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Create space4time site configuration object (s4t_config)

Source: R/s4t_config.R
s4t_config.Rd

Create the space4time site configuration object (s4t_config) using custom site configuration. For a simple configuration where there is only one initial release site use linear_s4t_config(), which assumes that the sites are arranged in a simple sequence. If there are multiple initial release sites that are immediately connected to a simple sequence then simplebranch_s4t_config() can be used. Otherwise, use this function to create a custom site configuration. See details or (LINK VIGNETTE) for more detailed instructions.

Usage

s4t_config(
  sites_names,
  sites_config,
  holdover_config,
  min_a,
  max_a,
  sites_to_pool = NULL
)

Arguments

sites_names

a character vector of the site names

sites_config

a matrix that determine how sites are linked together. Must be in the same order as sites_names. See LINK VIGNETTE and details.

holdover_config

a matrix that determine whether individuals can holdover in between sites. In the same format as sites_configs. See LINK VIGNETTE and details.

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 examples, LINK VIGNETTE, and details.

Value

A s4t_config object, which contains

Details

Additional details... sites_to_pool is either a named list or a list of character vectors. If it is unnamed, than the name, min_a, max_a values are used from the first site listed. If the list is named, than the name, min_a, and max_a are used from the site in the name.

Examples

site_arrangement <- s4t_config(sites_names = c("A","B","C","D"),
                               min_a = c(1,1,1,1),
                               max_a = c(3,4,4,4),
                               sites_config = matrix(
                                       c(0,1,0,0,
                                         0,0,1,0,
                                         0,0,0,1,
                                         0,0,0,0),
                                         nrow = 4,
                                         ncol = 4,
                                         byrow = TRUE,
                                         dimnames = list(c("A","B","C","D"),
                                         c("A","B","C","D"))),
                               holdover_config = matrix(
                                        c(0,1,0,0,
                                          0,0,0,0,
                                          0,0,0,0,
                                          0,0,0,0),
                                          nrow = 4,
                                          ncol = 4,
                                          byrow = TRUE,
                                          dimnames = list(c("A","B","C","D"),
                                          c("A","B","C","D")))
)