spanner
Utilities to support landscape-, forest-, and tree-related data collection, manipulation, analysis, modelling, and visualization.
Science Score: 59.0%
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
Found .zenodo.json file -
✓DOI references
Found 11 DOI reference(s) in README -
✓Academic publication links
Links to: sciencedirect.com, springer.com, zenodo.org -
✓Committers with academic emails
1 of 3 committers (33.3%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.1%) to scientific vocabulary
Repository
Utilities to support landscape-, forest-, and tree-related data collection, manipulation, analysis, modelling, and visualization.
Basic Info
- Host: GitHub
- Owner: bi0m3trics
- License: gpl-3.0
- Language: C++
- Default Branch: master
- Size: 56.4 MB
Statistics
- Stars: 28
- Watchers: 5
- Forks: 8
- Open Issues: 0
- Releases: 2
Metadata Files
README.md
spanner 
Definition of spanner
1 (chiefly British): WRENCH
2: a wrench that has a hole, projection, or hook at one or both ends of the head for engaging with a corresponding device on the object that is to be turned
3: utilities to support landscape-, forest-, and tree-related data collection, manipulation, analysis, modelling, and visualization.
Install spanner
Get the latest released version of spanner from github.
r
remotes::install_github('bi0m3trics/spanner')
Workflows
Terrestial Lidar Tree Attributes and Segmentation
The following is the full processing pipeline described in Donager et al. (2021), and provides an example from downloading an example dataset, preprocesing it using lidR's functionality, estimating tree locations and DBH by rasterizing individual point cloud values of relative neighborhood density (at 0.3 and 1 m radius) and verticality within a slice of the normalized point cloud around breast height to
(1.37 m), to individual tree segmentation following ecological principles for “growing” trees based on input locations in a graph-theory approach. Relies heavily on work of Roussel et al (2020), Tao and others (2015), and de Conto et al. (2017).
Citation: Donager, Jonathon J., Andrew J. Sánchez Meador, and Ryan C. Blackburn 2021. Adjudicating Perspectives on Forest Structure: How Do Airborne, Terrestrial, and Mobile Lidar-Derived Estimates Compare? Remote Sensing 13, no. 12: 2297. https://doi.org/10.3390/rs13122297
PatchMorph: Patch Delineation Algorithm
The patchwoRk function implements a patch delineation algorithm [at present it only implements 'PatchMorph' (Girvetz & Greco 2007), which can delineate patches across a range of spatial scales based on three organism-specific thresholds - (1) land cover density threshold, (2) habitat gap maximum thickness (gap threshold), and (3) habitat patch minimum thickness (spur threshold)].
Citation: Girvetz EH, and Greco SE. 2007. How to define a patch: a spatial model for hierarchically delineating organism-specific habitat patches. Landscape Ecology 22: 1131-1142. http://dx.doi.org/10.1007/s10980-007-9104-8
Owner
- Name: Andrew Sánchez Meador
- Login: bi0m3trics
- Kind: user
- Location: Flagstaff, AZ
- Company: Ecological Restoration Inst. and School of Forestry, Northern Arizona Univ.
- Website: https://directory.nau.edu/person/ajm69
- Twitter: bi0m3trics
- Repositories: 12
- Profile: https://github.com/bi0m3trics
Exec. Director of Ecological Restoration Institute and Professor in the School of Forestry at Northern Arizona University in Flagstaff, AZ
GitHub Events
Total
- Watch event: 4
- Delete event: 1
- Push event: 15
- Pull request event: 2
- Gollum event: 5
- Fork event: 1
- Create event: 2
Last Year
- Watch event: 4
- Delete event: 1
- Push event: 15
- Pull request event: 2
- Gollum event: 5
- Fork event: 1
- Create event: 2
Committers
Last synced: 8 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Andrew Sánchez Meador | a****r@n****u | 100 |
| JDonager | j****r@g****m | 9 |
| Jeffery B Cannon | 3****n | 5 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 4
- Total pull requests: 5
- Average time to close issues: 20 days
- Average time to close pull requests: 3 days
- Total issue authors: 3
- Total pull request authors: 2
- Average comments per issue: 7.75
- Average comments per pull request: 0.0
- Merged pull requests: 4
- 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: 6 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
- cingularities (2)
- rdeinin (1)
- summitbri (1)
Pull Request Authors
- jbcannon (4)
- bi0m3trics (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- data.table * depends
- lidR * depends
- magrittr * depends
- FNN * imports
- RANN * imports
- Rcpp * imports
- Rfast * imports
- conicfit * imports
- cppRouting * imports
- data.table * imports
- dbscan * imports
- dplyr * imports
- igraph * imports
- lidR * imports
- lwgeom * imports
- mathjaxr * imports
- sf * imports
- sfheaders * imports
- stringr * imports
- terra * imports
- testthat >= 3.0.0 suggests