Package: occumb 1.1.0

Keiichi Fukaya

occumb: Site Occupancy Modeling for Environmental DNA Metabarcoding

Fits multispecies 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>.

Authors:Keiichi Fukaya [aut, cre], Ken Kellner [cph]

occumb_1.1.0.tar.gz
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occumb_1.1.0.tgz(r-4.4-emscripten)occumb_1.1.0.tgz(r-4.3-emscripten)
occumb.pdf |occumb.html✨
occumb/json (API)
NEWS

# Install 'occumb' in R:
install.packages('occumb', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/fukayak/occumb/issues

Pkgdown site:https://fukayak.github.io

Uses libs:
  • jags– Just Another Gibbs Sampler for Bayesian MCMC
  • c++– GNU Standard C++ Library v3
Datasets:
  • fish - Fish eDNA metabarcoding dataset
  • fish_raw - Fish eDNA metabarcoding dataset

jagscpp

3.30 score 10 scripts 228 downloads 12 exports 12 dependencies

Last updated 9 months agofrom:32b1262fa2. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 22 2024
R-4.5-linuxOKDec 22 2024

Exports:eval_util_Leval_util_Rget_post_samplesget_post_summarygoflist_cond_Llist_cond_RoccumboccumbDataplotpredictsummary

Dependencies:backportscheckmatecodacrayonevaluatehighrjagsUIknitrlatticerjagsxfunyaml

Introduction to occumb

Rendered fromoccumb.Rmdusingknitr::rmarkdownon Dec 22 2024.

Last update: 2024-03-27
Started: 2023-09-23

Model specification in occumb()

Rendered frommodel_specification.Rmdusingknitr::rmarkdownon Dec 22 2024.

Last update: 2024-03-27
Started: 2023-09-23