Package: eDNAjoint 0.3.3
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 gear scaling coefficients for traditional gear types. Models are implemented with a Bayesian framework (Markov chain Monte Carlo) using the 'Stan' probabilistic programming language.
Authors:
eDNAjoint_0.3.3.tar.gz
eDNAjoint_0.3.3.zip(r-4.7)eDNAjoint_0.3.3.zip(r-4.6)eDNAjoint_0.3.3.zip(r-4.5)
eDNAjoint_0.3.3.tgz(r-4.6-x86_64)eDNAjoint_0.3.3.tgz(r-4.6-arm64)eDNAjoint_0.3.3.tgz(r-4.5-x86_64)eDNAjoint_0.3.3.tgz(r-4.5-arm64)
eDNAjoint_0.3.3.tar.gz(r-4.7-arm64)eDNAjoint_0.3.3.tar.gz(r-4.7-x86_64)eDNAjoint_0.3.3.tar.gz(r-4.6-arm64)eDNAjoint_0.3.3.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
card.svg |card.png
eDNAjoint/json (API)
NEWS
| # Install 'eDNAjoint' in R: |
| install.packages('eDNAjoint', repos = c('https://packages.ropensci.org', 'https://cloud.r-project.org')) |
Reviews:rOpenSci Software Review #642
Bug tracker:https://github.com/ropensci/ednajoint/issues
Pkgdown/docs site:https://docs.ropensci.org
- goby_data - Goby_data
- green_crab_data - Green_crab_data
Last updated from:e86c3017c6 (on master). Checks:11 NOTE, 2 OK, 1 FAIL. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | NOTE | 422 | ||
| linux-devel-x86_64 | NOTE | 427 | ||
| pkgdown docs | OK | 1271 | ||
| source / vignettes | OK | 451 | ||
| linux-release-arm64 | NOTE | 427 | ||
| linux-release-x86_64 | NOTE | 434 | ||
| macos-release-arm64 | NOTE | 269 | ||
| macos-release-x86_64 | NOTE | 656 | ||
| macos-oldrel-arm64 | NOTE | 279 | ||
| macos-oldrel-x86_64 | NOTE | 458 | ||
| windows-devel | NOTE | 514 | ||
| windows-release | NOTE | 530 | ||
| windows-oldrel | NOTE | 574 | ||
| wasm-release | FAIL | 182 |
Exports:detection_calculatedetection_plotjoint_modeljoint_selectjoint_summarizemu_criticaltraditional_model
Dependencies:abindbackportsbayestestRBHcallrcheckmateclicpp11data.tabledatawizarddescdistributionaldplyrfarvergenericsggplot2gluegridExtragtableinlineinsightisobandjsonlitelabelinglifecycleloomagrittrmatrixStatsnumDerivpillarpkgbuildpkgconfigposteriorprocessxpspurrrQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelrlangrlistrstanrstantoolsS7scalesStanHeadersstringistringrtensorAtibbletidyrtidyselectutf8vctrsviridisLitewithrXMLyaml
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 |
