Function reference • occumb

Setup dataset

Functions for building a dataset object used for model-fitting.

occumbData(): Constructor for occumbData data class.

Model fitting

Functions for fitting a model.

occumb(): Model-fitting function.

Model assessment

Functions for assessment of the fitted model.

get_post_samples() get_post_summary(): Extract posterior samples or summary of parameters from a model-fit object.

gof(): Goodness-of-fit assessment of the fitted model.

Study design for effective species detection

Functions for the model-based assessment of study design.

eval_util_L(): Expected utility for local species diversity assessments.

eval_util_R(): Expected utility for regional species diversity assessments.

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 values.

S4 methods

Generic function methods applied to occumb package outputs.

plot(<occumbFit>): Plot method for occumbFit class.

plot(<occumbGof>): Plot method for occumbGof class.

predict(<occumbFit>): Predict method for occumbFit class.

summary(<occumbData>): Summary method for occumbData class.

summary(<occumbFit>): Summary method for occumbFit class.

Dataset

Example dataset to illustrate function usage.

fish: Fish eDNA metabarcoding dataset

fish_raw: Fish eDNA metabarcoding dataset