Science Score: 23.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
○codemeta.json file
-
○.zenodo.json file
-
✓DOI references
Found 3 DOI reference(s) in README -
○Academic publication links
-
✓Committers with academic emails
3 of 7 committers (42.9%) from academic institutions -
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (11.6%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: carlos-alberto-silva
- Language: R
- Default Branch: master
- Size: 200 MB
Statistics
- Stars: 119
- Watchers: 10
- Forks: 39
- Open Issues: 5
- Releases: 0
Metadata Files
README.md
Treetop: A Shiny-based Application for Extracting Forest Information from LiDAR data.
Authors: Carlos Alberto Silva, Andrew T. Hudak, Lee A. Vierling, Ruben Valbuena, Adrian Cardil, Midhun Mohan, Danilo Roberti Alves de Almeida, Eben N. Broadbent, Angelica M. Almeyda Zambrano, Ben Wilkinson, Ajay Sharma, Jason B. Drake, Paul B. Medley, Jason G. Vogel, Gabriel Atticciati Prata, Jeff Atkins, Caio Hamamura, Carine Klauberg.
The treetop application provides options for i) detecting individual trees from LiDAR-derived canopy height models (CHM), ii) extract crown-level attributes (e.g. location, crown height and area), iii) assessing forest uniformity and individual tree spatial distribution, iv) exporting extracted crown-level products, v) visualizing CHM and crown-level products in 2D and 3D.
Getting Started
Install R, Git and Rtools40
i) R (>= 4.0.0): https://www.r-project.org/
ii) Git: https://git-scm.com/
iii) Rtools40: https://cran.r-project.org/bin/windows/Rtools/
Treetop installation
```r
The CRAN version:
install.packages("treetop")
The development version:
install.packages("remotes")
library(remotes) install_github("https://github.com/carlos-alberto-silva/weblidar-treetop", dependencies = TRUE)
```
Loading and launching treetop application
```r library(treetop) launchApp(launch.browser = TRUE)
```
References
Chang, W., Cheng, J., Allaire, J. J., Xie, Y., & McPherson, J. (2021). shiny: Web Application Framework for R. https://cran.r-project.org/web/packages/shiny/index.html
Leite, R.V.; Silva, C.A.; Mohan, M.; Cardil, A.; Almeida, D.R.A.d.; Carvalho, S.d.P.C.e; Jaafar, W.S.W.M.; Guerra-Hernández, J.; Weiskittel, A.; Hudak, A.T.; Broadbent, E.N.; Prata, G.; Valbuena, R.; Leite, H.G.; Taquetti, M.F.; Soares, A.A.V.; Scolforo, H.F.; Amaral, C.H.d.; Dalla Corte, A.P.; Klauberg, C. (2020). Individual Tree Attribute Estimation and Uniformity Assessment in Fast-Growing Eucalyptus spp. Forest Plantations Using Lidar and Linear Mixed-Effects Models. Remote Sens. 12, 3599. doi:10.3390/rs12213599
R Core Team. (2021). R: A Language and Environment for Statistical Computing; R Core Team: Vienna, Austria. https://www.r-project.org/
Silva, C. A., Hudak, A. T., Vierling, L. A., Loudermilk, E. L., O’Brien, J. J., Hiers, J. K., Khosravipour, A. (2016). Imputation of Individual Longleaf Pine (Pinus palustris Mill.) Tree Attributes from Field and LiDAR Data. Canadian Journal of Remote Sensing, 42(5), 554–573. doi:10.1080/07038992.2016.1196582
Roussel, J.R., Auty, D., Coops, N. C., Tompalski, P., Goodbody, T. R. H., Sánchez Meador, A., Bourdon, J.F., De Boissieu, F., Achim, A. (2020). lidR : An R package for analysis of Airborne Laser Scanning (ALS) data. Remote Sensing of Environment, 251 (August), 112061. doi:10.1016/j.rse.2020.112061.
Acknowledgements
We gratefully acknowledge funding from the National Counsel of Technological and Scientific Development (CNPq) and Department of Defense Strategic Environmental Research and Development Program (SERDP), grant RC-2243, RC19-1064 and RC20-1346.
