occumb1.2.1 package

Site Occupancy Modeling for Environmental DNA Metabarcoding

eval_util_L

Expected utility for local species diversity assessments.

eval_util_R

Expected utility for regional species diversity assessments.

get_posterior

Extract posterior samples or summary of parameters from a model-fit ob...

gof

Goodness-of-fit assessment of the fitted model.

list_cond_L

Conditions for local assessment under certain budget and cost values.

list_cond_R

Conditions for regional assessment under certain budget and cost value...

occumb

Model-fitting function.

occumbData

Constructor for occumbData data class.

plot-occumbFit-method

Plot method for occumbFit class.

plot-occumbGof-method

Plot method for occumbGof class.

predict-occumbFit-method

Predict method for occumbFit class.

summary-occumbData-method

Summary method for occumbData class.

summary-occumbFit-method

Summary method for occumbFit class.

Download source packageRead PDF manual

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>.

  • Maintainer: Keiichi Fukaya
  • License: GPL (>= 3)
  • Last published: 2025-07-16

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