commOccu objects

commOccu objects

Value

commOccu object

Slots

modelText

JAGS model code as a character vector (made up of code chunks, use cat() to print)

params

Parameters to monitor in the model runs

inits_fun

Function to create start values for the MCMC chains. It being a function ensures different values in each chain

data

List with data needed to run the model (detection & effort matrices, site covariates, number of species / stations / occasions)

input

Input data_list (unchanged)

nimble

logical indicator for whether it is a Nimble model

modelFile

Path of the text file containing the model code

covariate_info

Data frame containing information about covariates. Only used internally in plot_* and predict methods

model

character indicating whether it is a standard "Occupancy" model or Royle-Nichols ("RN") occupancy model

Note

The data slot is a list of model input data. While the exact content depends on function input, it can be summarized as:

y	array of detection histories. Dimensions are: y[species, station, occasion]
effort_binary	matrix of binary (1/0) survey effort. Only used to ensure p = 0 when effort = 0. Dimensions are: effort_binary[station, occasion]
site-occasion covariates	The required content of data_list$obsCovs as named matrices with dimensions [station, occasion]
site covariates	The required columns of data_list$siteCovs as named vectors (length = number of stations)
M	Number of species
J	Number of stations
maxocc	Number of occasions

For categorical site-occasion covariates, an addition matrix containing an integer representation of the character matrix with suffix "_integer" is stored in the data slot.