 |
| jo | j****h | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 4
- Total pull requests: 2
- Average time to close issues: 3 months
- Average time to close pull requests: 12 minutes
- Total issue authors: 4
- Total pull request authors: 2
- Average comments per issue: 2.0
- Average comments per pull request: 1.0
- Merged pull requests: 2
- 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
- bznes (1)
- brmagalis (1)
- mretier (1)
- Pereiraehs (1)
Pull Request Authors
- michbur (1)
- jotech (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- cran 529 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 9
- Total maintainers: 1
cran.r-project.org: growthrates
Estimate Growth Rates from Experimental Data
- Homepage: https://github.com/tpetzoldt/growthrates
- Documentation: http://cran.r-project.org/web/packages/growthrates/growthrates.pdf
- License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
-
Latest release: 0.8.5
published 10 months ago
Rankings
Maintainers (1)
Dependencies
- R >= 3.2 depends
- deSolve * depends
- lattice * depends
- FME * imports
- graphics * imports
- methods * imports
- parallel * imports
- stats * imports
- utils * imports
- knitr * suggests
- rmarkdown * suggests