Science Score: 59.0%
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Found 2 DOI reference(s) in README -
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2 of 2 committers (100.0%) from academic institutions -
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○Scientific vocabulary similarity
Low similarity (17.8%) to scientific vocabulary
Keywords
Repository
shadia: dam passage performance standard models for R
Basic Info
- Host: GitHub
- Owner: danStich
- License: gpl-3.0
- Language: R
- Default Branch: master
- Homepage: https://shadia-ui.github.io/index.html
- Size: 46.3 MB
Statistics
- Stars: 7
- Watchers: 1
- Forks: 1
- Open Issues: 1
- Releases: 2
Topics
Metadata Files
README.md
shadia
Package containing functions and data for American shad population modeling (click here for project website).
Note
This is the development version of the shadia package for R (shadia v2.0). This package is under continual development at this time, as it is part of ongoing research and management. For that reason, it is important to correspond with package developers before using the dam passage performance standard models in decision making or research.
Frozen (stable) versions of the software are provided for consistency during dam relisencing studies and reproducibility of research through the shadia website. The site now also provides up-to-date information about the status of all models.
Please check regularly for updates, changes, and bug patches. Please submit issues directly to this repository using the links above.
Installation
The development version of shadia can be installed with devtools in R using the repository url:
devtools::install_github("danStich/shadia")
To install shadia, you will need to have devtools installed ahead of time in R, but that requires some special tools. To install on Windows, you will need to download and install the appropriate version of Rtools. To install on Mac, you will need to have the XCode command-line tools installed. And, if running from Linux, you will need to install the developer version of R (r-base-dev) if you have not already.
Use
The purpose of this package is to distribute code used to run dam passage performance standard models for anadromous alosines (shad and herring). Currently, the model is implemented for the Connecticut, Kennebec, Merrimack, Mohawk and Hudson, Penobscot, Saco, and Susquehanna rivers, USA, but we are actively adding new rivers.
The main package functions can be run without any arguments to estimate population abundance in various reaches or in whole rivers under 'no dam' passage scenarios (see examples). Alternatively, the user can pass one or more values for upstream and downstream fish passage at a given dam which can then be applied throughout the watershed, or separately at each dam. Outputs include population abundance of spawners in the watersheds, within specific production units of each river, and the proportion of repeat spawners in each age class.
The models take several (10-30) seconds to run for one iteration on most standard workstations.
Warning
Management decisions should not be based on a single model run. The models rely on stochastic inputs for parameterization, as detailed in Stich et al. (2019). As such, any two model runs might result in substantially different predictions, even under the same passage scenario. We recommend at least 100 model runs per scenario to provide a minimal characterization of stochasticity, and a cursory understanding of variability in the response(s) of interest. In these cases, we strongly recommend running the model using the snowfall package as demonstrated in the help file for each model, which can be accessed by typing ?...RiverModel (where '...' is the name of each river in lowercase) in the console and pressing < Enter >.
Directories
data/ Contains built-in data sets for the package
man/ help files and documentation
R/ R functions in scripts
src/ C++ source files written with Rcpp
Owner
- Login: danStich
- Kind: user
- Location: Oneonta, NY
- Company: SUNY Oneonta
- Website: https://danstich.github.io/stich/
- Repositories: 31
- Profile: https://github.com/danStich
Associate professor, Biology. Research focuses on development and application of quantitative tools for informing natural resource sciences and management.
GitHub Events
Total
- Watch event: 1
- Push event: 2
Last Year
- Watch event: 1
- Push event: 2
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| danStich | d****h@o****u | 340 |
| Erin Gilligan | g****9@o****u | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 35
- Total pull requests: 15
- Average time to close issues: 5 months
- Average time to close pull requests: 4 minutes
- Total issue authors: 1
- Total pull request authors: 1
- Average comments per issue: 1.49
- Average comments per pull request: 0.07
- Merged pull requests: 15
- 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
- danStich (35)
Pull Request Authors
- danStich (15)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
- Total downloads: unknown
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Total dependent packages: 0
(may contain duplicates) -
Total dependent repositories: 0
(may contain duplicates) - Total versions: 4
proxy.golang.org: github.com/danStich/shadia
- Documentation: https://pkg.go.dev/github.com/danStich/shadia#section-documentation
- License: gpl-3.0
-
Latest release: v2.1.0+incompatible
published over 1 year ago
Rankings
proxy.golang.org: github.com/danstich/shadia
- Documentation: https://pkg.go.dev/github.com/danstich/shadia#section-documentation
- License: gpl-3.0
-
Latest release: v2.1.0+incompatible
published over 1 year ago
Rankings
Dependencies
- MASS * imports
- geosphere * imports
- lubridate * imports
- methods * imports
- plyr * imports
- tidyverse * imports
- zoo * imports
- rlecuyer * suggests
- snowfall * suggests