Create site configuration for simple branching site arrangement

This is only for when there are two or more initial sites where individuals can be released, and then the next site is for all sites. After this shared site, there should be at least one additional site in order to estimate transitions and apparent survival (because detection probability cannot be estimated for the last site).

Usage

simplebranch_s4t_config(
  sites_names,
  branch_sites,
  holdover_sites = NULL,
  min_a,
  max_a,
  sites_to_pool = NULL
)

Arguments

sites_names

a character vector of the site names. Order indicates the direction of movement.

branch_sites

a character vector of the initial branching sites

holdover_sites

a character vector of the sites where after passing, individuals can holdover (take 1 or more time intervals) before reaching the next site.

min_a

a vector of the minimum ageclass individuals in a site can be. Must be the same length and order as sites_names

max_a

a vector of the maximum ageclass individuals in a site can be. Must be the same length and order as sites_names

sites_to_pool

a named list of character vectors that contain the names of sites to be pooled together and treated as one site. See LINK VIGNETTE and details.