eDNAjoint: R package for interpreting paired environmental DNA and traditional surveys

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Submitting Author Name: Abigail Keller Submitting Author Github Handle: @abigailkeller Repository: https://github.com/abigailkeller/eDNAjoint Version submitted: 0.1 Submission type: Stats Badge grade: silver Editor: @emitanaka Reviewers: @chitrams, @smwindecker

Due date for @chitrams: 2024-07-02

Due date for @smwindecker: 2024-07-02 Archive: TBD Version accepted: TBD Language: en

• Paste the full DESCRIPTION file inside a code block below:

Package: eDNAjoint
Title: Joint Modeling of Traditional and Environmental DNA Survey Data
Version: 0.1
Maintainer: Abigail G. Keller <[email protected]>
Author: Abigail G. Keller
Authors@R: 
    c(person("Abigail G.", "Keller", role = c("aut", "cre"), email="[email protected]"),
    person("Ryan P.", "Kelly", role = "ctb", email="[email protected]"))
Description: Models integrate environmental DNA (eDNA) detection data and traditional survey data to jointly estimate species catch rate (see package vignette: https://bookdown.org/abigailkeller/eDNAjoint_vignette/). Models can be used with count data via traditional survey methods (i.e., trapping, electrofishing, visual) and replicated eDNA detection/nondetection data via polymerase chain reaction (i.e., PCR or qPCR) from multiple survey locations. Estimated parameters include probability of a false positive eDNA detection, a site-level covariates that scale the sensitivity of eDNA surveys relative to traditional surveys, and catchability coefficients for traditional gear types. Models are implemented with a Bayesian framework (Markov chain Monte Carlo) using the 'Stan' probabilistic programming language.
License: GPL-3
URL: https://github.com/abigailkeller/eDNAjoint
BugReports: https://github.com/abigailkeller/eDNAjoint/issues
Encoding: UTF-8
Roxygen: list(markdown = TRUE, roclets = c ("namespace", "rd", "srr::srr_stats_roclet"))
RoxygenNote: 7.3.1
Biarch: true
Depends: 
    R (>= 3.4.0)
Imports: 
    bayestestR,
    dplyr,
    ggplot2,
    loo,
    magrittr,
    methods,
    Rcpp (>= 0.12.0),
    RcppParallel (>= 5.0.1), 
    rlist,
    rstan (>= 2.26.23),
    rstantools (>= 2.3.1.1),
    tidyr
LinkingTo: 
    BH (>= 1.66.0),
    Rcpp (>= 0.12.0),
    RcppEigen (>= 0.3.3.3.0),
    RcppParallel (>= 5.0.1),
    rstan (>= 2.26.23),
    StanHeaders (>= 2.26.22)
SystemRequirements: GNU make
LazyData: true
Suggests: 
    bayesplot,
    knitr,
    rmarkdown,
    testthat (>= 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3

Scope

• Please indicate which of our statistical package categories this package falls under. (Please check one appropriate box below):

  Statistical Packages

  • [x] Bayesian and Monte Carlo Routines
  • [ ] Dimensionality Reduction, Clustering, and Unsupervised Learning
  • [ ] Machine Learning
  • [ ] Regression and Supervised Learning
  • [ ] Exploratory Data Analysis (EDA) and Summary Statistics
  • [ ] Spatial Analyses
  • [ ] Time Series Analyses
  • [x] Probability Distributions

Pre-submission Inquiry

• [x] A pre-submission inquiry has been approved in issue 628

General Information

• Who is the target audience and what are scientific applications of this package?

The package eDNAjoint is useful for interpreting observations from paired environmental DNA (eDNA) and traditional surveys. The package runs a Bayesian model that integrates these two data streams to jointly estimate parameters like the false positive probability of eDNA detection and expected catch rate at a site. The package allows users to access pre-compiled models written in Stan. The target audience is environmental science researchers or managers who want to interpret environmental DNA data but do not have experience writing and implementing custom Bayesian models.

• Paste your responses to our General Standard G1.1 here, describing whether your software is:

This is the first implementation of a model/algorithm developed in Keller et al. 2022.

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Silver

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Compliance with a good number of standards beyond those identified as minimally necessary.

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• [x] I have read the author guide and I expect to maintain this package for at least 2 years or have another maintainer identified.
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