TrenchR
Facilitates microclimate modeling to translate weather station data into the environmental conditions experienced by organisms and biophysical modeling to predict organismal body temperatures given the environmental conditions.
https://github.com/trenchproject/trenchr
Category: Biosphere
Sub Category: Ecological and Environmental Modeling
Keywords from Contributors
thermal-ecology biophysics bookdown ecology-modelling educational-resources
Last synced: about 18 hours ago
JSON representation
Repository metadata
an R package for transparent environmental and ecological biophysics
- Host: GitHub
- URL: https://github.com/trenchproject/trenchr
- Owner: trenchproject
- License: other
- Created: 2017-01-04T23:09:28.000Z (over 8 years ago)
- Default Branch: main
- Last Pushed: 2023-09-29T20:08:23.000Z (over 1 year ago)
- Last Synced: 2025-04-10T06:39:01.108Z (18 days ago)
- Language: R
- Homepage: https://trenchproject.github.io/TrenchR/
- Size: 51.7 MB
- Stars: 13
- Watchers: 5
- Forks: 7
- Open Issues: 2
- Releases: 3
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
README.md
TrenchR: an R package for transparent environmental and ecological biophysics
Author: TrEnCh project, Buckley Lab, Department of Biology, University of Washington
Description
The TrenchR package aids in Translating Environmental Change into organismal responses. The package facilitates microclimate modeling to translate weather station data into the environmental conditions experienced by organisms and biophysical modeling to predict organismal body temperatures given the environmental conditions. The package aims to introduce and enable microclimate and biophysical modeling to improve ecological and evolutionary forecasting and includes tutorials and well as a series of educational modules introducing microclimate and biophysical modeling. The package focuses on transparent and modular functions but also includes some biophysical models for particular organisms. The package complements and integrates with the NicheMapR package, which contains more complex functions that are generally not intended for modular use.
Installation
You can install the TrenchR package from CRAN:
install.packages("TrenchR")
The latest version of the package can be installed from the github repository:
install.packages("devtools")
devtools::install_github("trenchproject/TrenchR")
Using the package
The package encompasses simple functions that can be combined to estimate environmental conditions and their impacts on organisms.
Many of the functions are adapted from biophysical ecology texts including the following:
- Gates DM. 1980. Biophysical Ecology.
- Campbell GS and Norman JM. 2000. An introduction to environmental biophysics.
Package Vignettes
We introduce functions in categorically grouped tutorials. A good place to start is the Allometry and conversions tutorial, which provides tools for preparing data such as estimating additional dimensions of organisms from measured dimensions.
vignette("AllometryAndConversionsTutorial.Rmd", package = "TrenchR")
The Estimating microclimates tutorial provides resources for estimating the environmental conditions experienced by organisms. This includes estimating solar radiation and its components, diurnal variation in temperature and radiation, temperature and wind speed profiles, and soil temperatures and profiles.
vignette("MicroclimateTutorial", package = "TrenchR")
Finally, the core biophysical modeling functions are described in a tutorial on Using energy balances to estimate body temperatures. Components of an energy budget can be estimated using individual functions and then operative environmental temperatures, Te, can be solved for using either a generic energy balance or taxa specific biophysical models.
vignette("TeTutorial", package = "TrenchR")
Future Directions
We welcome code contributions, fixes, and comments. Code (scripts and functions) will be accepted in any programming language and thorough commenting will be appreciated. We would also appreciate your including a header that describes the intent, input, and output of your scripts and functions.
Citation
If you use this package, We would appreciate a citation. You can see an up to date citation information with citation("TrenchR"). You can cite either the package or the accompanying journal article.
Developer notes
Please see the Contributor Notes and Code of Conduct.
We use Rdpack to facilitate package documentation with BibTeX citations. See the documentation workflow document for more details about building package manual components.
Owner metadata
- Name: TRanslating ENvironmental CHange
- Login: trenchproject
- Email:
- Kind: organization
- Description: We build computational and visualization tools to translate environmental change into organismal responses.
