Package: occumb 1.3.0
Keiichi Fukaya
occumb: Site Occupancy Modeling for Environmental DNA Metabarcoding
Fits community site occupancy models to environmental DNA metabarcoding data collected using spatially-replicated survey design. Model fitting results can be used to evaluate and compare the effectiveness of species detection to find an efficient survey design. Reference: Fukaya et al. (2022) <doi:10.1111/2041-210X.13732>, Fukaya and Hasebe (2025) <doi:10.1002/1438-390X.12219>.
Authors:
occumb_1.3.0.tar.gz
occumb_1.3.0.tar.gz(r-4.7-any)occumb_1.3.0.tar.gz(r-4.6-any)
occumb_1.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
occumb/json (API)
NEWS
| # Install 'occumb' in R: |
| install.packages('occumb', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/fukayak/occumb/issues
Pkgdown/docs site:https://fukayak.github.io
Last updated from:f19b843f6b. Checks:4 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 165 | ||
| source / vignettes | OK | 186 | ||
| linux-release-x86_64 | OK | 153 | ||
| wasm-release | OK | 126 |
Exports:eval_util_Leval_util_Rget_post_samplesget_post_summarygoflist_cond_Llist_cond_RoccumboccumbDataplotpredictsummary
Dependencies:backportscheckmatecodacrayonevaluatehighrjagsUIknitrlatticerjagsxfunyaml
Introduction to occumb
Rendered fromoccumb.Rmdusingknitr::rmarkdownon Jun 14 2026.Last update: 2026-04-06
Started: 2023-09-23
Model specification in occumb()
Rendered frommodel_specification.Rmdusingknitr::rmarkdownon Jun 14 2026.Last update: 2025-07-16
Started: 2023-09-23
Options for MCMC engines in occumb()
Rendered frommcmc_engine_options.Rmdusingknitr::rmarkdownon Jun 14 2026.Last update: 2026-04-06
Started: 2026-04-06
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Expected utility for local species diversity assessments. | eval_util_L |
| Expected utility for regional species diversity assessments. | eval_util_R |
| Fish eDNA metabarcoding dataset | fish |
| Fish eDNA metabarcoding dataset | fish_raw |
| Extract posterior samples or summary of parameters from a model-fit object. | get_posterior get_post_samples get_post_summary |
| Goodness-of-fit assessment of the fitted model. | gof |
| Conditions for local assessment under certain budget and cost values. | list_cond_L |
| Conditions for regional assessment under certain budget and cost values. | list_cond_R |
| Model-fitting function. | occumb |
| Constructor for occumbData data class. | occumbData |
| Plot method for occumbFit class. | plot,occumbFit-method |
| Plot method for occumbGof class. | plot,occumbGof-method |
| Predict method for occumbFit class. | predict,occumbFit-method |
| Summary method for occumbData class. | summary,occumbData-method |
| Summary method for occumbFit class. | summary,occumbFit-method |
