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sporeg

Regularization of sporadic detection data with tests for associated bias and uncertainty

https://github.com/mebowers5/sporeg

Science Score: 67.0%

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Regularization of sporadic detection data with tests for associated bias and uncertainty

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  • Stars: 7
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  • Open Issues: 3
  • Releases: 1
Created over 2 years ago · Last pushed 12 months ago
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Readme License Citation

README.md

sporeg

DOI

The goal of sporeg is to reconstruct passive telemetry tracks using movement models and measure the accuracy of the reconstructions. This provides information on the reliability of ecological conclusions such as population distribution.

Installation

Sporeg requires R version >= 4.3.2. The latest version of sporeg can be installed from GitHub using the following:

To install sporeg, first install the remotes and pathroutr packages.

r install.packages("remotes") library(remotes) remotes::install_github('jmlondon/pathroutr') remotes::install_github('mebowers5/sporeg', build_vignettes = TRUE, dependencies = TRUE)

Step-by-step guide

The vignette(s) for this package can be accessed via GitHub pages (https://mebowers5.github.io/sporeg/articles/sporeg_workflow.html) or the following code:

r browseVignettes(package = "sporeg")

Have a suggestion? Found a bug?

For any suggestions or problems, please create a new issue on the sporeg GitHub page (https://github.com/mebowers5/sporeg/issues).

You don't have any experience documenting issues on GitHub? No problem! Start here: https://docs.github.com/en/issues/tracking-your-work-with-issues/quickstart.

Acknowledgements

The creation of this package was made possible by the helpful, supportive hosts and attendees of Ocean Tracking Network Study Hall, particularly Mike O'Brien, Ben Hlina, Jon Pye, and Sarah Popova. In addition, I thank Josh London for help with pathroutr code and encouragement. I also thank Brian J. Smith for introducing me to the world of movement modeling and for all his help and encouragement early on.

Owner

  • Name: Beth Bowers
  • Login: mebowers5
  • Kind: user

Citation (CITATION.cff) 

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "sporeg" in publications use:'
type: software
license: MIT
title: 'sporeg: A package to reconstruct sporadic passive tracking data and measure
  the bias and uncertainty incurred through the process'
version: 0.1.0
abstract: This package is the corresponding code for the Methods in Ecology and Evolution
  article, "A novel process to infer the reliability of ecological information derived
  from passive acoustic telemetry track reconstruction". The intended workflow is
  to simulate tracks inside a specified polygon, calculate quadrat counts inside grid
  cells, derive passive detection data from the simulated tracks using geolocations
  of listening stations, reconstruct the tracks using continuous-time correlated random
  walk models, re-route any spurious track intersections with a specified boundary,
  calculate quadrat counts of reconstructed tracks within grid cells, and compare
  quadrat counts between simulated and reconstructed tracks. This process is designed
  to be iterated to achieve statistical power. The user can then proceed with modeling
  the relationship between environmental variables and a desirable result (i.e., a
  good fit) to determine what environmental variables affect the odds of a good fit
  in grid cells.
authors:
- family-names: Bowers
  given-names: Mary E.
  email: mebowers5@gmail.com
  orcid: https://orcid.org/0000-0002-5823-186X
contact:
- family-names: Bowers
  given-names: Mary E.
  email: mebowers5@gmail.com
  orcid: https://orcid.org/0000-0002-5823-186X
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    orcid: https://orcid.org/0000-0003-0645-5666
  year: '2024'
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    given-names: Matt
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    given-names: Arun
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  - family-names: Gorecki
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  - family-names: Chirico
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    given-names: Hadley
    email: hadley@posit.co
    orcid: https://orcid.org/0000-0003-4757-117X
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    given-names: Romain
    orcid: https://orcid.org/0000-0002-2444-4226
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    given-names: Lionel
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    orcid: https://orcid.org/0000-0002-1416-3412
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  url: https://github.com/ocean-tracking-network/glatos
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  - family-names: Holbrook
    given-names: Christopher
    email: cholbrook@usgs.gov
  - family-names: Hayden
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    given-names: Josh
    email: josh.london@noaa.gov
    orcid: https://orcid.org/0000-0002-3647-5046
  year: '2024'
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  repository: https://CRAN.R-project.org/package=sf
  authors:
  - family-names: Pebesma
    given-names: Edzer
    email: edzer.pebesma@uni-muenster.de
    orcid: https://orcid.org/0000-0001-8049-7069
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  repository: https://CRAN.R-project.org/package=momentuHMM
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  repository: https://CRAN.R-project.org/package=purrr
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    given-names: Hadley
    email: hadley@rstudio.com
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  repository: https://CRAN.R-project.org/package=tidyr
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  - family-names: Mailund
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    email: mailund@birc.au.dk
  - family-names: Kalinowski
    given-names: Tomasz
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    given-names: Stefan Milton
    email: stefan@stefanbache.dk
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  institution:
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    address: Vienna, Austria
  year: '2024'
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  title: 'R: A Language and Environment for Statistical Computing'
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  url: https://www.R-project.org/
  authors:
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  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2024'
  version: '>= 3.5.0'

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