- Website: https://trenchproject.com
- Location: Biology Department, University of Washington, Seattle, WA
- Twitter:
- Company:
- Icon url: https://avatars.githubusercontent.com/u/22244755?v=4
- Repositories: 25
- Last ynced at: 2023-08-05T12:20:51.686Z
- Profile URL: https://github.com/trenchproject
GitHub Events
Total
- Watch event: 1
- Fork event: 1
Last Year
- Watch event: 1
- Fork event: 1
Committers metadata
Last synced: 8 days ago
Total Commits: 657
Total Committers: 12
Avg Commits per committer: 54.75
Development Distribution Score (DDS): 0.728
Commits in past year: 17
Committers in past year: 2
Avg Commits per committer in past year: 8.5
Development Distribution Score (DDS) in past year: 0.059
| Name | Commits | |
|---|---|---|
| L Buckley | l****y@g****m | 179 |
| juniperlsimonis | d****s@g****m | 158 |
| Aji John | a****n@g****m | 126 |
| Lauren Buckley | l****y@g****m | 58 |
| Yutaro Sakairi | y****i@g****m | 49 |
| Isaac Caruso | 4****1 | 38 |
| Lauren Buckley | l****y@D****u | 21 |
| Abby Meyer | a****r@A****l | 17 |
| Bryan Briones Ortiz | b****4@u****u | 6 |
| Ofir Levy | l****i@g****m | 2 |
| Eric Riddell | 3****y | 2 |
| Lauren Buckley | l****y@L****l | 1 |
Committer domains:
Issue and Pull Request metadata
Last synced: 2 days ago
Total issues: 39
Total pull requests: 63
Average time to close issues: 4 months
Average time to close pull requests: about 6 hours
Total issue authors: 7
Total pull request authors: 4
Average comments per issue: 1.77
Average comments per pull request: 0.49
Merged pull request: 61
Bot issues: 0
Bot pull requests: 0
Past year issues: 0
Past year pull requests: 0
Past year average time to close issues: N/A
Past year average time to close pull requests: N/A
Past year issue authors: 0
Past year pull request authors: 0
Past year average comments per issue: 0
Past year average comments per pull request: 0
Past year merged pull request: 0
Past year bot issues: 0
Past year bot pull requests: 0
Top Issue Authors
- juniperlsimonis (25)
- icaruso21 (5)
- lbuckley (4)
- henningte (2)
- ys634 (1)
- aeiche01 (1)
- mladencucak (1)
Top Pull Request Authors
- juniperlsimonis (49)
- icaruso21 (11)
- ecophysiology (2)
- lbuckley (1)
Top Issue Labels
Top Pull Request Labels
Package metadata
- Total packages: 1
-
Total downloads:
- cran: 178 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 3
- Total maintainers: 1
cran.r-project.org: TrenchR
Tools for Microclimate and Biophysical Ecology
- Homepage: https://trenchproject.github.io/TrenchR/
- Documentation: http://cran.r-project.org/web/packages/TrenchR/TrenchR.pdf
- Licenses: MIT + file LICENSE
- Latest release: 1.1.1 (published over 1 year ago)
- Last Synced: 2025-04-26T14:35:13.668Z (2 days ago)
- Versions: 3
- Dependent Packages: 0
- Dependent Repositories: 1
- Downloads: 178 Last month
-
Rankings:
- Forks count: 9.635%
- Stargazers count: 17.386%
- Dependent repos count: 23.981%
- Average: 26.403%
- Dependent packages count: 28.751%
- Downloads: 52.262%
- Maintainers (1)
Dependencies
- actions/checkout v2 composite
- r-lib/actions/setup-pandoc v1 composite
- r-lib/actions/setup-r v1 composite
- r-lib/actions/setup-r-dependencies v1 composite
- actions/checkout v2 composite
- r-lib/actions/check-r-package v2 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
- r-lib/actions/setup-r-dependencies v2 composite
- actions/cache v2 composite
- actions/checkout v2 composite
- r-lib/actions/setup-pandoc v1 composite
- r-lib/actions/setup-r v1 composite
- R >= 3.3.1 depends
- Rdpack >= 0.7 imports
- deSolve * imports
- msm * imports
- stats * imports
- zoo * imports
- covr * suggests
- knitr * suggests
- rmarkdown * suggests
- testthat * suggests
Score: 10.38591370178042