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btspas

Bayesian Time Stratified Petersen Analysis System

https://github.com/cschwarz-stat-sfu-ca/btspas

Science Score: 26.0%

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    CITATION.cff file
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    codemeta.json file
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    .zenodo.json file
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    DOI references
    Found 4 DOI reference(s) in README
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    Scientific vocabulary similarity
    Low similarity (8.8%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Bayesian Time Stratified Petersen Analysis System

Basic Info
  • Host: GitHub
  • Owner: cschwarz-stat-sfu-ca
  • Language: HTML
  • Default Branch: master
  • Size: 37.7 MB
Statistics
  • Stars: 1
  • Watchers: 4
  • Forks: 3
  • Open Issues: 6
  • Releases: 0
Created over 7 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog

README.md

BTSPAS

Bayesian Time Stratified Petersen Analysis System

Versions and installation

  • Github To install the latest development version from Github, install the newest version of the devtools package; then run devtools::install_github("cschwarz-stat-sfu-ca/BTSPAS", dependencies = TRUE, build_vignettes = TRUE)

Features

Provides advanced Bayesian methods to estimate abundance and run-timing from temporally-stratified Petersen mark-recapture experiments as described in Bonner and Schwarz(2011). Methods include hierarchical modelling of the capture probabilities and spline smoothing of the daily run size. This version uses JAGS to sample from the posterior distribution.

This is a more specific application of a stratified Petersen (Darroch, 1961; Plante et al 1988; Schwarz and Taylor, 1998) where, for example, fish are tagged a a fish wheel over a series of weeks, migrate, and then are recaptured. The stratification is temporal rather than geographical. This temporal stratification enable estimation of the run profile and various other parameters of interest such as abundance.

References

Bonner Simon, J., & Schwarz Carl, J. (2011). Smoothing Population Size Estimates for Time-Stratified MarkRecapture Experiments Using Bayesian P-Splines. Biometrics, 67, 1498–1507. https://doi.org/10.1111/j.1541-0420.2011.01599.x

Darroch, J. N. (1961). The two-sample capture-recapture census when tagging and sampling are stratified. Biometrika, 48, 241–260. https://www.jstor.org/stable/2332748

Plante, N., L.-P Rivest, and G. Tremblay. (1988). Stratified Capture-Recapture Estimation of the Size of a Closed Population. Biometrics 54, 47-60. https://www.jstor.org/stable/2533994

Schwarz, C. J., & Dempson, J. B. (1994). Mark-recapture estimation of a salmon smolt population. Biometrics, 50, 98–108.

Schwarz, C. J., & Taylor, C. G. (1998). The use of the stratified-Petersen estimator in fisheries management with an illustration of estimating the number of pink salmon (Oncorhynchus gorbuscha) that return to spawn in the Fraser River. Canadian Journal of Fisheries and Aquatic Sciences, 55, 281–296. https://doi.org/10.1139/f97-238

Owner

  • Name: Carl Schwarz
  • Login: cschwarz-stat-sfu-ca
  • Kind: user
  • Location: Port Moody, BC
  • Company: StatMathComp Consulting by Schwarz (retired from Simon Fraser University)

GitHub Events

Total
  • Push event: 3
Last Year
  • Push event: 3

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 81
  • Total Committers: 5
  • Avg Commits per committer: 16.2
  • Development Distribution Score (DDS): 0.222
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
cschwarz-stat-sfu-ca c****z@s****a 63
cschwarz-stat-sfu-ca c****a@g****m 12
Carl Schwarz c****z@C****l 4
Carl Schwarz c****z@C****n 1
Erik Suring 5****g 1
Committer Domains (Top 20 + Academic)
carls-mbp.lan: 1 stat.sfu.ca: 1

Issues and Pull Requests

Last synced: almost 2 years ago

All Time
  • Total issues: 31
  • Total pull requests: 1
  • Average time to close issues: 3 months
  • Average time to close pull requests: about 1 month
  • Total issue authors: 3
  • Total pull request authors: 1
  • Average comments per issue: 1.77
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: 1 minute
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 2.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • cschwarz-stat-sfu-ca (28)
  • kalebentley (2)
  • ErikSuring (1)
Pull Request Authors
  • ErikSuring (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 785 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 19
  • Total maintainers: 1
cran.r-project.org: BTSPAS

Bayesian Time-Stratified Population Analysis

  • Versions: 19
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 785 Last month
Rankings
Forks count: 14.2%
Downloads: 23.6%
Dependent repos count: 23.9%
Average: 24.2%
Dependent packages count: 28.7%
Stargazers count: 30.8%
Maintainers (1)
cschwarz.stat.sfu.ca@gmail.com
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • R2jags * imports
  • actuar * imports
  • coda * imports
  • data.table * imports
  • ggforce * imports
  • ggplot2 * imports
  • grDevices * imports
  • graphics * imports
  • gridExtra * imports
  • plyr * imports
  • reshape2 * imports
  • scales * imports
  • splines * imports
  • stats * imports
  • utils * imports
  • R.rsp * suggests