Package: eDNAjoint 0.3
Abigail G. Keller
eDNAjoint: Joint Modeling of Traditional and Environmental DNA Survey Data in a Bayesian Framework
Models integrate environmental DNA (eDNA) detection data and traditional survey data to jointly estimate species catch rate (see package vignette: <https://ednajoint.netlify.app/>). 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.
Authors:
eDNAjoint_0.3.tar.gz
eDNAjoint_0.3.zip(r-4.5)eDNAjoint_0.3.zip(r-4.4)eDNAjoint_0.3.zip(r-4.3)
eDNAjoint_0.3.tgz(r-4.4-x86_64)eDNAjoint_0.3.tgz(r-4.4-arm64)eDNAjoint_0.3.tgz(r-4.3-x86_64)eDNAjoint_0.3.tgz(r-4.3-arm64)
eDNAjoint_0.3.tar.gz(r-4.5-noble)eDNAjoint_0.3.tar.gz(r-4.4-noble)
eDNAjoint.pdf |eDNAjoint.html✨
eDNAjoint/json (API)
NEWS
| # Install 'eDNAjoint' in R: |
| install.packages('eDNAjoint', repos = c('https://ropensci.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ropensci/ednajoint/issues
Pkgdown site:https://docs.ropensci.org
- goby_data - Goby_data
- green_crab_data - Green_crab_data
Last updated 2 hours agofrom:0d64443826 (on master). Checks:1 OK, 8 NOTE. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Jan 18 2025 |
| R-4.5-win-x86_64 | NOTE | Jan 18 2025 |
| R-4.5-linux-x86_64 | NOTE | Jan 18 2025 |
| R-4.4-win-x86_64 | NOTE | Jan 18 2025 |
| R-4.4-mac-x86_64 | NOTE | Jan 18 2025 |
| R-4.4-mac-aarch64 | NOTE | Jan 18 2025 |
| R-4.3-win-x86_64 | NOTE | Jan 18 2025 |
| R-4.3-mac-x86_64 | NOTE | Jan 18 2025 |
| R-4.3-mac-aarch64 | NOTE | Jan 18 2025 |
Exports:detection_calculatedetection_plotjoint_modeljoint_selectjoint_summarizemu_criticaltraditional_model
Dependencies:abindbackportsbayestestRBHcallrcheckmateclicolorspacecpp11data.tabledatawizarddescdistributionaldplyrfansifarvergenericsggplot2gluegridExtragtableinlineinsightisobandjsonlitelabelinglatticelifecycleloomagrittrMASSMatrixmatrixStatsmgcvmunsellnlmenumDerivpillarpkgbuildpkgconfigposteriorprocessxpspurrrQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelrlangrlistrstanrstantoolsscalesStanHeadersstringistringrtensorAtibbletidyrtidyselectutf8vctrsviridisLitewithrXMLyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| The 'eDNAjoint' package. | eDNAjoint-package eDNAjoint |
| Calculate the survey effort necessary to detect species presence, given the species expected catch rate. | detection_calculate |
| Plot the survey effort necessary to detect species presence, given the species expected catch rate. | detection_plot |
| goby_data | goby_data |
| green_crab_data | green_crab_data |
| Specify and fit joint model using count data from traditional surveys and eDNA PCR data | joint_model |
| Perform model selection using leave one out cross validation of model objects | joint_select |
| Summarize posterior distributions of model parameters. | joint_summarize |
| Calculate mu_critical | mu_critical |
| Specify and fit model using count data from traditional, non eDNA surveys | traditional_model |
