Summarise spOccupancy occupancy estimates

spOccupancy produces estimates of detection probability for each visit and occupancy probabilities for each site. This functions takes these predictions and creates detection probabilities, occupancy probabilities and realized occupancy probabilities (occupancy probabilities conditional on observed data) for each site.

Usage

summariseSpOccu(pred_p, pred_psi, quants)

Arguments

pred_p

Detection probabilities estimated from a spOccupancy model. It must be a matrix (or mcmc object) with each row corresponding to an MCMC sample and each column corresponding to a visit. This object must contain a "pentad" attribute indicating which pentad each column correspond to, an attribute "year" indicating what year the probabilities correspond to, and an attribute "obs" indicating whether the species was detected in the visit or not. Outputs from predictSpOccu, should be readily appropriate.

pred_psi

Occupancy probabilities estimated from an a spOccupancy model. It must be a matrix (or mcmc object) with each row corresponding to an MCMC sample and each column corresponding to a pentad. This object must contain a "pentad" attribute indicating which pentad each column correspond to, and an attribute "year" indicating what year the probabilities correspond to. Outputs from predictSpOccu, should be readily appropriate.

quants

Quantiles to summarise predictions distribution passed as c("lower", "med", "upper").

Value

A tibble with estimates and/or quantiles for each pentad in site_data:

• psi: occupancy probability,

• p: detection probability,

• occu: realized occupancy (occupancy conditional on data).