Reporting Issues
Please report any issue regarding the Treetop app to Dr. Carlos A. Silva (carlos_engflorestal@outlook.com)
Citing treetop application
Silva, C.A.; Hudak, A.T; Vierling, L.A.; Valbuena, R.; Cardil, A.; Mohan, M.; Almeida, D. A.; Broadbent,E.N.; Zambrano,A. M. A.; Wilkinson, B., Sharma,A., Drake,J. B.; Medley,P. B., Vogel, J. G.; Prata,G. A.; Atkins, J.; Hamamura,C.; Klauberg, C. 2021. TreeTop: A Shiny-based Application for Extracting Forest Information from LiDAR data for Ecologists and Conservationists. Methods in Ecology and Evolution (In prep).
Silva, C.A.; Hudak, A.T; Vierling, L.A.; Valbuena, R.; Cardil, A.; Mohan, M.; Almeida, D. A.; Broadbent,E.N.; Zambrano,A. M. A.; Wilkinson, B., Sharma,A., Drake,J. B.; Medley,P. B., Vogel, J. G.; Prata,G. A.; Atkins, J.; Hamamura,C.; Klauberg, C. Treetop: A Shiny-based Application for Extracting Forest Information from LiDAR data. Version 0.0.1, accessed on March. 13 2021, available at: https://CRAN.R-project.org/package=treetop
Example datasets:
The example datasets used for the case studies can be downloaded herein: https://drive.google.com/drive/folders/1AjzIMGbI2BPPjnyOI5mSVFsyqbCgwxkm?usp=sharing
Disclaimer
Treetop has been developed using the Shiny (Chang et al. 2021) package in R (R Core Team 2021). It comes with no guarantee, expressed or implied, and the authors hold no responsibility for its use or reliability of its outputs.
Owner
- Name: Carlos Alberto Silva
- Login: carlos-alberto-silva
- Kind: user
- Company: University of Florida
- Website: https://carlos-alberto-silva.github.io/silvalab/home.html
- Twitter: Web_LiDAR
- Repositories: 100
- Profile: https://github.com/carlos-alberto-silva
GitHub Events
Total
- Watch event: 5
- Pull request event: 2
- Fork event: 1
Last Year
- Watch event: 5
- Pull request event: 2
- Fork event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Carlos | c****l@o****m | 94 |
| Caio Hamamura | c****a@g****m | 12 |
| rubenvalpue | r****a@b****k | 7 |
| Silva | c****a@u****u | 3 |
| atkinsjeff | j****6@v****u | 3 |
| Duncan Murdoch | m****n@g****m | 1 |
| rubak | r****k@m****k | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: about 1 year ago
All Time
- Total issues: 7
- Total pull requests: 10
- Average time to close issues: 8 months
- Average time to close pull requests: 3 months
- Total issue authors: 6
- Total pull request authors: 5
- Average comments per issue: 1.14
- Average comments per pull request: 0.0
- Merged pull requests: 9
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: 23 days
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- atkinsjeff (2)
- Phome95 (1)
- AAmeen112 (1)
- Saadi4469 (1)
- rsbivand (1)
- tahirsaeed13 (1)
Pull Request Authors
- rubenvalpue (6)
- briandrye (2)
- rubak (1)
- atkinsjeff (1)
- dmurdoch (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
-
Total downloads:
- cran 300 last-month
-
Total dependent packages: 0
(may contain duplicates) -
Total dependent repositories: 0
(may contain duplicates) - Total versions: 7
- Total maintainers: 1
proxy.golang.org: github.com/carlos-alberto-silva/weblidar-treetop
- Documentation: https://pkg.go.dev/github.com/carlos-alberto-silva/weblidar-treetop#section-documentation
-
Latest release: v0.0.5
published over 4 years ago
Rankings
cran.r-project.org: treetop
A Shiny-Based Application for Extracting Forest Information from LiDAR Data
- Homepage: https://github.com/carlos-alberto-silva/weblidar-treetop
- Documentation: http://cran.r-project.org/web/packages/treetop/treetop.pdf
- License: GPL-3
- Status: removed
-
Latest release: 0.0.5
published over 3 years ago
Rankings
Maintainers (1)
Dependencies
- R >= 4.0 depends
- RColorBrewer * imports
- geometry * imports
- lidR * imports
- pryr * imports
- raster * imports
- rasterVis * imports
- rgdal * imports
- rgeos * imports
- rgl * imports
- sf * imports
- shiny * imports
- sp * imports
- spatstat.core * imports
- spatstat.geom * imports
- stars * imports
- rmarkdown * suggests